Diff for /imach/src/imach.c between versions 1.41 and 1.115

version 1.41, 2002/05/07 15:53:01 version 1.115, 2006/02/27 12:17:45
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.115  2006/02/27 12:17:45  brouard
      (Module): One freematrix added in mlikeli! 0.98c
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.114  2006/02/26 12:57:58  brouard
   first survey ("cross") where individuals from different ages are    (Module): Some improvements in processing parameter
   interviewed on their health status or degree of disability (in the    filename with strsep.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.113  2006/02/24 14:20:24  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Memory leaks checks with valgrind and:
   computed from the time spent in each health state according to a    datafile was not closed, some imatrix were not freed and on matrix
   model. More health states you consider, more time is necessary to reach the    allocation too.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.112  2006/01/30 09:55:26  brouard
   probability to be observed in state j at the second wave    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.111  2006/01/25 20:38:18  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): Lots of cleaning and bugs added (Gompertz)
   complex model than "constant and age", you should modify the program    (Module): Comments can be added in data file. Missing date values
   where the markup *Covariates have to be included here again* invites    can be a simple dot '.'.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.109  2006/01/24 19:37:15  brouard
   identical for each individual. Also, if a individual missed an    (Module): Comments (lines starting with a #) are allowed in data.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
   hPijx is the probability to be observed in state i at age x+h    To be fixed
   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 1.107  2006/01/19 16:20:37  brouard
   states. This elementary transition (by month or quarter trimester,    Test existence of gnuplot in imach path
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.106  2006/01/19 13:24:36  brouard
   and the contribution of each individual to the likelihood is simply    Some cleaning and links added in html output
   hPijx.  
     Revision 1.105  2006/01/05 20:23:19  lievre
   Also this programme outputs the covariance matrix of the parameters but also    *** empty log message ***
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.104  2005/09/30 16:11:43  lievre
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): sump fixed, loop imx fixed, and simplifications.
            Institut national d'études démographiques, Paris.    (Module): If the status is missing at the last wave but we know
   This software have been partly granted by Euro-REVES, a concerted action    that the person is alive, then we can code his/her status as -2
   from the European Union.    (instead of missing=-1 in earlier versions) and his/her
   It is copyrighted identically to a GNU software product, ie programme and    contributions to the likelihood is 1 - Prob of dying from last
   software can be distributed freely for non commercial use. Latest version    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   can be accessed at http://euroreves.ined.fr/imach .    the healthy state at last known wave). Version is 0.98
   **********************************************************************/  
      Revision 1.103  2005/09/30 15:54:49  lievre
 #include <math.h>    (Module): sump fixed, loop imx fixed, and simplifications.
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.102  2004/09/15 17:31:30  brouard
 #include <unistd.h>    Add the possibility to read data file including tab characters.
   
 #define MAXLINE 256    Revision 1.101  2004/09/15 10:38:38  brouard
 #define GNUPLOTPROGRAM "wgnuplot"    Fix on curr_time
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.100  2004/07/12 18:29:06  brouard
 /*#define DEBUG*/    Add version for Mac OS X. Just define UNIX in Makefile
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.99  2004/06/05 08:57:40  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    *** empty log message ***
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.98  2004/05/16 15:05:56  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 #define NINTERVMAX 8    state at each age, but using a Gompertz model: log u =a + b*age .
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    This is the basic analysis of mortality and should be done before any
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    other analysis, in order to test if the mortality estimated from the
 #define NCOVMAX 8 /* Maximum number of covariates */    cross-longitudinal survey is different from the mortality estimated
 #define MAXN 20000    from other sources like vital statistic data.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    The same imach parameter file can be used but the option for mle should be -3.
 #define AGEBASE 40  
     Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
 int erreur; /* Error number */  
 int nvar;    The output is very simple: only an estimate of the intercept and of
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    the slope with 95% confident intervals.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Current limitations:
 int ndeath=1; /* Number of dead states */    A) Even if you enter covariates, i.e. with the
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int popbased=0;    B) There is no computation of Life Expectancy nor Life Table.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.97  2004/02/20 13:25:42  lievre
 int maxwav; /* Maxim number of waves */    Version 0.96d. Population forecasting command line is (temporarily)
 int jmin, jmax; /* min, max spacing between 2 waves */    suppressed.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.96  2003/07/15 15:38:55  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 double jmean; /* Mean space between 2 waves */    rewritten within the same printf. Workaround: many printfs.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.95  2003/07/08 07:54:34  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    * imach.c (Repository):
 FILE *ficgp,*ficresprob,*ficpop;    (Repository): Using imachwizard code to output a more meaningful covariance
 FILE *ficreseij;    matrix (cov(a12,c31) instead of numbers.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.94  2003/06/27 13:00:02  brouard
   char fileresv[FILENAMELENGTH];    Just cleaning
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define NR_END 1    exist so I changed back to asctime which exists.
 #define FREE_ARG char*    (Module): Version 0.96b
 #define FTOL 1.0e-10  
     Revision 1.92  2003/06/25 16:30:45  brouard
 #define NRANSI    (Module): On windows (cygwin) function asctime_r doesn't
 #define ITMAX 200    exist so I changed back to asctime which exists.
   
 #define TOL 2.0e-4    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 #define CGOLD 0.3819660    (Repository): Elapsed time after each iteration is now output. It
 #define ZEPS 1.0e-10    helps to forecast when convergence will be reached. Elapsed time
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.90  2003/06/24 12:34:15  brouard
 #define TINY 1.0e-20    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 static double maxarg1,maxarg2;    of the covariance matrix to be input.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.89  2003/06/24 12:30:52  brouard
      (Module): Some bugs corrected for windows. Also, when
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    mle=-1 a template is output in file "or"mypar.txt with the design
 #define rint(a) floor(a+0.5)    of the covariance matrix to be input.
   
 static double sqrarg;    Revision 1.88  2003/06/23 17:54:56  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * 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.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.87  2003/06/18 12:26:01  brouard
 int imx;    Version 0.96
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 int estepm;    routine fileappend.
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.85  2003/06/17 13:12:43  brouard
 int m,nb;    * imach.c (Repository): Check when date of death was earlier that
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    current date of interview. It may happen when the death was just
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    prior to the death. In this case, dh was negative and likelihood
 double **pmmij, ***probs, ***mobaverage;    was wrong (infinity). We still send an "Error" but patch by
 double dateintmean=0;    assuming that the date of death was just one stepm after the
     interview.
 double *weight;    (Repository): Because some people have very long ID (first column)
 int **s; /* Status */    we changed int to long in num[] and we added a new lvector for
 double *agedc, **covar, idx;    memory allocation. But we also truncated to 8 characters (left
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    truncation)
     (Repository): No more line truncation errors.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 /**************** split *************************/    place. It differs from routine "prevalence" which may be called
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    many times. Probs is memory consuming and must be used with
 {    parcimony.
    char *s;                             /* pointer */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    int  l1, l2;                         /* length counters */  
     Revision 1.83  2003/06/10 13:39:11  lievre
    l1 = strlen( path );                 /* length of path */    *** empty log message ***
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.82  2003/06/05 15:57:20  brouard
    s = strrchr( path, '\\' );           /* find last / */    Add log in  imach.c and  fullversion number is now printed.
 #else  
    s = strrchr( path, '/' );            /* find last / */  */
 #endif  /*
    if ( s == NULL ) {                   /* no directory, so use current */     Interpolated Markov Chain
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Short summary of the programme:
     
       if ( getwd( dirc ) == NULL ) {    This program computes Healthy Life Expectancies from
 #else    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
       extern char       *getcwd( );    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    case of a health survey which is our main interest) -2- at least a
 #endif    second wave of interviews ("longitudinal") which measure each change
          return( GLOCK_ERROR_GETCWD );    (if any) in individual health status.  Health expectancies are
       }    computed from the time spent in each health state according to a
       strcpy( name, path );             /* we've got it */    model. More health states you consider, more time is necessary to reach the
    } else {                             /* strip direcotry from path */    Maximum Likelihood of the parameters involved in the model.  The
       s++;                              /* after this, the filename */    simplest model is the multinomial logistic model where pij is the
       l2 = strlen( s );                 /* length of filename */    probability to be observed in state j at the second wave
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    conditional to be observed in state i at the first wave. Therefore
       strcpy( name, s );                /* save file name */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    'age' is age and 'sex' is a covariate. If you want to have a more
       dirc[l1-l2] = 0;                  /* add zero */    complex model than "constant and age", you should modify the program
    }    where the markup *Covariates have to be included here again* invites
    l1 = strlen( dirc );                 /* length of directory */    you to do it.  More covariates you add, slower the
 #ifdef windows    convergence.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    The advantage of this computer programme, compared to a simple
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    multinomial logistic model, is clear when the delay between waves is not
 #endif    identical for each individual. Also, if a individual missed an
    s = strrchr( name, '.' );            /* find last / */    intermediate interview, the information is lost, but taken into
    s++;    account using an interpolation or extrapolation.  
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    hPijx is the probability to be observed in state i at age x+h
    l2= strlen( s)+1;    conditional to the observed state i at age x. The delay 'h' can be
    strncpy( finame, name, l1-l2);    split into an exact number (nh*stepm) of unobserved intermediate
    finame[l1-l2]= 0;    states. This elementary transition (by month, quarter,
    return( 0 );                         /* we're done */    semester or year) is modelled as a multinomial logistic.  The hPx
 }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
     hPijx.
 /******************************************/  
     Also this programme outputs the covariance matrix of the parameters but also
 void replace(char *s, char*t)    of the life expectancies. It also computes the stable prevalence. 
 {    
   int i;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   int lg=20;             Institut national d'études démographiques, Paris.
   i=0;    This software have been partly granted by Euro-REVES, a concerted action
   lg=strlen(t);    from the European Union.
   for(i=0; i<= lg; i++) {    It is copyrighted identically to a GNU software product, ie programme and
     (s[i] = t[i]);    software can be distributed freely for non commercial use. Latest version
     if (t[i]== '\\') s[i]='/';    can be accessed at http://euroreves.ined.fr/imach .
   }  
 }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int nbocc(char *s, char occ)    
 {    **********************************************************************/
   int i,j=0;  /*
   int lg=20;    main
   i=0;    read parameterfile
   lg=strlen(s);    read datafile
   for(i=0; i<= lg; i++) {    concatwav
   if  (s[i] == occ ) j++;    freqsummary
   }    if (mle >= 1)
   return j;      mlikeli
 }    print results files
     if mle==1 
 void cutv(char *u,char *v, char*t, char occ)       computes hessian
 {    read end of parameter file: agemin, agemax, bage, fage, estepm
   int i,lg,j,p=0;        begin-prev-date,...
   i=0;    open gnuplot file
   for(j=0; j<=strlen(t)-1; j++) {    open html file
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    stable prevalence
   }     for age prevalim()
     h Pij x
   lg=strlen(t);    variance of p varprob
   for(j=0; j<p; j++) {    forecasting if prevfcast==1 prevforecast call prevalence()
     (u[j] = t[j]);    health expectancies
   }    Variance-covariance of DFLE
      u[p]='\0';    prevalence()
      movingaverage()
    for(j=0; j<= lg; j++) {    varevsij() 
     if (j>=(p+1))(v[j-p-1] = t[j]);    if popbased==1 varevsij(,popbased)
   }    total life expectancies
 }    Variance of stable prevalence
    end
 /********************** nrerror ********************/  */
   
 void nrerror(char error_text[])  
 {  
   fprintf(stderr,"ERREUR ...\n");   
   fprintf(stderr,"%s\n",error_text);  #include <math.h>
   exit(1);  #include <stdio.h>
 }  #include <stdlib.h>
 /*********************** vector *******************/  #include <string.h>
 double *vector(int nl, int nh)  #include <unistd.h>
 {  
   double *v;  #include <limits.h>
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #include <sys/types.h>
   if (!v) nrerror("allocation failure in vector");  #include <sys/stat.h>
   return v-nl+NR_END;  #include <errno.h>
 }  extern int errno;
   
 /************************ free vector ******************/  /* #include <sys/time.h> */
 void free_vector(double*v, int nl, int nh)  #include <time.h>
 {  #include "timeval.h"
   free((FREE_ARG)(v+nl-NR_END));  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  #define MAXLINE 256
 {  
   int *v;  #define GNUPLOTPROGRAM "gnuplot"
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   if (!v) nrerror("allocation failure in ivector");  #define FILENAMELENGTH 132
   return v-nl+NR_END;  
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 /******************* imatrix *******************************/  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define NCOVMAX 8 /* Maximum number of covariates */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define MAXN 20000
 {  #define YEARM 12. /* Number of months per year */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define AGESUP 130
   int **m;  #define AGEBASE 40
    #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   /* allocate pointers to rows */  #ifdef UNIX
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define DIRSEPARATOR '/'
   if (!m) nrerror("allocation failure 1 in matrix()");  #define CHARSEPARATOR "/"
   m += NR_END;  #define ODIRSEPARATOR '\\'
   m -= nrl;  #else
    #define DIRSEPARATOR '\\'
    #define CHARSEPARATOR "\\"
   /* allocate rows and set pointers to them */  #define ODIRSEPARATOR '/'
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #endif
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /* $Id$ */
   m[nrl] -= ncl;  /* $State$ */
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
    char fullversion[]="$Revision$ $Date$"; 
   /* return pointer to array of pointers to rows */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   return m;  int nvar;
 }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 /****************** free_imatrix *************************/  int nlstate=2; /* Number of live states */
 void free_imatrix(m,nrl,nrh,ncl,nch)  int ndeath=1; /* Number of dead states */
       int **m;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       long nch,ncl,nrh,nrl;  int popbased=0;
      /* free an int matrix allocated by imatrix() */  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int maxwav; /* Maxim number of waves */
   free((FREE_ARG) (m+nrl-NR_END));  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 
 /******************* matrix *******************************/                     to the likelihood and the sum of weights (done by funcone)*/
 double **matrix(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 */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double **m;  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. */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double jmean; /* Mean space between 2 waves */
   if (!m) nrerror("allocation failure 1 in matrix()");  double **oldm, **newm, **savm; /* Working pointers to matrices */
   m += NR_END;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m -= nrl;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int globpr; /* Global variable for printing or not */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double fretone; /* Only one call to likelihood */
   m[nrl] += NR_END;  long ipmx; /* Number of contributions */
   m[nrl] -= ncl;  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   return m;  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /*************************free matrix ************************/  FILE *fichtm, *fichtmcov; /* Html File */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE  *ficresvij;
   free((FREE_ARG)(m+nrl-NR_END));  char fileresv[FILENAMELENGTH];
 }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 /******************* ma3x *******************************/  char title[MAXLINE];
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double ***m;  char command[FILENAMELENGTH];
   int  outcmd=0;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   m += NR_END;  
   m -= nrl;  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fileregp[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char popfile[FILENAMELENGTH];
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  extern int gettimeofday();
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   m[nrl][ncl] += NR_END;  long time_value;
   m[nrl][ncl] -= nll;  extern long time();
   for (j=ncl+1; j<=nch; j++)  char strcurr[80], strfor[80];
     m[nrl][j]=m[nrl][j-1]+nlay;  
    char *endptr;
   for (i=nrl+1; i<=nrh; i++) {  long lval;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  #define NR_END 1
       m[i][j]=m[i][j-1]+nlay;  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
   return m;  
 }  #define NRANSI 
   #define ITMAX 200 
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define TOL 2.0e-4 
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define CGOLD 0.3819660 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define ZEPS 1.0e-10 
   free((FREE_ARG)(m+nrl-NR_END));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /***************** f1dim *************************/  #define GLIMIT 100.0 
 extern int ncom;  #define TINY 1.0e-20 
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  static double maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double f1dim(double x)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   int j;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   double f;  #define rint(a) floor(a+0.5)
   double *xt;  
    static double sqrarg;
   xt=vector(1,ncom);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   f=(*nrfunc)(xt);  int agegomp= AGEGOMP;
   free_vector(xt,1,ncom);  
   return f;  int imx; 
 }  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int estepm;
 {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   int iter;  
   double a,b,d,etemp;  int m,nb;
   double fu,fv,fw,fx;  long *num;
   double ftemp;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double e=0.0;  double **pmmij, ***probs;
    double *ageexmed,*agecens;
   a=(ax < cx ? ax : cx);  double dateintmean=0;
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  double *weight;
   fw=fv=fx=(*f)(x);  int **s; /* Status */
   for (iter=1;iter<=ITMAX;iter++) {  double *agedc, **covar, idx;
     xm=0.5*(a+b);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double *lsurv, *lpop, *tpop;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 #ifdef DEBUG  double ftolhess; /* Tolerance for computing hessian */
     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)))) { */  /**************** split *************************/
 #endif  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  {
       *xmin=x;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       return fx;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     }    */ 
     ftemp=fu;    char  *ss;                            /* pointer */
     if (fabs(e) > tol1) {    int   l1, l2;                         /* length counters */
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    l1 = strlen(path );                   /* length of path */
       p=(x-v)*q-(x-w)*r;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       q=2.0*(q-r);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       if (q > 0.0) p = -p;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       q=fabs(q);      strcpy( name, path );               /* we got the fullname name because no directory */
       etemp=e;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       e=d;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      /* get current working directory */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      /*    extern  char* getcwd ( char *buf , int len);*/
       else {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         d=p/q;        return( GLOCK_ERROR_GETCWD );
         u=x+d;      }
         if (u-a < tol2 || b-u < tol2)      /* got dirc from getcwd*/
           d=SIGN(tol1,xm-x);      printf(" DIRC = %s \n",dirc);
       }    } else {                              /* strip direcotry from path */
     } else {      ss++;                               /* after this, the filename */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      l2 = strlen( ss );                  /* length of filename */
     }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      strcpy( name, ss );         /* save file name */
     fu=(*f)(u);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     if (fu <= fx) {      dirc[l1-l2] = 0;                    /* add zero */
       if (u >= x) a=x; else b=x;      printf(" DIRC2 = %s \n",dirc);
       SHFT(v,w,x,u)    }
         SHFT(fv,fw,fx,fu)    /* We add a separator at the end of dirc if not exists */
         } else {    l1 = strlen( dirc );                  /* length of directory */
           if (u < x) a=u; else b=u;    if( dirc[l1-1] != DIRSEPARATOR ){
           if (fu <= fw || w == x) {      dirc[l1] =  DIRSEPARATOR;
             v=w;      dirc[l1+1] = 0; 
             w=u;      printf(" DIRC3 = %s \n",dirc);
             fv=fw;    }
             fw=fu;    ss = strrchr( name, '.' );            /* find last / */
           } else if (fu <= fv || v == x || v == w) {    if (ss >0){
             v=u;      ss++;
             fv=fu;      strcpy(ext,ss);                     /* save extension */
           }      l1= strlen( name);
         }      l2= strlen(ss)+1;
   }      strncpy( finame, name, l1-l2);
   nrerror("Too many iterations in brent");      finame[l1-l2]= 0;
   *xmin=x;    }
   return fx;  
 }    return( 0 );                          /* we're done */
   }
 /****************** mnbrak ***********************/  
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /******************************************/
             double (*func)(double))  
 {  void replace_back_to_slash(char *s, char*t)
   double ulim,u,r,q, dum;  {
   double fu;    int i;
      int lg=0;
   *fa=(*func)(*ax);    i=0;
   *fb=(*func)(*bx);    lg=strlen(t);
   if (*fb > *fa) {    for(i=0; i<= lg; i++) {
     SHFT(dum,*ax,*bx,dum)      (s[i] = t[i]);
       SHFT(dum,*fb,*fa,dum)      if (t[i]== '\\') s[i]='/';
       }    }
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  int nbocc(char *s, char occ)
     r=(*bx-*ax)*(*fb-*fc);  {
     q=(*bx-*cx)*(*fb-*fa);    int i,j=0;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    int lg=20;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    i=0;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    lg=strlen(s);
     if ((*bx-u)*(u-*cx) > 0.0) {    for(i=0; i<= lg; i++) {
       fu=(*func)(u);    if  (s[i] == occ ) j++;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    }
       fu=(*func)(u);    return j;
       if (fu < *fc) {  }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  void cutv(char *u,char *v, char*t, char occ)
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       u=ulim;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       fu=(*func)(u);       gives u="abcedf" and v="ghi2j" */
     } else {    int i,lg,j,p=0;
       u=(*cx)+GOLD*(*cx-*bx);    i=0;
       fu=(*func)(u);    for(j=0; j<=strlen(t)-1; j++) {
     }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     SHFT(*ax,*bx,*cx,u)    }
       SHFT(*fa,*fb,*fc,fu)  
       }    lg=strlen(t);
 }    for(j=0; j<p; j++) {
       (u[j] = t[j]);
 /*************** linmin ************************/    }
        u[p]='\0';
 int ncom;  
 double *pcom,*xicom;     for(j=0; j<= lg; j++) {
 double (*nrfunc)(double []);      if (j>=(p+1))(v[j-p-1] = t[j]);
      }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  }
 {  
   double brent(double ax, double bx, double cx,  /********************** nrerror ********************/
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  void nrerror(char error_text[])
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  {
               double *fc, double (*func)(double));    fprintf(stderr,"ERREUR ...\n");
   int j;    fprintf(stderr,"%s\n",error_text);
   double xx,xmin,bx,ax;    exit(EXIT_FAILURE);
   double fx,fb,fa;  }
    /*********************** vector *******************/
   ncom=n;  double *vector(int nl, int nh)
   pcom=vector(1,n);  {
   xicom=vector(1,n);    double *v;
   nrfunc=func;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for (j=1;j<=n;j++) {    if (!v) nrerror("allocation failure in vector");
     pcom[j]=p[j];    return v-nl+NR_END;
     xicom[j]=xi[j];  }
   }  
   ax=0.0;  /************************ free vector ******************/
   xx=1.0;  void free_vector(double*v, int nl, int nh)
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    free((FREE_ARG)(v+nl-NR_END));
 #ifdef DEBUG  }
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  /************************ivector *******************************/
   for (j=1;j<=n;j++) {  int *ivector(long nl,long nh)
     xi[j] *= xmin;  {
     p[j] += xi[j];    int *v;
   }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   free_vector(xicom,1,n);    if (!v) nrerror("allocation failure in ivector");
   free_vector(pcom,1,n);    return v-nl+NR_END;
 }  }
   
 /*************** powell ************************/  /******************free ivector **************************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  void free_ivector(int *v, long nl, long nh)
             double (*func)(double []))  {
 {    free((FREE_ARG)(v+nl-NR_END));
   void linmin(double p[], double xi[], int n, double *fret,  }
               double (*func)(double []));  
   int i,ibig,j;  /************************lvector *******************************/
   double del,t,*pt,*ptt,*xit;  long *lvector(long nl,long nh)
   double fp,fptt;  {
   double *xits;    long *v;
   pt=vector(1,n);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   ptt=vector(1,n);    if (!v) nrerror("allocation failure in ivector");
   xit=vector(1,n);    return v-nl+NR_END;
   xits=vector(1,n);  }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  /******************free lvector **************************/
   for (*iter=1;;++(*iter)) {  void free_lvector(long *v, long nl, long nh)
     fp=(*fret);  {
     ibig=0;    free((FREE_ARG)(v+nl-NR_END));
     del=0.0;  }
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /******************* imatrix *******************************/
       printf(" %d %.12f",i, p[i]);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     printf("\n");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for (i=1;i<=n;i++) {  { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       fptt=(*fret);    int **m; 
 #ifdef DEBUG    
       printf("fret=%lf \n",*fret);    /* allocate pointers to rows */ 
 #endif    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       printf("%d",i);fflush(stdout);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       linmin(p,xit,n,fret,func);    m += NR_END; 
       if (fabs(fptt-(*fret)) > del) {    m -= nrl; 
         del=fabs(fptt-(*fret));    
         ibig=i;    
       }    /* allocate rows and set pointers to them */ 
 #ifdef DEBUG    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       printf("%d %.12e",i,(*fret));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for (j=1;j<=n;j++) {    m[nrl] += NR_END; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m[nrl] -= ncl; 
         printf(" x(%d)=%.12e",j,xit[j]);    
       }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       for(j=1;j<=n;j++)    
         printf(" p=%.12e",p[j]);    /* return pointer to array of pointers to rows */ 
       printf("\n");    return m; 
 #endif  } 
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  /****************** free_imatrix *************************/
 #ifdef DEBUG  void free_imatrix(m,nrl,nrh,ncl,nch)
       int k[2],l;        int **m;
       k[0]=1;        long nch,ncl,nrh,nrl; 
       k[1]=-1;       /* free an int matrix allocated by imatrix() */ 
       printf("Max: %.12e",(*func)(p));  { 
       for (j=1;j<=n;j++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         printf(" %.12e",p[j]);    free((FREE_ARG) (m+nrl-NR_END)); 
       printf("\n");  } 
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /******************* matrix *******************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double **matrix(long nrl, long nrh, long ncl, long nch)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double **m;
       }  
 #endif    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
       free_vector(xit,1,n);    m -= nrl;
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       free_vector(pt,1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       return;    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       ptt[j]=2.0*p[j]-pt[j];    return m;
       xit[j]=p[j]-pt[j];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       pt[j]=p[j];     */
     }  }
     fptt=(*func)(ptt);  
     if (fptt < fp) {  /*************************free matrix ************************/
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       if (t < 0.0) {  {
         linmin(p,xit,n,fret,func);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         for (j=1;j<=n;j++) {    free((FREE_ARG)(m+nrl-NR_END));
           xi[j][ibig]=xi[j][n];  }
           xi[j][n]=xit[j];  
         }  /******************* ma3x *******************************/
 #ifdef DEBUG  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
           printf(" %.12e",xit[j]);    double ***m;
         printf("\n");  
 #endif    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
   }    m -= nrl;
 }  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /**** Prevalence limit ****************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    m[nrl] -= ncl;
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
      matrix by transitions matrix until convergence is reached */  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   int i, ii,j,k;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double min, max, maxmin, maxmax,sumnew=0.;    m[nrl][ncl] += NR_END;
   double **matprod2();    m[nrl][ncl] -= nll;
   double **out, cov[NCOVMAX], **pmij();    for (j=ncl+1; j<=nch; j++) 
   double **newm;      m[nrl][j]=m[nrl][j-1]+nlay;
   double agefin, delaymax=50 ; /* Max number of years to converge */    
     for (i=nrl+1; i<=nrh; i++) {
   for (ii=1;ii<=nlstate+ndeath;ii++)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     for (j=1;j<=nlstate+ndeath;j++){      for (j=ncl+1; j<=nch; j++) 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        m[i][j]=m[i][j-1]+nlay;
     }    }
     return m; 
    cov[1]=1.;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
               &(m[i][j][k]) <=> *((*(m+i) + j)+k)
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  }
     newm=savm;  
     /* Covariates have to be included here again */  /*************************free ma3x ************************/
      cov[2]=agefin;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
    {
       for (k=1; k<=cptcovn;k++) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         /*      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]]);*/    free((FREE_ARG)(m+nrl-NR_END));
       }  }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /*************** function subdirf ***********/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  char *subdirf(char fileres[])
   {
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    /* Caution optionfilefiname is hidden */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    strcpy(tmpout,optionfilefiname);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    strcat(tmpout,"/"); /* Add to the right */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    strcat(tmpout,fileres);
     return tmpout;
     savm=oldm;  }
     oldm=newm;  
     maxmax=0.;  /*************** function subdirf2 ***********/
     for(j=1;j<=nlstate;j++){  char *subdirf2(char fileres[], char *preop)
       min=1.;  {
       max=0.;    
       for(i=1; i<=nlstate; i++) {    /* Caution optionfilefiname is hidden */
         sumnew=0;    strcpy(tmpout,optionfilefiname);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    strcat(tmpout,"/");
         prlim[i][j]= newm[i][j]/(1-sumnew);    strcat(tmpout,preop);
         max=FMAX(max,prlim[i][j]);    strcat(tmpout,fileres);
         min=FMIN(min,prlim[i][j]);    return tmpout;
       }  }
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);  /*************** function subdirf3 ***********/
     }  char *subdirf3(char fileres[], char *preop, char *preop2)
     if(maxmax < ftolpl){  {
       return prlim;    
     }    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/");
     strcat(tmpout,preop);
 /*************** transition probabilities ***************/    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    return tmpout;
 {  }
   double s1, s2;  
   /*double t34;*/  /***************** f1dim *************************/
   int i,j,j1, nc, ii, jj;  extern int ncom; 
   extern double *pcom,*xicom;
     for(i=1; i<= nlstate; i++){  extern double (*nrfunc)(double []); 
     for(j=1; j<i;j++){   
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double f1dim(double x) 
         /*s2 += param[i][j][nc]*cov[nc];*/  { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int j; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    double f;
       }    double *xt; 
       ps[i][j]=s2;   
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for(j=i+1; j<=nlstate+ndeath;j++){    f=(*nrfunc)(xt); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free_vector(xt,1,ncom); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    return f; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  } 
       }  
       ps[i][j]=s2;  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   }  { 
     /*ps[3][2]=1;*/    int iter; 
     double a,b,d,etemp;
   for(i=1; i<= nlstate; i++){    double fu,fv,fw,fx;
      s1=0;    double ftemp;
     for(j=1; j<i; j++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       s1+=exp(ps[i][j]);    double e=0.0; 
     for(j=i+1; j<=nlstate+ndeath; j++)   
       s1+=exp(ps[i][j]);    a=(ax < cx ? ax : cx); 
     ps[i][i]=1./(s1+1.);    b=(ax > cx ? ax : cx); 
     for(j=1; j<i; j++)    x=w=v=bx; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    fw=fv=fx=(*f)(x); 
     for(j=i+1; j<=nlstate+ndeath; j++)    for (iter=1;iter<=ITMAX;iter++) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      xm=0.5*(a+b); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   } /* end i */      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      fprintf(ficlog,".");fflush(ficlog);
     for(jj=1; jj<= nlstate+ndeath; jj++){  #ifdef DEBUG
       ps[ii][jj]=0;      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);
       ps[ii][ii]=1;      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);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   }  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        return fx; 
     for(jj=1; jj<= nlstate+ndeath; jj++){      } 
      printf("%lf ",ps[ii][jj]);      ftemp=fu;
    }      if (fabs(e) > tol1) { 
     printf("\n ");        r=(x-w)*(fx-fv); 
     }        q=(x-v)*(fx-fw); 
     printf("\n ");printf("%lf ",cov[2]);*/        p=(x-v)*q-(x-w)*r; 
 /*        q=2.0*(q-r); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        if (q > 0.0) p = -p; 
   goto end;*/        q=fabs(q); 
     return ps;        etemp=e; 
 }        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 /**************** Product of 2 matrices ******************/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          d=p/q; 
 {          u=x+d; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          if (u-a < tol2 || b-u < tol2) 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */            d=SIGN(tol1,xm-x); 
   /* in, b, out are matrice of pointers which should have been initialized        } 
      before: only the contents of out is modified. The function returns      } else { 
      a pointer to pointers identical to out */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   long i, j, k;      } 
   for(i=nrl; i<= nrh; i++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for(k=ncolol; k<=ncoloh; k++)      fu=(*f)(u); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      if (fu <= fx) { 
         out[i][k] +=in[i][j]*b[j][k];        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
   return out;          SHFT(fv,fw,fx,fu) 
 }          } else { 
             if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
 /************* Higher Matrix Product ***************/              v=w; 
               w=u; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )              fv=fw; 
 {              fw=fu; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month            } else if (fu <= fv || v == x || v == w) { 
      duration (i.e. until              v=u; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.              fv=fu; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step            } 
      (typically every 2 years instead of every month which is too big).          } 
      Model is determined by parameters x and covariates have to be    } 
      included manually here.    nrerror("Too many iterations in brent"); 
     *xmin=x; 
      */    return fx; 
   } 
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  /****************** mnbrak ***********************/
   double **newm;  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   /* Hstepm could be zero and should return the unit matrix */              double (*func)(double)) 
   for (i=1;i<=nlstate+ndeath;i++)  { 
     for (j=1;j<=nlstate+ndeath;j++){    double ulim,u,r,q, dum;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double fu; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);   
     }    *fa=(*func)(*ax); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    *fb=(*func)(*bx); 
   for(h=1; h <=nhstepm; h++){    if (*fb > *fa) { 
     for(d=1; d <=hstepm; d++){      SHFT(dum,*ax,*bx,dum) 
       newm=savm;        SHFT(dum,*fb,*fa,dum) 
       /* Covariates have to be included here again */        } 
       cov[1]=1.;    *cx=(*bx)+GOLD*(*bx-*ax); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    *fc=(*func)(*cx); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    while (*fb > *fc) { 
       for (k=1; k<=cptcovage;k++)      r=(*bx-*ax)*(*fb-*fc); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      q=(*bx-*cx)*(*fb-*fa); 
       for (k=1; k<=cptcovprod;k++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        fu=(*func)(u); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        fu=(*func)(u); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        if (fu < *fc) { 
       savm=oldm;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       oldm=newm;            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
     for(i=1; i<=nlstate+ndeath; i++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for(j=1;j<=nlstate+ndeath;j++) {        u=ulim; 
         po[i][j][h]=newm[i][j];        fu=(*func)(u); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      } else { 
          */        u=(*cx)+GOLD*(*cx-*bx); 
       }        fu=(*func)(u); 
   } /* end h */      } 
   return po;      SHFT(*ax,*bx,*cx,u) 
 }        SHFT(*fa,*fb,*fc,fu) 
         } 
   } 
 /*************** log-likelihood *************/  
 double func( double *x)  /*************** linmin ************************/
 {  
   int i, ii, j, k, mi, d, kk;  int ncom; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  double *pcom,*xicom;
   double **out;  double (*nrfunc)(double []); 
   double sw; /* Sum of weights */   
   double lli; /* Individual log likelihood */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   long ipmx;  { 
   /*extern weight */    double brent(double ax, double bx, double cx, 
   /* We are differentiating ll according to initial status */                 double (*f)(double), double tol, double *xmin); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double f1dim(double x); 
   /*for(i=1;i<imx;i++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     printf(" %d\n",s[4][i]);                double *fc, double (*func)(double)); 
   */    int j; 
   cov[1]=1.;    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   for(k=1; k<=nlstate; k++) ll[k]=0.;   
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    ncom=n; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    pcom=vector(1,n); 
     for(mi=1; mi<= wav[i]-1; mi++){    xicom=vector(1,n); 
       for (ii=1;ii<=nlstate+ndeath;ii++)    nrfunc=func; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for (j=1;j<=n;j++) { 
       for(d=0; d<dh[mi][i]; d++){      pcom[j]=p[j]; 
         newm=savm;      xicom[j]=xi[j]; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    } 
         for (kk=1; kk<=cptcovage;kk++) {    ax=0.0; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    xx=1.0; 
         }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
            *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  #ifdef DEBUG
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         savm=oldm;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         oldm=newm;  #endif
            for (j=1;j<=n;j++) { 
              xi[j] *= xmin; 
       } /* end mult */      p[j] += xi[j]; 
          } 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    free_vector(xicom,1,n); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    free_vector(pcom,1,n); 
       ipmx +=1;  } 
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  char *asc_diff_time(long time_sec, char ascdiff[])
     } /* end of wave */  {
   } /* end of individual */    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    sec_left = (time_sec) % (60*60*24);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    hours = (sec_left) / (60*60) ;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    sec_left = (sec_left) %(60*60);
   return -l;    minutes = (sec_left) /60;
 }    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
 /*********** Maximum Likelihood Estimation ***************/  }
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  /*************** powell ************************/
 {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   int i,j, iter;              double (*func)(double [])) 
   double **xi,*delti;  { 
   double fret;    void linmin(double p[], double xi[], int n, double *fret, 
   xi=matrix(1,npar,1,npar);                double (*func)(double [])); 
   for (i=1;i<=npar;i++)    int i,ibig,j; 
     for (j=1;j<=npar;j++)    double del,t,*pt,*ptt,*xit;
       xi[i][j]=(i==j ? 1.0 : 0.0);    double fp,fptt;
   printf("Powell\n");    double *xits;
   powell(p,xi,npar,ftol,&iter,&fret,func);    int niterf, itmp;
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    pt=vector(1,n); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    ptt=vector(1,n); 
     xit=vector(1,n); 
 }    xits=vector(1,n); 
     *fret=(*func)(p); 
 /**** Computes Hessian and covariance matrix ***/    for (j=1;j<=n;j++) pt[j]=p[j]; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    for (*iter=1;;++(*iter)) { 
 {      fp=(*fret); 
   double  **a,**y,*x,pd;      ibig=0; 
   double **hess;      del=0.0; 
   int i, j,jk;      last_time=curr_time;
   int *indx;      (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);
   double hessii(double p[], double delta, int theta, double delti[]);      /*    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);
   double hessij(double p[], double delti[], int i, int j);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      */
   void ludcmp(double **a, int npar, int *indx, double *d) ;     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
   hess=matrix(1,npar,1,npar);        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   printf("\nCalculation of the hessian matrix. Wait...\n");      }
   for (i=1;i<=npar;i++){      printf("\n");
     printf("%d",i);fflush(stdout);      fprintf(ficlog,"\n");
     hess[i][i]=hessii(p,ftolhess,i,delti);      fprintf(ficrespow,"\n");fflush(ficrespow);
     /*printf(" %f ",p[i]);*/      if(*iter <=3){
     /*printf(" %lf ",hess[i][i]);*/        tm = *localtime(&curr_time.tv_sec);
   }        strcpy(strcurr,asctime(&tm));
    /*       asctime_r(&tm,strcurr); */
   for (i=1;i<=npar;i++) {        forecast_time=curr_time; 
     for (j=1;j<=npar;j++)  {        itmp = strlen(strcurr);
       if (j>i) {        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         printf(".%d%d",i,j);fflush(stdout);          strcurr[itmp-1]='\0';
         hess[i][j]=hessij(p,delti,i,j);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         hess[j][i]=hess[i][j];            fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         /*printf(" %lf ",hess[i][j]);*/        for(niterf=10;niterf<=30;niterf+=10){
       }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     }          tmf = *localtime(&forecast_time.tv_sec);
   }  /*      asctime_r(&tmf,strfor); */
   printf("\n");          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          if(strfor[itmp-1]=='\n')
            strfor[itmp-1]='\0';
   a=matrix(1,npar,1,npar);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   y=matrix(1,npar,1,npar);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   x=vector(1,npar);        }
   indx=ivector(1,npar);      }
   for (i=1;i<=npar;i++)      for (i=1;i<=n;i++) { 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   ludcmp(a,npar,indx,&pd);        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);
       matcov[i][j]=x[i];        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
           ibig=i; 
   printf("\n#Hessian matrix#\n");        } 
   for (i=1;i<=npar;i++) {  #ifdef DEBUG
     for (j=1;j<=npar;j++) {        printf("%d %.12e",i,(*fret));
       printf("%.3e ",hess[i][j]);        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     printf("\n");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   }          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   /* Recompute Inverse */        }
   for (i=1;i<=npar;i++)        for(j=1;j<=n;j++) {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          printf(" p=%.12e",p[j]);
   ludcmp(a,npar,indx,&pd);          fprintf(ficlog," p=%.12e",p[j]);
         }
   /*  printf("\n#Hessian matrix recomputed#\n");        printf("\n");
         fprintf(ficlog,"\n");
   for (j=1;j<=npar;j++) {  #endif
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     lubksb(a,npar,indx,x);  #ifdef DEBUG
     for (i=1;i<=npar;i++){        int k[2],l;
       y[i][j]=x[i];        k[0]=1;
       printf("%.3e ",y[i][j]);        k[1]=-1;
     }        printf("Max: %.12e",(*func)(p));
     printf("\n");        fprintf(ficlog,"Max: %.12e",(*func)(p));
   }        for (j=1;j<=n;j++) {
   */          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   free_matrix(a,1,npar,1,npar);        }
   free_matrix(y,1,npar,1,npar);        printf("\n");
   free_vector(x,1,npar);        fprintf(ficlog,"\n");
   free_ivector(indx,1,npar);        for(l=0;l<=1;l++) {
   free_matrix(hess,1,npar,1,npar);          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]);
 }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
 /*************** hessian matrix ****************/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 double hessii( double x[], double delta, int theta, double delti[])          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 {        }
   int i;  #endif
   int l=1, lmax=20;  
   double k1,k2;  
   double p2[NPARMAX+1];        free_vector(xit,1,n); 
   double res;        free_vector(xits,1,n); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        free_vector(ptt,1,n); 
   double fx;        free_vector(pt,1,n); 
   int k=0,kmax=10;        return; 
   double l1;      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   fx=func(x);      for (j=1;j<=n;j++) { 
   for (i=1;i<=npar;i++) p2[i]=x[i];        ptt[j]=2.0*p[j]-pt[j]; 
   for(l=0 ; l <=lmax; l++){        xit[j]=p[j]-pt[j]; 
     l1=pow(10,l);        pt[j]=p[j]; 
     delts=delt;      } 
     for(k=1 ; k <kmax; k=k+1){      fptt=(*func)(ptt); 
       delt = delta*(l1*k);      if (fptt < fp) { 
       p2[theta]=x[theta] +delt;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       k1=func(p2)-fx;        if (t < 0.0) { 
       p2[theta]=x[theta]-delt;          linmin(p,xit,n,fret,func); 
       k2=func(p2)-fx;          for (j=1;j<=n;j++) { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */            xi[j][ibig]=xi[j][n]; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            xi[j][n]=xit[j]; 
                }
 #ifdef DEBUG  #ifdef DEBUG
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 #endif          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          for(j=1;j<=n;j++){
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            printf(" %.12e",xit[j]);
         k=kmax;            fprintf(ficlog," %.12e",xit[j]);
       }          }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          printf("\n");
         k=kmax; l=lmax*10.;          fprintf(ficlog,"\n");
       }  #endif
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        }
         delts=delt;      } 
       }    } 
     }  } 
   }  
   delti[theta]=delts;  /**** Prevalence limit (stable prevalence)  ****************/
   return res;  
    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
 double hessij( double x[], double delti[], int thetai,int thetaj)       matrix by transitions matrix until convergence is reached */
 {  
   int i;    int i, ii,j,k;
   int l=1, l1, lmax=20;    double min, max, maxmin, maxmax,sumnew=0.;
   double k1,k2,k3,k4,res,fx;    double **matprod2();
   double p2[NPARMAX+1];    double **out, cov[NCOVMAX], **pmij();
   int k;    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   fx=func(x);  
   for (k=1; k<=2; k++) {    for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1;i<=npar;i++) p2[i]=x[i];      for (j=1;j<=nlstate+ndeath;j++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      }
     k1=func(p2)-fx;  
       cov[1]=1.;
     p2[thetai]=x[thetai]+delti[thetai]/k;   
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     k2=func(p2)-fx;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
        newm=savm;
     p2[thetai]=x[thetai]-delti[thetai]/k;      /* Covariates have to be included here again */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       cov[2]=agefin;
     k3=func(p2)-fx;    
          for (k=1; k<=cptcovn;k++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     k4=func(p2)-fx;        }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 #ifdef DEBUG        for (k=1; k<=cptcovprod;k++)
     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);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 #endif  
   }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   return res;        /*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]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)      savm=oldm;
 {      oldm=newm;
   int i,imax,j,k;      maxmax=0.;
   double big,dum,sum,temp;      for(j=1;j<=nlstate;j++){
   double *vv;        min=1.;
          max=0.;
   vv=vector(1,n);        for(i=1; i<=nlstate; i++) {
   *d=1.0;          sumnew=0;
   for (i=1;i<=n;i++) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     big=0.0;          prlim[i][j]= newm[i][j]/(1-sumnew);
     for (j=1;j<=n;j++)          max=FMAX(max,prlim[i][j]);
       if ((temp=fabs(a[i][j])) > big) big=temp;          min=FMIN(min,prlim[i][j]);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        }
     vv[i]=1.0/big;        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {      if(maxmax < ftolpl){
       sum=a[i][j];        return prlim;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      }
       a[i][j]=sum;    }
     }  }
     big=0.0;  
     for (i=j;i<=n;i++) {  /*************** transition probabilities ***************/ 
       sum=a[i][j];  
       for (k=1;k<j;k++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         sum -= a[i][k]*a[k][j];  {
       a[i][j]=sum;    double s1, s2;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    /*double t34;*/
         big=dum;    int i,j,j1, nc, ii, jj;
         imax=i;  
       }      for(i=1; i<= nlstate; i++){
     }        for(j=1; j<i;j++){
     if (j != imax) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<=n;k++) {            /*s2 += param[i][j][nc]*cov[nc];*/
         dum=a[imax][k];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         a[imax][k]=a[j][k];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
         a[j][k]=dum;          }
       }          ps[i][j]=s2;
       *d = -(*d);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       vv[imax]=vv[j];        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
     indx[j]=imax;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     if (a[j][j] == 0.0) a[j][j]=TINY;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     if (j != n) {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       dum=1.0/(a[j][j]);          }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          ps[i][j]=s2;
     }        }
   }      }
   free_vector(vv,1,n);  /* Doesn't work */      /*ps[3][2]=1;*/
 ;      
 }      for(i=1; i<= nlstate; i++){
         s1=0;
 void lubksb(double **a, int n, int *indx, double b[])        for(j=1; j<i; j++)
 {          s1+=exp(ps[i][j]);
   int i,ii=0,ip,j;        for(j=i+1; j<=nlstate+ndeath; j++)
   double sum;          s1+=exp(ps[i][j]);
          ps[i][i]=1./(s1+1.);
   for (i=1;i<=n;i++) {        for(j=1; j<i; j++)
     ip=indx[i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     sum=b[ip];        for(j=i+1; j<=nlstate+ndeath; j++)
     b[ip]=b[i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     if (ii)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      } /* end i */
     else if (sum) ii=i;      
     b[i]=sum;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   }        for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=n;i>=1;i--) {          ps[ii][jj]=0;
     sum=b[i];          ps[ii][ii]=1;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        }
     b[i]=sum/a[i][i];      }
   }      
 }  
   /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 /************ Frequencies ********************/  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  /*         printf("ddd %lf ",ps[ii][jj]); */
 {  /* Some frequencies */  /*       } */
    /*       printf("\n "); */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  /*        } */
   double ***freq; /* Frequencies */  /*        printf("\n ");printf("%lf ",cov[2]); */
   double *pp;         /*
   double pos, k2, dateintsum=0,k2cpt=0;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   FILE *ficresp;        goto end;*/
   char fileresp[FILENAMELENGTH];      return ps;
    }
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /**************** Product of 2 matrices ******************/
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   if((ficresp=fopen(fileresp,"w"))==NULL) {  {
     printf("Problem with prevalence resultfile: %s\n", fileresp);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     exit(0);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   }    /* in, b, out are matrice of pointers which should have been initialized 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       before: only the contents of out is modified. The function returns
   j1=0;       a pointer to pointers identical to out */
      long i, j, k;
   j=cptcoveff;    for(i=nrl; i<= nrh; i++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
   for(k1=1; k1<=j;k1++){          out[i][k] +=in[i][j]*b[j][k];
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;    return out;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  }
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    /************* Higher Matrix Product ***************/
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
        {
       dateintsum=0;    /* Computes the transition matrix starting at age 'age' over 
       k2cpt=0;       'nhstepm*hstepm*stepm' months (i.e. until
       for (i=1; i<=imx; i++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         bool=1;       nhstepm*hstepm matrices. 
         if  (cptcovn>0) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           for (z1=1; z1<=cptcoveff; z1++)       (typically every 2 years instead of every month which is too big 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       for the memory).
               bool=0;       Model is determined by parameters x and covariates have to be 
         }       included manually here. 
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){       */
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    int i, j, d, h, k;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double **out, cov[NCOVMAX];
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double **newm;
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /* Hstepm could be zero and should return the unit matrix */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    for (i=1;i<=nlstate+ndeath;i++)
               }      for (j=1;j<=nlstate+ndeath;j++){
                      oldm[i][j]=(i==j ? 1.0 : 0.0);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
                 dateintsum=dateintsum+k2;      }
                 k2cpt++;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
               }    for(h=1; h <=nhstepm; h++){
             }      for(d=1; d <=hstepm; d++){
           }        newm=savm;
         }        /* Covariates have to be included here again */
       }        cov[1]=1.;
                cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
       if  (cptcovn>0) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         fprintf(ficresp, "\n#********** Variable ");        for (k=1; k<=cptcovprod;k++)
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         fprintf(ficresp, "**********\n#");  
       }  
       for(i=1; i<=nlstate;i++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       fprintf(ficresp, "\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                           pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=(int)agemin; i <= (int)agemax+3; i++){        savm=oldm;
         if(i==(int)agemax+3)        oldm=newm;
           printf("Total");      }
         else      for(i=1; i<=nlstate+ndeath; i++)
           printf("Age %d", i);        for(j=1;j<=nlstate+ndeath;j++) {
         for(jk=1; jk <=nlstate ; jk++){          po[i][j][h]=newm[i][j];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
             pp[jk] += freq[jk][m][i];           */
         }        }
         for(jk=1; jk <=nlstate ; jk++){    } /* end h */
           for(m=-1, pos=0; m <=0 ; m++)    return po;
             pos += freq[jk][m][i];  }
           if(pp[jk]>=1.e-10)  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
           else  /*************** log-likelihood *************/
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  double func( double *x)
         }  {
     int i, ii, j, k, mi, d, kk;
         for(jk=1; jk <=nlstate ; jk++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double **out;
             pp[jk] += freq[jk][m][i];    double sw; /* Sum of weights */
         }    double lli; /* Individual log likelihood */
     int s1, s2;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double bbh, survp;
           pos += pp[jk];    long ipmx;
         for(jk=1; jk <=nlstate ; jk++){    /*extern weight */
           if(pos>=1.e-5)    /* We are differentiating ll according to initial status */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           else    /*for(i=1;i<imx;i++) 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      printf(" %d\n",s[4][i]);
           if( i <= (int) agemax){    */
             if(pos>=1.e-5){    cov[1]=1.;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;    for(k=1; k<=nlstate; k++) ll[k]=0.;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
             }    if(mle==1){
             else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        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++){
         for(jk=-1; jk <=nlstate+ndeath; jk++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=-1; m <=nlstate+ndeath; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            }
         if(i <= (int) agemax)          for(d=0; d<dh[mi][i]; d++){
           fprintf(ficresp,"\n");            newm=savm;
         printf("\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   dateintmean=dateintsum/k2cpt;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fclose(ficresp);            savm=oldm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            oldm=newm;
   free_vector(pp,1,nlstate);          } /* end mult */
          
   /* End of Freq */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 }          /* But now since version 0.9 we anticipate for bias at large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
 /************ Prevalence ********************/           * (in months) between two waves is not a multiple of stepm, we rounded to 
 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)           * the nearest (and in case of equal distance, to the lowest) interval but now
 {  /* Some frequencies */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           * probability in order to take into account the bias as a fraction of the way
   double ***freq; /* Frequencies */           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   double *pp;           * -stepm/2 to stepm/2 .
   double pos, k2;           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
   pp=vector(1,nlstate);           */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          bbh=(double)bh[mi][i]/(double)stepm; 
   j1=0;          /* bias bh is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   j=cptcoveff;           */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            if( s2 > nlstate){ 
  for(k1=1; k1<=j;k1++){            /* i.e. if s2 is a death state and if the date of death is known 
     for(i1=1; i1<=ncodemax[k1];i1++){               then the contribution to the likelihood is the probability to 
       j1++;               die between last step unit time and current  step unit time, 
                 which is also equal to probability to die before dh 
       for (i=-1; i<=nlstate+ndeath; i++)                 minus probability to die before dh-stepm . 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                 In version up to 0.92 likelihood was computed
           for(m=agemin; m <= agemax+3; m++)          as if date of death was unknown. Death was treated as any other
             freq[i][jk][m]=0;          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=1; i<=imx; i++) {          to consider that at each interview the state was recorded
         bool=1;          (healthy, disable or death) and IMaCh was corrected; but when we
         if  (cptcovn>0) {          introduced the exact date of death then we should have modified
           for (z1=1; z1<=cptcoveff; z1++)          the contribution of an exact death to the likelihood. This new
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          contribution is smaller and very dependent of the step unit
               bool=0;          stepm. It is no more the probability to die between last interview
         }          and month of death but the probability to survive from last
         if (bool==1) {          interview up to one month before death multiplied by the
           for(m=firstpass; m<=lastpass; m++){          probability to die within a month. Thanks to Chris
             k2=anint[m][i]+(mint[m][i]/12.);          Jackson for correcting this bug.  Former versions increased
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          mortality artificially. The bad side is that we add another loop
               if(agev[m][i]==0) agev[m][i]=agemax+1;          which slows down the processing. The difference can be up to 10%
               if(agev[m][i]==1) agev[m][i]=agemax+2;          lower mortality.
               if (m<lastpass)            */
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            lli=log(out[s1][s2] - savm[s1][s2]);
               else  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          } else if  (s2==-2) {
             }            for (j=1,survp=0. ; j<=nlstate; j++) 
           }              survp += out[s1][j];
         }            lli= survp;
       }          }
         for(i=(int)agemin; i <= (int)agemax+3; i++){          
           for(jk=1; jk <=nlstate ; jk++){          else if  (s2==-4) {
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            for (j=3,survp=0. ; j<=nlstate; j++) 
               pp[jk] += freq[jk][m][i];              survp += out[s1][j];
           }            lli= survp;
           for(jk=1; jk <=nlstate ; jk++){          }
             for(m=-1, pos=0; m <=0 ; m++)          
             pos += freq[jk][m][i];          else if  (s2==-5) {
         }            for (j=1,survp=0. ; j<=2; j++) 
                      survp += out[s1][j];
          for(jk=1; jk <=nlstate ; jk++){            lli= survp;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          }
              pp[jk] += freq[jk][m][i];  
          }  
                    else{
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            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 */
          for(jk=1; jk <=nlstate ; jk++){                    } 
            if( i <= (int) agemax){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
              if(pos>=1.e-5){          /*if(lli ==000.0)*/
                probs[i][jk][j1]= pp[jk]/pos;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
              }          ipmx +=1;
            }          sw += weight[i];
          }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                  } /* end of wave */
         }      } /* end of individual */
     }    }  else if(mle==2){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_vector(pp,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }  /* End of Freq */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 /************* Waves Concatenation ***************/          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      Death is a valid wave (if date is known).            }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      and mw[mi+1][i]. dh depends on stepm.            savm=oldm;
      */            oldm=newm;
           } /* end mult */
   int i, mi, m;        
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          s1=s[mw[mi][i]][i];
      double sum=0., jmean=0.;*/          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   int j, k=0,jk, ju, jl;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double sum=0.;          ipmx +=1;
   jmin=1e+5;          sw += weight[i];
   jmax=-1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   jmean=0.;        } /* end of wave */
   for(i=1; i<=imx; i++){      } /* end of individual */
     mi=0;    }  else if(mle==3){  /* exponential inter-extrapolation */
     m=firstpass;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     while(s[m][i] <= nlstate){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if(s[m][i]>=1)        for(mi=1; mi<= wav[i]-1; mi++){
         mw[++mi][i]=m;          for (ii=1;ii<=nlstate+ndeath;ii++)
       if(m >=lastpass)            for (j=1;j<=nlstate+ndeath;j++){
         break;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         m++;            }
     }/* end while */          for(d=0; d<dh[mi][i]; d++){
     if (s[m][i] > nlstate){            newm=savm;
       mi++;     /* Death is another wave */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       /* if(mi==0)  never been interviewed correctly before death */            for (kk=1; kk<=cptcovage;kk++) {
          /* Only death is a correct wave */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       mw[mi][i]=m;            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     wav[i]=mi;            savm=oldm;
     if(mi==0)            oldm=newm;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          } /* end mult */
   }        
           s1=s[mw[mi][i]][i];
   for(i=1; i<=imx; i++){          s2=s[mw[mi+1][i]][i];
     for(mi=1; mi<wav[i];mi++){          bbh=(double)bh[mi][i]/(double)stepm; 
       if (stepm <=0)          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 */
         dh[mi][i]=1;          ipmx +=1;
       else{          sw += weight[i];
         if (s[mw[mi+1][i]][i] > nlstate) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if (agedc[i] < 2*AGESUP) {        } /* end of wave */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      } /* end of individual */
           if(j==0) j=1;  /* Survives at least one month after exam */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           k=k+1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if (j >= jmax) jmax=j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (j <= jmin) jmin=j;        for(mi=1; mi<= wav[i]-1; mi++){
           sum=sum+j;          for (ii=1;ii<=nlstate+ndeath;ii++)
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            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);
         else{            }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          for(d=0; d<dh[mi][i]; d++){
           k=k+1;            newm=savm;
           if (j >= jmax) jmax=j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           else if (j <= jmin)jmin=j;            for (kk=1; kk<=cptcovage;kk++) {
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           sum=sum+j;            }
         }          
         jk= j/stepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         jl= j -jk*stepm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         ju= j -(jk+1)*stepm;            savm=oldm;
         if(jl <= -ju)            oldm=newm;
           dh[mi][i]=jk;          } /* end mult */
         else        
           dh[mi][i]=jk+1;          s1=s[mw[mi][i]][i];
         if(dh[mi][i]==0)          s2=s[mw[mi+1][i]][i];
           dh[mi][i]=1; /* At least one step */          if( s2 > nlstate){ 
       }            lli=log(out[s1][s2] - savm[s1][s2]);
     }          }else{
   }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   jmean=sum/k;          }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          ipmx +=1;
  }          sw += weight[i];
 /*********** Tricode ****************************/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 void tricode(int *Tvar, int **nbcode, int imx)  /*      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 */
   int Ndum[20],ij=1, k, j, i;      } /* end of individual */
   int cptcode=0;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   cptcoveff=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (k=0; k<19; k++) Ndum[k]=0;        for(mi=1; mi<= wav[i]-1; mi++){
   for (k=1; k<=7; k++) ncodemax[k]=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1; i<=imx; i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=(int)(covar[Tvar[j]][i]);            }
       Ndum[ij]++;          for(d=0; d<dh[mi][i]; d++){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            newm=savm;
       if (ij > cptcode) cptcode=ij;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (i=0; i<=cptcode; i++) {            }
       if(Ndum[i]!=0) ncodemax[j]++;          
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     ij=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
     for (i=1; i<=ncodemax[j]; i++) {          } /* end mult */
       for (k=0; k<=19; k++) {        
         if (Ndum[k] != 0) {          s1=s[mw[mi][i]][i];
           nbcode[Tvar[j]][ij]=k;          s2=s[mw[mi+1][i]][i];
                    lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ij++;          ipmx +=1;
         }          sw += weight[i];
         if (ij > ncodemax[j]) break;          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]);*/
     }        } /* end of wave */
   }        } /* end of individual */
     } /* End of if */
  for (k=0; k<19; k++) Ndum[k]=0;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  for (i=1; i<=ncovmodel-2; i++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       ij=Tvar[i];    return -l;
       Ndum[ij]++;  }
     }  
   /*************** log-likelihood *************/
  ij=1;  double funcone( double *x)
  for (i=1; i<=10; i++) {  {
    if((Ndum[i]!=0) && (i<=ncovcol)){    /* Same as likeli but slower because of a lot of printf and if */
      Tvaraff[ij]=i;    int i, ii, j, k, mi, d, kk;
      ij++;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
    }    double **out;
  }    double lli; /* Individual log likelihood */
      double llt;
     cptcoveff=ij-1;    int s1, s2;
 }    double bbh, survp;
     /*extern weight */
 /*********** Health Expectancies ****************/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 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 )    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 {    */
   /* Health expectancies */    cov[1]=1.;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  
   double age, agelim, hf;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *xp;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **gp, **gm;      for(mi=1; mi<= wav[i]-1; mi++){
   double ***gradg, ***trgradg;        for (ii=1;ii<=nlstate+ndeath;ii++)
   int theta;          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate*2,1,npar);        for(d=0; d<dh[mi][i]; d++){
   doldm=matrix(1,nlstate*2,1,nlstate*2);          newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficreseij,"# Health expectancies\n");          for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficreseij,"# Age");            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=nlstate;j++)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficreseij," %1d-%1d (SE)",i,j);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficreseij,"\n");          savm=oldm;
           oldm=newm;
   if(estepm < stepm){        } /* end mult */
     printf ("Problem %d lower than %d\n",estepm, stepm);        
   }        s1=s[mw[mi][i]][i];
   else  hstepm=estepm;          s2=s[mw[mi+1][i]][i];
   /* We compute the life expectancy from trapezoids spaced every estepm months        bbh=(double)bh[mi][i]/(double)stepm; 
    * This is mainly to measure the difference between two models: for example        /* bias is positive if real duration
    * if stepm=24 months pijx are given only every 2 years and by summing them         * is higher than the multiple of stepm and negative otherwise.
    * we are calculating an estimate of the Life Expectancy assuming a linear         */
    * progression inbetween and thus overestimating or underestimating according        if( s2 > nlstate && (mle <5) ){  /* Jackson */
    * to the curvature of the survival function. If, for the same date, we          lli=log(out[s1][s2] - savm[s1][s2]);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        } else if (mle==1){
    * to compare the new estimate of Life expectancy with the same linear          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
    * hypothesis. A more precise result, taking into account a more precise        } else if(mle==2){
    * curvature will be obtained if estepm is as small as 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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
   /* For example we decided to compute the life expectancy with the smallest unit */          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 */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        } else if (mle==4){  /* mle=4 no inter-extrapolation */
      nhstepm is the number of hstepm from age to agelim          lli=log(out[s1][s2]); /* Original formula */
      nstepm is the number of stepm from age to agelin.        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
      Look at hpijx to understand the reason of that which relies in memory size          lli=log(out[s1][s2]); /* Original formula */
      and note for a fixed period like estepm months */        } /* End of if */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        ipmx +=1;
      survival function given by stepm (the optimization length). Unfortunately it        sw += weight[i];
      means that if the survival funtion is printed only each two years of age and if        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  /*       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]); */
      results. So we changed our mind and took the option of the best precision.        if(globpr){
   */          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */   %10.6f %10.6f %10.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   agelim=AGESUP;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     /* nhstepm age range expressed in number of stepm */            llt +=ll[k]*gipmx/gsw;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          }
     /* if (stepm >= YEARM) hstepm=1;*/          fprintf(ficresilk," %10.6f\n", -llt);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end of wave */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    } /* end of individual */
     gp=matrix(0,nhstepm,1,nlstate*2);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     gm=matrix(0,nhstepm,1,nlstate*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 */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    if(globpr==0){ /* First time we count the contributions and weights */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      gipmx=ipmx;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        gsw=sw;
      }
     return -l;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  }
   
     /* Computing Variances of health expectancies */  
   /*************** function likelione ***********/
      for(theta=1; theta <=npar; theta++){  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<=npar; i++){  {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* This routine should help understanding what is done with 
       }       the selection of individuals/waves and
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         to check the exact contribution to the likelihood.
         Plotting could be done.
       cptj=0;     */
       for(j=1; j<= nlstate; j++){    int k;
         for(i=1; i<=nlstate; i++){  
           cptj=cptj+1;    if(*globpri !=0){ /* Just counts and sums, no printings */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      strcpy(fileresilk,"ilk"); 
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      strcat(fileresilk,fileres);
           }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         }        printf("Problem with resultfile: %s\n", fileresilk);
       }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
            }
            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");
       for(i=1; i<=npar; i++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(k=1; k<=nlstate; k++) 
              fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       cptj=0;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       for(j=1; j<= nlstate; j++){    }
         for(i=1;i<=nlstate;i++){  
           cptj=cptj+1;    *fretone=(*funcone)(p);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    if(*globpri !=0){
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      fclose(ficresilk);
           }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         }      fflush(fichtm); 
       }    } 
          return;
      }
   
       for(j=1; j<= nlstate*2; j++)  
         for(h=0; h<=nhstepm-1; h++){  /*********** Maximum Likelihood Estimation ***************/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
      }    int i,j, iter;
        double **xi;
 /* End theta */    double fret;
     double fretone; /* Only one call to likelihood */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
      for(h=0; h<=nhstepm-1; h++)    for (i=1;i<=npar;i++)
       for(j=1; j<=nlstate*2;j++)      for (j=1;j<=npar;j++)
         for(theta=1; theta <=npar; theta++)        xi[i][j]=(i==j ? 1.0 : 0.0);
         trgradg[h][j][theta]=gradg[h][theta][j];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
      for(i=1;i<=nlstate*2;i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       for(j=1;j<=nlstate*2;j++)      printf("Problem with resultfile: %s\n", filerespow);
         varhe[i][j][(int)age] =0.;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     for(h=0;h<=nhstepm-1;h++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       for(k=0;k<=nhstepm-1;k++){    for (i=1;i<=nlstate;i++)
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      for(j=1;j<=nlstate+ndeath;j++)
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         for(i=1;i<=nlstate*2;i++)    fprintf(ficrespow,"\n");
           for(j=1;j<=nlstate*2;j++)  
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    powell(p,xi,npar,ftol,&iter,&fret,func);
       }  
     }    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
          printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     /* Computing expectancies */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(i=1; i<=nlstate;i++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(j=1; j<=nlstate;j++)  
         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;  
            /**** Computes Hessian and covariance matrix ***/
 /* 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]);*/  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
         }    double  **a,**y,*x,pd;
     double **hess;
     fprintf(ficreseij,"%3.0f",age );    int i, j,jk;
     cptj=0;    int *indx;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         cptj++;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    void lubksb(double **a, int npar, int *indx, double b[]) ;
       }    void ludcmp(double **a, int npar, int *indx, double *d) ;
     fprintf(ficreseij,"\n");    double gompertz(double p[]);
        hess=matrix(1,npar,1,npar);
     free_matrix(gm,0,nhstepm,1,nlstate*2);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);    printf("\nCalculation of the hessian matrix. Wait...\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    for (i=1;i<=npar;i++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("%d",i);fflush(stdout);
   }      fprintf(ficlog,"%d",i);fflush(ficlog);
   free_vector(xp,1,npar);     
   free_matrix(dnewm,1,nlstate*2,1,npar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      /*  printf(" %f ",p[i]);
 }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
 /************ Variance ******************/    
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    for (i=1;i<=npar;i++) {
 {      for (j=1;j<=npar;j++)  {
   /* Variance of health expectancies */        if (j>i) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          printf(".%d%d",i,j);fflush(stdout);
   double **newm;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double **dnewm,**doldm;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   int i, j, nhstepm, hstepm, h, nstepm ;          
   int k, cptcode;          hess[j][i]=hess[i][j];    
   double *xp;          /*printf(" %lf ",hess[i][j]);*/
   double **gp, **gm;        }
   double ***gradg, ***trgradg;      }
   double ***p3mat;    }
   double age,agelim, hf;    printf("\n");
   int theta;    fprintf(ficlog,"\n");
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficresvij,"# Age");    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   for(i=1; i<=nlstate;i++)    
     for(j=1; j<=nlstate;j++)    a=matrix(1,npar,1,npar);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    y=matrix(1,npar,1,npar);
   fprintf(ficresvij,"\n");    x=vector(1,npar);
     indx=ivector(1,npar);
   xp=vector(1,npar);    for (i=1;i<=npar;i++)
   dnewm=matrix(1,nlstate,1,npar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   doldm=matrix(1,nlstate,1,nlstate);    ludcmp(a,npar,indx,&pd);
    
   if(estepm < stepm){    for (j=1;j<=npar;j++) {
     printf ("Problem %d lower than %d\n",estepm, stepm);      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
   else  hstepm=estepm;        lubksb(a,npar,indx,x);
   /* For example we decided to compute the life expectancy with the smallest unit */      for (i=1;i<=npar;i++){ 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        matcov[i][j]=x[i];
      nhstepm is the number of hstepm from age to agelim      }
      nstepm is the number of stepm from age to agelin.    }
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */    printf("\n#Hessian matrix#\n");
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    fprintf(ficlog,"\n#Hessian matrix#\n");
      survival function given by stepm (the optimization length). Unfortunately it    for (i=1;i<=npar;i++) { 
      means that if the survival funtion is printed only each two years of age and if      for (j=1;j<=npar;j++) { 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        printf("%.3e ",hess[i][j]);
      results. So we changed our mind and took the option of the best precision.        fprintf(ficlog,"%.3e ",hess[i][j]);
   */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      printf("\n");
   agelim = AGESUP;      fprintf(ficlog,"\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    /* Recompute Inverse */
     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]=matcov[i][j];
     gp=matrix(0,nhstepm,1,nlstate);    ludcmp(a,npar,indx,&pd);
     gm=matrix(0,nhstepm,1,nlstate);  
     /*  printf("\n#Hessian matrix recomputed#\n");
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    for (j=1;j<=npar;j++) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        lubksb(a,npar,indx,x);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
       if (popbased==1) {        printf("%.3e ",y[i][j]);
         for(i=1; i<=nlstate;i++)        fprintf(ficlog,"%.3e ",y[i][j]);
           prlim[i][i]=probs[(int)age][i][ij];      }
       }      printf("\n");
        fprintf(ficlog,"\n");
       for(j=1; j<= nlstate; j++){    }
         for(h=0; h<=nhstepm; h++){    */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    free_matrix(a,1,npar,1,npar);
         }    free_matrix(y,1,npar,1,npar);
       }    free_vector(x,1,npar);
        free_ivector(indx,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    free_matrix(hess,1,npar,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
    
       if (popbased==1) {  /*************** hessian matrix ****************/
         for(i=1; i<=nlstate;i++)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           prlim[i][i]=probs[(int)age][i][ij];  {
       }    int i;
     int l=1, lmax=20;
       for(j=1; j<= nlstate; j++){    double k1,k2;
         for(h=0; h<=nhstepm; h++){    double p2[NPARMAX+1];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    double res;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         }    double fx;
       }    int k=0,kmax=10;
     double l1;
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; h++){    fx=func(x);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    for (i=1;i<=npar;i++) p2[i]=x[i];
         }    for(l=0 ; l <=lmax; l++){
     } /* End theta */      l1=pow(10,l);
       delts=delt;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
     for(h=0; h<=nhstepm; h++)        p2[theta]=x[theta] +delt;
       for(j=1; j<=nlstate;j++)        k1=func(p2)-fx;
         for(theta=1; theta <=npar; theta++)        p2[theta]=x[theta]-delt;
           trgradg[h][j][theta]=gradg[h][theta][j];        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     for(i=1;i<=nlstate;i++)        
       for(j=1;j<=nlstate;j++)  #ifdef DEBUG
         vareij[i][j][(int)age] =0.;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     for(h=0;h<=nhstepm;h++){  #endif
       for(k=0;k<=nhstepm;k++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          k=kmax;
         for(i=1;i<=nlstate;i++)        }
           for(j=1;j<=nlstate;j++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          k=kmax; l=lmax*10.;
       }        }
     }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
     fprintf(ficresvij,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++){    }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    delti[theta]=delts;
       }    return res; 
     fprintf(ficresvij,"\n");    
     free_matrix(gp,0,nhstepm,1,nlstate);  }
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i;
   } /* End age */    int l=1, l1, lmax=20;
      double k1,k2,k3,k4,res,fx;
   free_vector(xp,1,npar);    double p2[NPARMAX+1];
   free_matrix(doldm,1,nlstate,1,npar);    int k;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     fx=func(x);
 }    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
 /************ Variance of prevlim ******************/      p2[thetai]=x[thetai]+delti[thetai]/k;
 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)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 {      k1=func(p2)-fx;
   /* Variance of prevalence limit */    
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      p2[thetai]=x[thetai]+delti[thetai]/k;
   double **newm;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double **dnewm,**doldm;      k2=func(p2)-fx;
   int i, j, nhstepm, hstepm;    
   int k, cptcode;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double *xp;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double *gp, *gm;      k3=func(p2)-fx;
   double **gradg, **trgradg;    
   double age,agelim;      p2[thetai]=x[thetai]-delti[thetai]/k;
   int theta;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k4=func(p2)-fx;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   fprintf(ficresvpl,"# Age");  #ifdef DEBUG
   for(i=1; i<=nlstate;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(ficresvpl," %1d-%1d",i,i);      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);
   fprintf(ficresvpl,"\n");  #endif
     }
   xp=vector(1,npar);    return res;
   dnewm=matrix(1,nlstate,1,npar);  }
   doldm=matrix(1,nlstate,1,nlstate);  
    /************** Inverse of matrix **************/
   hstepm=1*YEARM; /* Every year of age */  void ludcmp(double **a, int n, int *indx, double *d) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  { 
   agelim = AGESUP;    int i,imax,j,k; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double big,dum,sum,temp; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double *vv; 
     if (stepm >= YEARM) hstepm=1;   
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    vv=vector(1,n); 
     gradg=matrix(1,npar,1,nlstate);    *d=1.0; 
     gp=vector(1,nlstate);    for (i=1;i<=n;i++) { 
     gm=vector(1,nlstate);      big=0.0; 
       for (j=1;j<=n;j++) 
     for(theta=1; theta <=npar; theta++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
       for(i=1; i<=npar; i++){ /* Computes gradient */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      vv[i]=1.0/big; 
       }    } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (j=1;j<=n;j++) { 
       for(i=1;i<=nlstate;i++)      for (i=1;i<j;i++) { 
         gp[i] = prlim[i][i];        sum=a[i][j]; 
            for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(i=1; i<=npar; i++) /* Computes gradient */        a[i][j]=sum; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      big=0.0; 
       for(i=1;i<=nlstate;i++)      for (i=j;i<=n;i++) { 
         gm[i] = prlim[i][i];        sum=a[i][j]; 
         for (k=1;k<j;k++) 
       for(i=1;i<=nlstate;i++)          sum -= a[i][k]*a[k][j]; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        a[i][j]=sum; 
     } /* End theta */        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
     trgradg =matrix(1,nlstate,1,npar);          imax=i; 
         } 
     for(j=1; j<=nlstate;j++)      } 
       for(theta=1; theta <=npar; theta++)      if (j != imax) { 
         trgradg[j][theta]=gradg[theta][j];        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
     for(i=1;i<=nlstate;i++)          a[imax][k]=a[j][k]; 
       varpl[i][(int)age] =0.;          a[j][k]=dum; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        } 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        *d = -(*d); 
     for(i=1;i<=nlstate;i++)        vv[imax]=vv[j]; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      } 
       indx[j]=imax; 
     fprintf(ficresvpl,"%.0f ",age );      if (a[j][j] == 0.0) a[j][j]=TINY; 
     for(i=1; i<=nlstate;i++)      if (j != n) { 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        dum=1.0/(a[j][j]); 
     fprintf(ficresvpl,"\n");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_vector(gp,1,nlstate);      } 
     free_vector(gm,1,nlstate);    } 
     free_matrix(gradg,1,npar,1,nlstate);    free_vector(vv,1,n);  /* Doesn't work */
     free_matrix(trgradg,1,nlstate,1,npar);  ;
   } /* End age */  } 
   
   free_vector(xp,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
   free_matrix(doldm,1,nlstate,1,npar);  { 
   free_matrix(dnewm,1,nlstate,1,nlstate);    int i,ii=0,ip,j; 
     double sum; 
 }   
     for (i=1;i<=n;i++) { 
 /************ Variance of one-step probabilities  ******************/      ip=indx[i]; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)      sum=b[ip]; 
 {      b[ip]=b[i]; 
   int i, j, i1, k1, j1, z1;      if (ii) 
   int k=0, cptcode;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double **dnewm,**doldm;      else if (sum) ii=i; 
   double *xp;      b[i]=sum; 
   double *gp, *gm;    } 
   double **gradg, **trgradg;    for (i=n;i>=1;i--) { 
   double age,agelim, cov[NCOVMAX];      sum=b[i]; 
   int theta;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   char fileresprob[FILENAMELENGTH];      b[i]=sum/a[i][i]; 
     } 
   strcpy(fileresprob,"prob");  } 
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  /************ Frequencies ********************/
     printf("Problem with resultfile: %s\n", fileresprob);  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[])
   }  {  /* Some frequencies */
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    
      int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    int first;
   fprintf(ficresprob,"# Age");    double ***freq; /* Frequencies */
   for(i=1; i<=nlstate;i++)    double *pp, **prop;
     for(j=1; j<=(nlstate+ndeath);j++)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
     
   fprintf(ficresprob,"\n");    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   xp=vector(1,npar);    strcat(fileresp,fileres);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   cov[1]=1;      exit(0);
   j=cptcoveff;    }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   j1=0;    j1=0;
   for(k1=1; k1<=1;k1++){    
     for(i1=1; i1<=ncodemax[k1];i1++){    j=cptcoveff;
     j1++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
     if  (cptcovn>0) {    first=1;
       fprintf(ficresprob, "\n#********** Variable ");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for(k1=1; k1<=j;k1++){
       fprintf(ficresprob, "**********\n#");      for(i1=1; i1<=ncodemax[k1];i1++){
     }        j1++;
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for (age=bage; age<=fage; age ++){          scanf("%d", i);*/
         cov[2]=age;        for (i=-5; i<=nlstate+ndeath; i++)  
         for (k=1; k<=cptcovn;k++) {          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            for(m=iagemin; m <= iagemax+3; m++)
                        freq[i][jk][m]=0;
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for (i=1; i<=nlstate; i++)  
         for (k=1; k<=cptcovprod;k++)        for(m=iagemin; m <= iagemax+3; m++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          prop[i][m]=0;
                
         gradg=matrix(1,npar,1,9);        dateintsum=0;
         trgradg=matrix(1,9,1,npar);        k2cpt=0;
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        for (i=1; i<=imx; i++) {
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          bool=1;
              if  (cptcovn>0) {
         for(theta=1; theta <=npar; theta++){            for (z1=1; z1<=cptcoveff; z1++) 
           for(i=1; i<=npar; i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);                bool=0;
                    }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          if (bool==1){
                      for(m=firstpass; m<=lastpass; m++){
           k=0;              k2=anint[m][i]+(mint[m][i]/12.);
           for(i=1; i<= (nlstate+ndeath); i++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             for(j=1; j<=(nlstate+ndeath);j++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               k=k+1;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               gp[k]=pmmij[i][j];                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
             }                if (m<lastpass) {
           }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                            freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           for(i=1; i<=npar; i++)                }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);                
                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                  dateintsum=dateintsum+k2;
           k=0;                  k2cpt++;
           for(i=1; i<=(nlstate+ndeath); i++){                }
             for(j=1; j<=(nlstate+ndeath);j++){                /*}*/
               k=k+1;            }
               gm[k]=pmmij[i][j];          }
             }        }
           }         
              /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  fprintf(ficresp, "#Local time at start: %s", strstart);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          if  (cptcovn>0) {
         }          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          fprintf(ficresp, "**********\n#");
           for(theta=1; theta <=npar; theta++)        }
             trgradg[j][theta]=gradg[theta][j];        for(i=1; i<=nlstate;i++) 
                  fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        fprintf(ficresp, "\n");
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        
                for(i=iagemin; i <= iagemax+3; i++){
         pmij(pmmij,cov,ncovmodel,x,nlstate);          if(i==iagemax+3){
                    fprintf(ficlog,"Total");
         k=0;          }else{
         for(i=1; i<=(nlstate+ndeath); i++){            if(first==1){
           for(j=1; j<=(nlstate+ndeath);j++){              first=0;
             k=k+1;              printf("See log file for details...\n");
             gm[k]=pmmij[i][j];            }
           }            fprintf(ficlog,"Age %d", i);
         }          }
                for(jk=1; jk <=nlstate ; jk++){
      /*printf("\n%d ",(int)age);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              pp[jk] += freq[jk][m][i]; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          }
      }*/          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
         fprintf(ficresprob,"\n%d ",(int)age);              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)              if(first==1){
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }
       }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }            }else{
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              if(first==1)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            }
   }          }
   free_vector(xp,1,npar);  
   fclose(ficresprob);          for(jk=1; jk <=nlstate ; jk++){
              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 }              pp[jk] += freq[jk][m][i];
           }       
 /******************* Printing html file ***********/          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \            pos += pp[jk];
  int lastpass, int stepm, int weightopt, char model[],\            posprop += prop[jk][i];
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \          }
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\          for(jk=1; jk <=nlstate ; jk++){
  char version[], int popforecast, int estepm ){            if(pos>=1.e-5){
   int jj1, k1, i1, cpt;              if(first==1)
   FILE *fichtm;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   /*char optionfilehtm[FILENAMELENGTH];*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
   strcpy(optionfilehtm,optionfile);              if(first==1)
   strcat(optionfilehtm,".htm");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("Problem with %s \n",optionfilehtm), exit(0);            }
   }            if( i <= iagemax){
               if(pos>=1.e-5){
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n                /*probs[i][jk][j1]= pp[jk]/pos;*/
 \n                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 Total number of observations=%d <br>\n              }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              else
 <hr  size=\"2\" color=\"#EC5E5E\">                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
  <ul><li>Outputs 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>\n          
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          for(jk=-1; jk <=nlstate+ndeath; jk++)
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n            for(m=-1; m <=nlstate+ndeath; m++)
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n              if(freq[jk][m][i] !=0 ) {
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
  fprintf(fichtm,"\n                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n              }
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n          if(i <= iagemax)
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n            fprintf(ficresp,"\n");
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n          if(first==1)
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);            printf("Others in log...\n");
           fprintf(ficlog,"\n");
  if(popforecast==1) fprintf(fichtm,"\n        }
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      }
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    }
         <br>",fileres,fileres,fileres,fileres);    dateintmean=dateintsum/k2cpt; 
  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);    fclose(ficresp);
 fprintf(fichtm," <li>Graphs</li><p>");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
  m=cptcoveff;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /* End of Freq */
   }
  jj1=0;  
  for(k1=1; k1<=m;k1++){  /************ Prevalence ********************/
    for(i1=1; i1<=ncodemax[k1];i1++){  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)
        jj1++;  {  
        if (cptcovn > 0) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");       in each health status at the date of interview (if between dateprev1 and dateprev2).
          for (cpt=1; cpt<=cptcoveff;cpt++)       We still use firstpass and lastpass as another selection.
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");   
        }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double ***freq; /* Frequencies */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        double *pp, **prop;
        for(cpt=1; cpt<nlstate;cpt++){    double pos,posprop; 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    double  y2; /* in fractional years */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    int iagemin, iagemax;
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {    iagemin= (int) agemin;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    iagemax= (int) agemax;
 interval) in state (%d): v%s%d%d.gif <br>    /*pp=vector(1,nlstate);*/
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      prop=matrix(1,nlstate,iagemin,iagemax+3); 
      }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      for(cpt=1; cpt<=nlstate;cpt++) {    j1=0;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    j=cptcoveff;
      }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.gif<br>    for(k1=1; k1<=j;k1++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      for(i1=1; i1<=ncodemax[k1];i1++){
 fprintf(fichtm,"\n</body>");        j1++;
    }        
    }        for (i=1; i<=nlstate; i++)  
 fclose(fichtm);          for(m=iagemin; m <= iagemax+3; m++)
 }            prop[i][m]=0.0;
        
 /******************* Gnuplot file **************/        for (i=1; i<=imx; i++) { /* Each individual */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          bool=1;
           if  (cptcovn>0) {
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   strcpy(optionfilegnuplot,optionfilefiname);                bool=0;
   strcat(optionfilegnuplot,".gp.txt");          } 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          if (bool==1) { 
     printf("Problem with file %s",optionfilegnuplot);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 #ifdef windows                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficgp,"cd \"%s\" \n",pathc);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 #endif                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
 m=pow(2,cptcoveff);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                    /*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]]);*/
  /* 1eme*/                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   for (cpt=1; cpt<= nlstate ; cpt ++) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
    for (k1=1; k1<= m ; k1 ++) {                } 
               }
 #ifdef windows            } /* end selection of waves */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          }
 #endif        }
 #ifdef unix        for(i=iagemin; i <= iagemax+3; i++){  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          
 #endif          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
 for (i=1; i<= nlstate ; i ++) {          } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){     
 }            if( i <=  iagemax){ 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              if(posprop>=1.e-5){ 
     for (i=1; i<= nlstate ; i ++) {                probs[i][jk][j1]= prop[jk][i]/posprop;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            } 
 }          }/* end jk */ 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        }/* end i */ 
      for (i=1; i<= nlstate ; i ++) {      } /* end i1 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } /* end k1 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /*free_vector(pp,1,nlstate);*/
 #ifdef unix    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 fprintf(ficgp,"\nset ter gif small size 400,300");  }  /* End of prevalence */
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  /************* Waves Concatenation ***************/
    }  
   }  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)
   /*2 eme*/  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   for (k1=1; k1<= m ; k1 ++) {       Death is a valid wave (if date is known).
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for (i=1; i<= nlstate+1 ; i ++) {       and mw[mi+1][i]. dh depends on stepm.
       k=2*i;       */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    int i, mi, m;
   if (j==i) 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;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    int j, k=0,jk, ju, jl;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double sum=0.;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    first=0;
       for (j=1; j<= nlstate+1 ; j ++) {    jmin=1e+5;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    jmax=-1;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    jmean=0.;
 }      for(i=1; i<=imx; i++){
       fprintf(ficgp,"\" t\"\" w l 0,");      mi=0;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      m=firstpass;
       for (j=1; j<= nlstate+1 ; j ++) {      while(s[m][i] <= nlstate){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          mw[++mi][i]=m;
 }          if(m >=lastpass)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          break;
       else fprintf(ficgp,"\" t\"\" w l 0,");        else
     }          m++;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      }/* end while */
   }      if (s[m][i] > nlstate){
          mi++;     /* Death is another wave */
   /*3eme*/        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
   for (k1=1; k1<= m ; k1 ++) {        mw[mi][i]=m;
     for (cpt=1; cpt<= nlstate ; cpt ++) {      }
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      wav[i]=mi;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      if(mi==0){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        nbwarn++;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        if(first==0){
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          first=1;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
         if(first==1){
 */          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],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);      } /* end mi==0 */
     } /* End individuals */
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
     }        if (stepm <=0)
            dh[mi][i]=1;
   /* CV preval stat */        else{
     for (k1=1; k1<= m ; k1 ++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     for (cpt=1; cpt<nlstate ; cpt ++) {            if (agedc[i] < 2*AGESUP) {
       k=3;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
       for (i=1; i< nlstate ; i ++)                nberr++;
         fprintf(ficgp,"+$%d",k+i+1);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                j=1; /* Temporary Dangerous patch */
                      printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       l=3+(nlstate+ndeath)*cpt;                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,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for (i=1; i< nlstate ; i ++) {              }
         l=3+(nlstate+ndeath)*cpt;              k=k+1;
         fprintf(ficgp,"+$%d",l+i+1);              if (j >= jmax){
       }                jmax=j;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  ijmax=i;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
     }              if (j <= jmin){
   }                  jmin=j;
                  ijmin=i;
   /* proba elementaires */              }
    for(i=1,jk=1; i <=nlstate; i++){              sum=sum+j;
     for(k=1; k <=(nlstate+ndeath); k++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       if (k != i) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for(j=1; j <=ncovmodel; j++){            }
                  }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          else{
           jk++;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           fprintf(ficgp,"\n");  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
         }  
       }            k=k+1;
     }            if (j >= jmax) {
     }              jmax=j;
               ijmax=i;
     for(jk=1; jk <=m; jk++) {            }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            else if (j <= jmin){
    i=1;              jmin=j;
    for(k2=1; k2<=nlstate; k2++) {              ijmin=i;
      k3=i;            }
      for(k=1; k<=(nlstate+ndeath); k++) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        if (k != k2){            /*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]);*/
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            if(j<0){
 ij=1;              nberr++;
         for(j=3; j <=ncovmodel; j++) {              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]);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
             ij++;            sum=sum+j;
           }          }
           else          jk= j/stepm;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          jl= j -jk*stepm;
         }          ju= j -(jk+1)*stepm;
           fprintf(ficgp,")/(1");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                    if(jl==0){
         for(k1=1; k1 <=nlstate; k1++){                dh[mi][i]=jk;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              bh[mi][i]=0;
 ij=1;            }else{ /* We want a negative bias in order to only have interpolation ie
           for(j=3; j <=ncovmodel; j++){                    * at the price of an extra matrix product in likelihood */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              dh[mi][i]=jk+1;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              bh[mi][i]=ju;
             ij++;            }
           }          }else{
           else            if(jl <= -ju){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              dh[mi][i]=jk;
           }              bh[mi][i]=jl;       /* bias is positive if real duration
           fprintf(ficgp,")");                                   * is higher than the multiple of stepm and negative otherwise.
         }                                   */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            else{
         i=i+ncovmodel;              dh[mi][i]=jk+1;
        }              bh[mi][i]=ju;
      }            }
    }            if(dh[mi][i]==0){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              dh[mi][i]=1; /* At least one step */
    }              bh[mi][i]=ju; /* At least one step */
                  /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   fclose(ficgp);            }
 }  /* end gnuplot */          } /* end if mle */
         }
       } /* end wave */
 /*************** Moving average **************/    }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   int i, cpt, cptcod;    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)   }
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  /*********** Tricode ****************************/
           mobaverage[(int)agedeb][i][cptcod]=0.;  void tricode(int *Tvar, int **nbcode, int imx)
      {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    
       for (i=1; i<=nlstate;i++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int cptcode=0;
           for (cpt=0;cpt<=4;cpt++){    cptcoveff=0; 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];   
           }    for (k=0; k<maxncov; k++) Ndum[k]=0;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    for (k=1; k<=7; k++) ncodemax[k]=0;
         }  
       }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                     modality*/ 
 }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 /************** Forecasting ******************/        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 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){                                         Tvar[j]. If V=sex and male is 0 and 
                                           female is 1, then  cptcode=1.*/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      }
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      for (i=0; i<=cptcode; i++) {
   double *popeffectif,*popcount;        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 */
   double ***p3mat;      }
   char fileresf[FILENAMELENGTH];  
       ij=1; 
  agelim=AGESUP;      for (i=1; i<=ncodemax[j]; i++) {
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            nbcode[Tvar[j]][ij]=k; 
              /* 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; */
              
   strcpy(fileresf,"f");            ij++;
   strcat(fileresf,fileres);          }
   if((ficresf=fopen(fileresf,"w"))==NULL) {          if (ij > ncodemax[j]) break; 
     printf("Problem with forecast resultfile: %s\n", fileresf);        }  
   }      } 
   printf("Computing forecasting: result on file '%s' \n", fileresf);    }  
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
   if (mobilav==1) {   for (i=1; i<=ncovmodel-2; i++) { 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     movingaverage(agedeb, fage, ageminpar, mobaverage);     ij=Tvar[i];
   }     Ndum[ij]++;
    }
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;   ij=1;
     for (i=1; i<= maxncov; i++) {
   agelim=AGESUP;     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
   hstepm=1;       ij++;
   hstepm=hstepm/stepm;     }
   yp1=modf(dateintmean,&yp);   }
   anprojmean=yp;   
   yp2=modf((yp1*12),&yp);   cptcoveff=ij-1; /*Number of simple covariates*/
   mprojmean=yp;  }
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;  /*********** Health Expectancies ****************/
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;  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,char strstart[] )
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  {
      /* Health expectancies */
   for(cptcov=1;cptcov<=i2;cptcov++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double age, agelim, hf;
       k=k+1;    double ***p3mat,***varhe;
       fprintf(ficresf,"\n#******");    double **dnewm,**doldm;
       for(j=1;j<=cptcoveff;j++) {    double *xp;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **gp, **gm;
       }    double ***gradg, ***trgradg;
       fprintf(ficresf,"******\n");    int theta;
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
          xp=vector(1,npar);
          dnewm=matrix(1,nlstate*nlstate,1,npar);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         fprintf(ficresf,"\n");    
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      fprintf(ficreseij,"# Local time at start: %s", strstart);
     fprintf(ficreseij,"# Health expectancies\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficreseij,"# Age");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for(i=1; i<=nlstate;i++)
           nhstepm = nhstepm/hstepm;      for(j=1; j<=nlstate;j++)
                  fprintf(ficreseij," %1d-%1d (SE)",i,j);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficreseij,"\n");
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
           for (h=0; h<=nhstepm; h++){    }
             if (h==(int) (calagedate+YEARM*cpt)) {    else  hstepm=estepm;   
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    /* We compute the life expectancy from trapezoids spaced every estepm months
             }     * This is mainly to measure the difference between two models: for example
             for(j=1; j<=nlstate+ndeath;j++) {     * if stepm=24 months pijx are given only every 2 years and by summing them
               kk1=0.;kk2=0;     * we are calculating an estimate of the Life Expectancy assuming a linear 
               for(i=1; i<=nlstate;i++) {                   * progression in between and thus overestimating or underestimating according
                 if (mobilav==1)     * to the curvature of the survival function. If, for the same date, we 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
                 else {     * to compare the new estimate of Life expectancy with the same linear 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];     * hypothesis. A more precise result, taking into account a more precise
                 }     * curvature will be obtained if estepm is as small as stepm. */
                  
               }    /* For example we decided to compute the life expectancy with the smallest unit */
               if (h==(int)(calagedate+12*cpt)){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                 fprintf(ficresf," %.3f", kk1);       nhstepm is the number of hstepm from age to agelim 
                               nstepm is the number of stepm from age to agelin. 
               }       Look at hpijx to understand the reason of that which relies in memory size
             }       and note for a fixed period like estepm months */
           }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       survival function given by stepm (the optimization length). Unfortunately it
         }       means that if the survival funtion is printed only each two years of age and if
       }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     }       results. So we changed our mind and took the option of the best precision.
   }    */
            hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     agelim=AGESUP;
   fclose(ficresf);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 }      /* nhstepm age range expressed in number of stepm */
 /************** Forecasting ******************/      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 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){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   int *popage;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   double *popeffectif,*popcount;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   double ***p3mat,***tabpop,***tabpopprev;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   char filerespop[FILENAMELENGTH];  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   agelim=AGESUP;   
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
        /* Computing  Variances of health expectancies */
    
   strcpy(filerespop,"pop");       for(theta=1; theta <=npar; theta++){
   strcat(filerespop,fileres);        for(i=1; i<=npar; i++){ 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("Problem with forecast resultfile: %s\n", filerespop);        }
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   printf("Computing forecasting: result on file '%s' \n", filerespop);    
         cptj=0;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   if (mobilav==1) {            cptj=cptj+1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     movingaverage(agedeb, fage, ageminpar, mobaverage);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   }            }
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   if (stepm<=12) stepsize=1;       
         
   agelim=AGESUP;        for(i=1; i<=npar; i++) 
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   hstepm=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   hstepm=hstepm/stepm;        
          cptj=0;
   if (popforecast==1) {        for(j=1; j<= nlstate; j++){
     if((ficpop=fopen(popfile,"r"))==NULL) {          for(i=1;i<=nlstate;i++){
       printf("Problem with population file : %s\n",popfile);exit(0);            cptj=cptj+1;
     }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     popcount=vector(0,AGESUP);            }
              }
     i=1;          }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        for(j=1; j<= nlstate*nlstate; j++)
              for(h=0; h<=nhstepm-1; h++){
     imx=i;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          }
   }       } 
      
   for(cptcov=1;cptcov<=i2;cptcov++){  /* End theta */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {       for(h=0; h<=nhstepm-1; h++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate*nlstate;j++)
       }          for(theta=1; theta <=npar; theta++)
       fprintf(ficrespop,"******\n");            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficrespop,"# Age");       
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");       for(i=1;i<=nlstate*nlstate;i++)
              for(j=1;j<=nlstate*nlstate;j++)
       for (cpt=0; cpt<=0;cpt++) {          varhe[i][j][(int)age] =0.;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
               printf("%d|",(int)age);fflush(stdout);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       for(h=0;h<=nhstepm-1;h++){
           nhstepm = nhstepm/hstepm;        for(k=0;k<=nhstepm-1;k++){
                    matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           oldm=oldms;savm=savms;          for(i=1;i<=nlstate*nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(j=1;j<=nlstate*nlstate;j++)
                      varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {      }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      /* Computing expectancies */
             }      for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {        for(j=1; j<=nlstate;j++)
               kk1=0.;kk2=0;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
               for(i=1; i<=nlstate;i++) {                          eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                 if (mobilav==1)            
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  /* 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]);*/
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 }  
               }      fprintf(ficreseij,"%3.0f",age );
               if (h==(int)(calagedate+12*cpt)){      cptj=0;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      for(i=1; i<=nlstate;i++)
                   /*fprintf(ficrespop," %.3f", kk1);        for(j=1; j<=nlstate;j++){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          cptj++;
               }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             }        }
             for(i=1; i<=nlstate;i++){      fprintf(ficreseij,"\n");
               kk1=0.;     
                 for(j=1; j<=nlstate;j++){      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                 }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    printf("\n");
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    fprintf(ficlog,"\n");
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(xp,1,npar);
         }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   /******/  }
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  /************ Variance ******************/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* Variance of health expectancies */
           nhstepm = nhstepm/hstepm;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
              /* double **newm;*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewm,**doldm;
           oldm=oldms;savm=savms;    double **dnewmp,**doldmp;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int i, j, nhstepm, hstepm, h, nstepm ;
           for (h=0; h<=nhstepm; h++){    int k, cptcode;
             if (h==(int) (calagedate+YEARM*cpt)) {    double *xp;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double **gp, **gm;  /* for var eij */
             }    double ***gradg, ***trgradg; /*for var eij */
             for(j=1; j<=nlstate+ndeath;j++) {    double **gradgp, **trgradgp; /* for var p point j */
               kk1=0.;kk2=0;    double *gpp, *gmp; /* for var p point j */
               for(i=1; i<=nlstate;i++) {                  double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        double ***p3mat;
               }    double age,agelim, hf;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    double ***mobaverage;
             }    int theta;
           }    char digit[4];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char digitp[25];
         }  
       }    char fileresprobmorprev[FILENAMELENGTH];
    }  
   }    if(popbased==1){
        if(mobilav!=0)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
   if (popforecast==1) {    }
     free_ivector(popage,0,AGESUP);    else 
     free_vector(popeffectif,0,AGESUP);      strcpy(digitp,"-stablbased-");
     free_vector(popcount,0,AGESUP);  
   }    if (mobilav!=0) {
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   fclose(ficrespop);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
 /***********************************************/    }
 /**************** Main Program *****************/  
 /***********************************************/    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
 int main(int argc, char *argv[])    /*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 */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    strcat(fileresprobmorprev,fileres);
   double agedeb, agefin,hf;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   double fret;    }
   double **xi,tmp,delta;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   double dum; /* Dummy variable */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double ***p3mat;    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   int *indx;    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);
   char line[MAXLINE], linepar[MAXLINE];    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   char title[MAXLINE];    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      fprintf(ficresprobmorprev," p.%-d SE",j);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    }  
     fprintf(ficresprobmorprev,"\n");
   char filerest[FILENAMELENGTH];    fprintf(ficgp,"\n# Routine varevsij");
   char fileregp[FILENAMELENGTH];    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   char popfile[FILENAMELENGTH];    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");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   int firstobs=1, lastobs=10;  /*   } */
   int sdeb, sfin; /* Status at beginning and end */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   int c,  h , cpt,l;   fprintf(ficresvij, "#Local time at start: %s", strstart);
   int ju,jl, mi;    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");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    fprintf(ficresvij,"# Age");
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    for(i=1; i<=nlstate;i++)
   int mobilav=0,popforecast=0;      for(j=1; j<=nlstate;j++)
   int hstepm, nhstepm;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    fprintf(ficresvij,"\n");
   
   double bage, fage, age, agelim, agebase;    xp=vector(1,npar);
   double ftolpl=FTOL;    dnewm=matrix(1,nlstate,1,npar);
   double **prlim;    doldm=matrix(1,nlstate,1,nlstate);
   double *severity;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   double ***param; /* Matrix of parameters */    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double  *p;  
   double **matcov; /* Matrix of covariance */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   double ***delti3; /* Scale */    gpp=vector(nlstate+1,nlstate+ndeath);
   double *delti; /* Scale */    gmp=vector(nlstate+1,nlstate+ndeath);
   double ***eij, ***vareij;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   double **varpl; /* Variances of prevalence limits by age */    
   double *epj, vepp;    if(estepm < stepm){
   double kk1, kk2;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    }
      else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   char *alph[]={"a","a","b","c","d","e"}, str[4];       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   char z[1]="c", occ;       and note for a fixed period like k years */
 #include <sys/time.h>    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 #include <time.h>       survival function given by stepm (the optimization length). Unfortunately it
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       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 
   /* long total_usecs;       results. So we changed our mind and took the option of the best precision.
   struct timeval start_time, end_time;    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    agelim = AGESUP;
   getcwd(pathcd, size);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   printf("\n%s",version);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if(argc <=1){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\nEnter the parameter file name: ");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     scanf("%s",pathtot);      gp=matrix(0,nhstepm,1,nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate);
   else{  
     strcpy(pathtot,argv[1]);  
   }      for(theta=1; theta <=npar; theta++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   /*cygwin_split_path(pathtot,path,optionfile);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        }
   /* cutv(path,optionfile,pathtot,'\\');*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        if (popbased==1) {
   chdir(path);          if(mobilav ==0){
   replace(pathc,path);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
 /*-------- arguments in the command line --------*/          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   strcpy(fileres,"r");              prlim[i][i]=mobaverage[(int)age][i][ij];
   strcat(fileres, optionfilefiname);          }
   strcat(fileres,".txt");    /* Other files have txt extension */        }
     
   /*---------arguments file --------*/        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     printf("Problem with optionfile %s\n",optionfile);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     goto end;          }
   }        }
         /* This for computing probability of death (h=1 means
   strcpy(filereso,"o");           computed over hstepm matrices product = hstepm*stepm months) 
   strcat(filereso,fileres);           as a weighted average of prlim.
   if((ficparo=fopen(filereso,"w"))==NULL) {        */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
   /* Reads comments: lines beginning with '#' */        }    
   while((c=getc(ficpar))=='#' && c!= EOF){        /* end probability of death */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     puts(line);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fputs(line,ficparo);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   ungetc(c,ficpar);   
         if (popbased==1) {
   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);          if(mobilav ==0){
   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);            for(i=1; i<=nlstate;i++)
   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);              prlim[i][i]=probs[(int)age][i][ij];
 while((c=getc(ficpar))=='#' && c!= EOF){          }else{ /* mobilav */ 
     ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              prlim[i][i]=mobaverage[(int)age][i][ij];
     puts(line);          }
     fputs(line,ficparo);        }
   }  
   ungetc(c,ficpar);        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
                for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   covar=matrix(0,NCOVMAX,1,n);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   cptcovn=0;          }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        }
         /* This for computing probability of death (h=1 means
   ncovmodel=2+cptcovn;           computed over hstepm matrices product = hstepm*stepm months) 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */           as a weighted average of prlim.
          */
   /* Read guess parameters */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /* Reads comments: lines beginning with '#' */          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   while((c=getc(ficpar))=='#' && c!= EOF){           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     ungetc(c,ficpar);        }    
     fgets(line, MAXLINE, ficpar);        /* end probability of death */
     puts(line);  
     fputs(line,ficparo);        for(j=1; j<= nlstate; j++) /* vareij */
   }          for(h=0; h<=nhstepm; h++){
   ungetc(c,ficpar);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     for(j=1; j <=nlstate+ndeath-1; j++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);      } /* End theta */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);      for(h=0; h<=nhstepm; h++) /* veij */
       }        for(j=1; j<=nlstate;j++)
       fscanf(ficpar,"\n");          for(theta=1; theta <=npar; theta++)
       printf("\n");            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficparo,"\n");  
     }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          trgradgp[j][theta]=gradgp[theta][j];
     
   p=param[1][1];  
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /* Reads comments: lines beginning with '#' */      for(i=1;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1;j<=nlstate;j++)
     ungetc(c,ficpar);          vareij[i][j][(int)age] =0.;
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(h=0;h<=nhstepm;h++){
     fputs(line,ficparo);        for(k=0;k<=nhstepm;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   ungetc(c,ficpar);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            for(j=1;j<=nlstate;j++)
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   for(i=1; i <=nlstate; i++){        }
     for(j=1; j <=nlstate+ndeath-1; j++){      }
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       printf("%1d%1d",i,j);      /* pptj */
       fprintf(ficparo,"%1d%1d",i1,j1);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       for(k=1; k<=ncovmodel;k++){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         printf(" %le",delti3[i][j][k]);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         fprintf(ficparo," %le",delti3[i][j][k]);          varppt[j][i]=doldmp[j][i];
       }      /* end ppptj */
       fscanf(ficpar,"\n");      /*  x centered again */
       printf("\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficparo,"\n");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     }   
   }      if (popbased==1) {
   delti=delti3[1][1];        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */            prlim[i][i]=probs[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){        }else{ /* mobilav */ 
     ungetc(c,ficpar);          for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);            prlim[i][i]=mobaverage[(int)age][i][ij];
     puts(line);        }
     fputs(line,ficparo);      }
   }               
   ungetc(c,ficpar);      /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   matcov=matrix(1,npar,1,npar);         as a weighted average of prlim.
   for(i=1; i <=npar; i++){      */
     fscanf(ficpar,"%s",&str);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     printf("%s",str);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     fprintf(ficparo,"%s",str);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     for(j=1; j <=i; j++){      }    
       fscanf(ficpar," %le",&matcov[i][j]);      /* end probability of death */
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fscanf(ficpar,"\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     printf("\n");        for(i=1; i<=nlstate;i++){
     fprintf(ficparo,"\n");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   }        }
   for(i=1; i <=npar; i++)      } 
     for(j=i+1;j<=npar;j++)      fprintf(ficresprobmorprev,"\n");
       matcov[i][j]=matcov[j][i];  
          fprintf(ficresvij,"%.0f ",age );
   printf("\n");      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     /*-------- Rewriting paramater file ----------*/        }
      strcpy(rfileres,"r");    /* "Rparameterfile */      fprintf(ficresvij,"\n");
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      free_matrix(gp,0,nhstepm,1,nlstate);
      strcat(rfileres,".");    /* */      free_matrix(gm,0,nhstepm,1,nlstate);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     if((ficres =fopen(rfileres,"w"))==NULL) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    } /* End age */
     fprintf(ficres,"#%s\n",version);    free_vector(gpp,nlstate+1,nlstate+ndeath);
        free_vector(gmp,nlstate+1,nlstate+ndeath);
     /*-------- data file ----------*/    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     if((fic=fopen(datafile,"r"))==NULL)    {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       printf("Problem with datafile: %s\n", datafile);goto end;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     n= lastobs;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     severity = vector(1,maxwav);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     outcome=imatrix(1,maxwav+1,1,n);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     num=ivector(1,n);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     moisnais=vector(1,n);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     annais=vector(1,n);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     moisdc=vector(1,n);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     andc=vector(1,n);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     agedc=vector(1,n);    /*  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);
     cod=ivector(1,n);  */
     weight=vector(1,n);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);    free_vector(xp,1,npar);
     s=imatrix(1,maxwav+1,1,n);    free_matrix(doldm,1,nlstate,1,nlstate);
     adl=imatrix(1,maxwav+1,1,n);        free_matrix(dnewm,1,nlstate,1,npar);
     tab=ivector(1,NCOVMAX);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ncodemax=ivector(1,8);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     i=1;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     while (fgets(line, MAXLINE, fic) != NULL)    {    fclose(ficresprobmorprev);
       if ((i >= firstobs) && (i <=lastobs)) {    fflush(ficgp);
            fflush(fichtm); 
         for (j=maxwav;j>=1;j--){  }  /* end varevsij */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);  /************ Variance of prevlim ******************/
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  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[])
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  {
         }    /* Variance of prevalence limit */
            /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double **newm;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    int k, cptcode;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double *xp;
     double *gp, *gm;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    double **gradg, **trgradg;
         for (j=ncovcol;j>=1;j--){    double age,agelim;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int theta;
         }    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
         num[i]=atol(stra);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
            fprintf(ficresvpl,"# Age");
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    for(i=1; i<=nlstate;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;}*/        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
         i=i+1;  
       }    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
     /* printf("ii=%d", ij);    doldm=matrix(1,nlstate,1,nlstate);
        scanf("%d",i);*/    
   imx=i-1; /* Number of individuals */    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   /* for (i=1; i<=imx; i++){    agelim = AGESUP;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      if (stepm >= YEARM) hstepm=1;
     }*/      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
    /*  for (i=1; i<=imx; i++){      gradg=matrix(1,npar,1,nlstate);
      if (s[4][i]==9)  s[4][i]=-1;      gp=vector(1,nlstate);
      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]));}*/      gm=vector(1,nlstate);
    
        for(theta=1; theta <=npar; theta++){
   /* Calculation of the number of parameter from char model*/        for(i=1; i<=npar; i++){ /* Computes gradient */
   Tvar=ivector(1,15);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   Tprod=ivector(1,15);        }
   Tvaraff=ivector(1,15);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   Tvard=imatrix(1,15,1,2);        for(i=1;i<=nlstate;i++)
   Tage=ivector(1,15);                gp[i] = prlim[i][i];
          
   if (strlen(model) >1){        for(i=1; i<=npar; i++) /* Computes gradient */
     j=0, j1=0, k1=1, k2=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     j=nbocc(model,'+');        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     j1=nbocc(model,'*');        for(i=1;i<=nlstate;i++)
     cptcovn=j+1;          gm[i] = prlim[i][i];
     cptcovprod=j1;  
            for(i=1;i<=nlstate;i++)
     strcpy(modelsav,model);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      } /* End theta */
       printf("Error. Non available option model=%s ",model);  
       goto end;      trgradg =matrix(1,nlstate,1,npar);
     }  
          for(j=1; j<=nlstate;j++)
     for(i=(j+1); i>=1;i--){        for(theta=1; theta <=npar; theta++)
       cutv(stra,strb,modelsav,'+');          trgradg[j][theta]=gradg[theta][j];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      for(i=1;i<=nlstate;i++)
       /*scanf("%d",i);*/        varpl[i][(int)age] =0.;
       if (strchr(strb,'*')) {      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         cutv(strd,strc,strb,'*');      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
         if (strcmp(strc,"age")==0) {      for(i=1;i<=nlstate;i++)
           cptcovprod--;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);      fprintf(ficresvpl,"%.0f ",age );
           cptcovage++;      for(i=1; i<=nlstate;i++)
             Tage[cptcovage]=i;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             /*printf("stre=%s ", stre);*/      fprintf(ficresvpl,"\n");
         }      free_vector(gp,1,nlstate);
         else if (strcmp(strd,"age")==0) {      free_vector(gm,1,nlstate);
           cptcovprod--;      free_matrix(gradg,1,npar,1,nlstate);
           cutv(strb,stre,strc,'V');      free_matrix(trgradg,1,nlstate,1,npar);
           Tvar[i]=atoi(stre);    } /* End age */
           cptcovage++;  
           Tage[cptcovage]=i;    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,npar);
         else {    free_matrix(dnewm,1,nlstate,1,nlstate);
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncovcol+k1;  }
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;  /************ Variance of one-step probabilities  ******************/
           Tvard[k1][1]=atoi(strc);  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[])
           Tvard[k1][2]=atoi(stre);  {
           Tvar[cptcovn+k2]=Tvard[k1][1];    int i, j=0,  i1, k1, l1, t, tj;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int k2, l2, j1,  z1;
           for (k=1; k<=lastobs;k++)    int k=0,l, cptcode;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    int first=1, first1;
           k1++;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           k2=k2+2;    double **dnewm,**doldm;
         }    double *xp;
       }    double *gp, *gm;
       else {    double **gradg, **trgradg;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double **mu;
        /*  scanf("%d",i);*/    double age,agelim, cov[NCOVMAX];
       cutv(strd,strc,strb,'V');    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       Tvar[i]=atoi(strc);    int theta;
       }    char fileresprob[FILENAMELENGTH];
       strcpy(modelsav,stra);      char fileresprobcov[FILENAMELENGTH];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    char fileresprobcor[FILENAMELENGTH];
         scanf("%d",i);*/  
     }    double ***varpij;
 }  
      strcpy(fileresprob,"prob"); 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    strcat(fileresprob,fileres);
   printf("cptcovprod=%d ", cptcovprod);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   scanf("%d ",i);*/      printf("Problem with resultfile: %s\n", fileresprob);
     fclose(fic);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     /*  if(mle==1){*/    strcpy(fileresprobcov,"probcov"); 
     if (weightopt != 1) { /* Maximisation without weights*/    strcat(fileresprobcov,fileres);
       for(i=1;i<=n;i++) weight[i]=1.0;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcov);
     /*-calculation of age at interview from date of interview and age at death -*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     agev=matrix(1,maxwav,1,imx);    }
     strcpy(fileresprobcor,"probcor"); 
     for (i=1; i<=imx; i++) {    strcat(fileresprobcor,fileres);
       for(m=2; (m<= maxwav); m++) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      printf("Problem with resultfile: %s\n", fileresprobcor);
          anint[m][i]=9999;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
          s[m][i]=-1;    }
        }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     }    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     for (i=1; i<=imx; i++)  {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fprintf(ficresprob, "#Local time at start: %s", strstart);
       for(m=1; (m<= maxwav); m++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         if(s[m][i] >0){    fprintf(ficresprob,"# Age");
           if (s[m][i] >= nlstate+1) {    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
             if(agedc[i]>0)    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficresprobcov,"# Age");
                 agev[m][i]=agedc[i];    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
            else {    fprintf(ficresprobcov,"# Age");
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    for(i=1; i<=nlstate;i++)
               }      for(j=1; j<=(nlstate+ndeath);j++){
             }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           else if(s[m][i] !=9){ /* Should no more exist */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      }  
             if(mint[m][i]==99 || anint[m][i]==9999)   /* fprintf(ficresprob,"\n");
               agev[m][i]=1;    fprintf(ficresprobcov,"\n");
             else if(agev[m][i] <agemin){    fprintf(ficresprobcor,"\n");
               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);*/   xp=vector(1,npar);
             }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             else if(agev[m][i] >agemax){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               agemax=agev[m][i];    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
             }    first=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(ficgp,"\n# Routine varprob");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           }    fprintf(fichtm,"\n");
           else { /* =9 */  
             agev[m][i]=1;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
             s[m][i]=-1;    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           }    file %s<br>\n",optionfilehtmcov);
         }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         else /*= 0 Unknown */  and drawn. It helps understanding how is the covariance between two incidences.\
           agev[m][i]=1;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
      It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     for (i=1; i<=imx; i++)  {  standard deviations wide on each axis. <br>\
       for(m=1; (m<= maxwav); m++){   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
         if (s[m][i] > (nlstate+ndeath)) {   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
           printf("Error: Wrong value in nlstate or ndeath\n");    To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
           goto end;  
         }    cov[1]=1;
       }    tj=cptcoveff;
     }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
     free_vector(severity,1,maxwav);        j1++;
     free_imatrix(outcome,1,maxwav+1,1,n);        if  (cptcovn>0) {
     free_vector(moisnais,1,n);          fprintf(ficresprob, "\n#********** Variable "); 
     free_vector(annais,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /* free_matrix(mint,1,maxwav,1,n);          fprintf(ficresprob, "**********\n#\n");
        free_matrix(anint,1,maxwav,1,n);*/          fprintf(ficresprobcov, "\n#********** Variable "); 
     free_vector(moisdc,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(andc,1,n);          fprintf(ficresprobcov, "**********\n#\n");
           
              fprintf(ficgp, "\n#********** Variable "); 
     wav=ivector(1,imx);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficgp, "**********\n#\n");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          
              
     /* Concatenates waves */          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
       Tcode=ivector(1,100);          fprintf(ficresprobcor, "\n#********** Variable ");    
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       ncodemax[1]=1;          fprintf(ficresprobcor, "**********\n#");    
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        }
              
    codtab=imatrix(1,100,1,10);        for (age=bage; age<=fage; age ++){ 
    h=0;          cov[2]=age;
    m=pow(2,cptcoveff);          for (k=1; k<=cptcovn;k++) {
              cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
    for(k=1;k<=cptcoveff; k++){          }
      for(i=1; i <=(m/pow(2,k));i++){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
        for(j=1; j <= ncodemax[k]; j++){          for (k=1; k<=cptcovprod;k++)
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            h++;          
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
          }          gp=vector(1,(nlstate)*(nlstate+ndeath));
        }          gm=vector(1,(nlstate)*(nlstate+ndeath));
      }      
    }          for(theta=1; theta <=npar; theta++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            for(i=1; i<=npar; i++)
       codtab[1][2]=1;codtab[2][2]=2; */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
    /* for(i=1; i <=m ;i++){            
       for(k=1; k <=cptcovn; k++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            
       }            k=0;
       printf("\n");            for(i=1; i<= (nlstate); i++){
       }              for(j=1; j<=(nlstate+ndeath);j++){
       scanf("%d",i);*/                k=k+1;
                    gp[k]=pmmij[i][j];
    /* Calculates basic frequencies. Computes observed prevalence at single age              }
        and prints on file fileres'p'. */            }
             
                for(i=1; i<=npar; i++)
                  xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k=0;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(i=1; i<=(nlstate); i++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              for(j=1; j<=(nlstate+ndeath);j++){
                      k=k+1;
     /* For Powell, parameters are in a vector p[] starting at p[1]                gm[k]=pmmij[i][j];
        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) */            }
        
     if(mle==1){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     }          }
      
     /*--------- results files --------------*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     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);            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
           
    jk=1;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
    for(i=1,jk=1; i <=nlstate; i++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
      for(k=1; k <=(nlstate+ndeath); k++){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        if (k != i)          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
          {  
            printf("%d%d ",i,k);          pmij(pmmij,cov,ncovmodel,x,nlstate);
            fprintf(ficres,"%1d%1d ",i,k);          
            for(j=1; j <=ncovmodel; j++){          k=0;
              printf("%f ",p[jk]);          for(i=1; i<=(nlstate); i++){
              fprintf(ficres,"%f ",p[jk]);            for(j=1; j<=(nlstate+ndeath);j++){
              jk++;              k=k+1;
            }              mu[k][(int) age]=pmmij[i][j];
            printf("\n");            }
            fprintf(ficres,"\n");          }
          }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
      }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
    }              varpij[i][j][(int)age] = doldm[i][j];
  if(mle==1){  
     /* Computing hessian and covariance matrix */          /*printf("\n%d ",(int)age);
     ftolhess=ftol; /* Usually correct */            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     hesscov(matcov, p, npar, delti, ftolhess, func);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            }*/
     printf("# Scales (for hessian or gradient estimation)\n");  
      for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresprob,"\n%d ",(int)age);
       for(j=1; j <=nlstate+ndeath; j++){          fprintf(ficresprobcov,"\n%d ",(int)age);
         if (j!=i) {          fprintf(ficresprobcor,"\n%d ",(int)age);
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           for(k=1; k<=ncovmodel;k++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
             printf(" %.5e",delti[jk]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficres," %.5e",delti[jk]);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             jk++;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }          }
           printf("\n");          i=0;
           fprintf(ficres,"\n");          for (k=1; k<=(nlstate);k++){
         }            for (l=1; l<=(nlstate+ndeath);l++){ 
       }              i=i++;
      }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
                  fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     k=1;              for (j=1; j<=i;j++){
     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(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     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(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     for(i=1;i<=npar;i++){              }
       /*  if (k>nlstate) k=1;            }
       i1=(i-1)/(ncovmodel*nlstate)+1;          }/* end of loop for state */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        } /* end of loop for age */
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);        /* Confidence intervalle of pij  */
       printf("%3d",i);        /*
       for(j=1; j<=i;j++){          fprintf(ficgp,"\nset noparametric;unset label");
         fprintf(ficres," %.5e",matcov[i][j]);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
         printf(" %.5e",matcov[i][j]);          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(ficres,"\n");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       printf("\n");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       k++;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     }        */
      
     while((c=getc(ficpar))=='#' && c!= EOF){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       ungetc(c,ficpar);        first1=1;
       fgets(line, MAXLINE, ficpar);        for (k2=1; k2<=(nlstate);k2++){
       puts(line);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       fputs(line,ficparo);            if(l2==k2) continue;
     }            j=(k2-1)*(nlstate+ndeath)+l2;
     ungetc(c,ficpar);            for (k1=1; k1<=(nlstate);k1++){
     estepm=0;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                if(l1==k1) continue;
     if (estepm==0 || estepm < stepm) estepm=stepm;                i=(k1-1)*(nlstate+ndeath)+l1;
     if (fage <= 2) {                if(i<=j) continue;
       bage = ageminpar;                for (age=bage; age<=fage; age ++){ 
       fage = agemaxpar;                  if ((int)age %5==0){
     }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                        v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    mu2=mu[j][(int) age]/stepm*YEARM;
                      c12=cv12/sqrt(v1*v2);
     while((c=getc(ficpar))=='#' && c!= EOF){                    /* Computing eigen value of matrix of covariance */
     ungetc(c,ficpar);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fgets(line, MAXLINE, ficpar);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     puts(line);                    /* Eigen vectors */
     fputs(line,ficparo);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   }                    /*v21=sqrt(1.-v11*v11); *//* error */
   ungetc(c,ficpar);                    v21=(lc1-v1)/cv12*v11;
                      v12=-v21;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    v22=v11;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    tnalp=v21/v11;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    if(first1==1){
                            first1=0;
   while((c=getc(ficpar))=='#' && c!= EOF){                      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);
     ungetc(c,ficpar);                    }
     fgets(line, MAXLINE, ficpar);                    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);
     puts(line);                    /*printf(fignu*/
     fputs(line,ficparo);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   ungetc(c,ficpar);                    if(first==1){
                        first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                      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);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   fscanf(ficpar,"pop_based=%d\n",&popbased);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   fprintf(ficparo,"pop_based=%d\n",popbased);    %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   fprintf(ficres,"pop_based=%d\n",popbased);                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     ungetc(c,ficpar);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     fgets(line, MAXLINE, ficpar);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     puts(line);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     fputs(line,ficparo);                      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",\
   ungetc(c,ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   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);                    }else{
 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);                      first=0;
 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);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
 while((c=getc(ficpar))=='#' && c!= EOF){                      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",\
     ungetc(c,ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fgets(line, MAXLINE, ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     puts(line);                    }/* if first */
     fputs(line,ficparo);                  } /* age mod 5 */
   }                } /* end loop age */
   ungetc(c,ficpar);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);              } /*l12 */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            } /* k12 */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          } /*l1 */
         }/* k1 */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      } /* loop covariates */
     }
 /*------------ gnuplot -------------*/    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 /*------------ free_vector  -------------*/    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
  chdir(path);    free_vector(xp,1,npar);
      fclose(ficresprob);
  free_ivector(wav,1,imx);    fclose(ficresprobcov);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    fclose(ficresprobcor);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      fflush(ficgp);
  free_ivector(num,1,n);    fflush(fichtmcov);
  free_vector(agedc,1,n);  }
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  
  fclose(ficparo);  
  fclose(ficres);  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 /*--------- index.htm --------*/                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                      double jprev2, double mprev2,double anprev2){
   /*--------------- Prevalence limit --------------*/    int jj1, k1, i1, cpt;
    
   strcpy(filerespl,"pl");     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   strcat(filerespl,fileres);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  </ul>");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   }   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
   fprintf(ficrespl,"#Prevalence limit\n");     fprintf(fichtm,"\
   fprintf(ficrespl,"#Age ");   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   fprintf(ficrespl,"\n");     fprintf(fichtm,"\
     - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
   prlim=matrix(1,nlstate,1,nlstate);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     fprintf(fichtm,"\
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   - Life expectancies by age and initial health status (estepm=%2d months): \
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     <a href=\"%s\">%s</a> <br>\n</li>",
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   agebase=ageminpar;  
   agelim=agemaxpar;   m=cptcoveff;
   ftolpl=1.e-10;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}   jj1=0;
    for(k1=1; k1<=m;k1++){
   for(cptcov=1;cptcov<=i1;cptcov++){     for(i1=1; i1<=ncodemax[k1];i1++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       jj1++;
         k=k+1;       if (cptcovn > 0) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         fprintf(ficrespl,"\n#******");         for (cpt=1; cpt<=cptcoveff;cpt++) 
         for(j=1;j<=cptcoveff;j++)           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         fprintf(ficrespl,"******\n");       }
               /* Pij */
         for (age=agebase; age<=agelim; age++){       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
           fprintf(ficrespl,"%.0f",age );       /* Quasi-incidences */
           for(i=1; i<=nlstate;i++)       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
           fprintf(ficrespl," %.5f", prlim[i][i]);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
           fprintf(ficrespl,"\n");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
         }         /* Stable prevalence in each health state */
       }         for(cpt=1; cpt<nlstate;cpt++){
     }           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   fclose(ficrespl);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
   /*------------- h Pij x at various ages ------------*/       for(cpt=1; cpt<=nlstate;cpt++) {
            fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;     } /* end i1 */
   }   }/* End k1 */
   printf("Computing pij: result on file '%s' \n", filerespij);   fprintf(fichtm,"</ul>");
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/   fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   agelim=AGESUP;   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   k=0;   fprintf(fichtm,"\
   for(cptcov=1;cptcov<=i1;cptcov++){   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");   fprintf(fichtm,"\
         for(j=1;j<=cptcoveff;j++)   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
         fprintf(ficrespij,"******\n");   fprintf(fichtm,"\
           - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   fprintf(fichtm,"\
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
           oldm=oldms;savm=savms;   fprintf(fichtm,"\
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
           fprintf(ficrespij,"# Age");           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)  /*  if(popforecast==1) fprintf(fichtm,"\n */
               fprintf(ficrespij," %1d-%1d",i,j);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
           fprintf(ficrespij,"\n");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
            for (h=0; h<=nhstepm; h++){  /*      <br>",fileres,fileres,fileres,fileres); */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  /*  else  */
             for(i=1; i<=nlstate;i++)  /*    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); */
               for(j=1; j<=nlstate+ndeath;j++)   fflush(fichtm);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
             fprintf(ficrespij,"\n");  
              }   m=cptcoveff;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           fprintf(ficrespij,"\n");  
         }   jj1=0;
     }   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   fclose(ficrespij);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /*---------- Forecasting ------------------*/       }
   if((stepm == 1) && (strcmp(model,".")==0)){       for(cpt=1; cpt<=nlstate;cpt++) {
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   else{       }
     erreur=108;       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     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);  health expectancies in states (1) and (2): %s%d.png<br>\
   }  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
       } /* end i1 */
    }/* End k1 */
   /*---------- Health expectancies and variances ------------*/   fprintf(fichtm,"</ul>");
    fflush(fichtm);
   strcpy(filerest,"t");  }
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {  /******************* Gnuplot file **************/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   strcpy(filerese,"e");  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   strcat(filerese,fileres);  /*     printf("Problem with file %s",optionfilegnuplot); */
   if((ficreseij=fopen(filerese,"w"))==NULL) {  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  /*   } */
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
  strcpy(fileresv,"v");      /*#endif */
   strcat(fileresv,fileres);    m=pow(2,cptcoveff);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    strcpy(dirfileres,optionfilefiname);
   }    strcpy(optfileres,"vpl");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   /* 1eme*/
   calagedate=-1;    for (cpt=1; cpt<= nlstate ; cpt ++) {
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   k=0;       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(ficgp,"set xlabel \"Age\" \n\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  set ylabel \"Probability\" \n\
       k=k+1;  set ter png small\n\
       fprintf(ficrest,"\n#****** ");  set size 0.65,0.65\n\
       for(j=1;j<=cptcoveff;j++)  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficreseij,"\n#****** ");         else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(j=1;j<=cptcoveff;j++)       }
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       fprintf(ficreseij,"******\n");       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficresvij,"\n#****** ");         else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(j=1;j<=cptcoveff;j++)       } 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
       fprintf(ficresvij,"******\n");       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       oldm=oldms;savm=savms;       }  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);         fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;    /*2 eme*/
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    
        for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
        fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      for (i=1; i<= nlstate+1 ; i ++) {
       fprintf(ficrest,"\n");        k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       epj=vector(1,nlstate+1);        for (j=1; j<= nlstate+1 ; j ++) {
       for(age=bage; age <=fage ;age++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         if (popbased==1) {        }   
           for(i=1; i<=nlstate;i++)        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
             prlim[i][i]=probs[(int)age][i][k];        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
                for (j=1; j<= nlstate+1 ; j ++) {
         fprintf(ficrest," %4.0f",age);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        }   
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        fprintf(ficgp,"\" t\"\" w l 0,");
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
           }        for (j=1; j<= nlstate+1 ; j ++) {
           epj[nlstate+1] +=epj[j];          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         }          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         for(i=1, vepp=0.;i <=nlstate;i++)        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
           for(j=1;j <=nlstate;j++)        else fprintf(ficgp,"\" t\"\" w l 0,");
             vepp += vareij[i][j][(int)age];      }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    }
         for(j=1;j <=nlstate;j++){    
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    /*3eme*/
         }    
         fprintf(ficrest,"\n");    for (k1=1; k1<= m ; k1 ++) { 
       }      for (cpt=1; cpt<= nlstate ; cpt ++) {
     }        k=2+nlstate*(2*cpt-2);
   }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
 free_matrix(mint,1,maxwav,1,n);        fprintf(ficgp,"set ter png small\n\
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  set size 0.65,0.65\n\
     free_vector(weight,1,n);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
   fclose(ficreseij);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   fclose(ficresvij);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   fclose(ficrest);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   fclose(ficpar);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   free_vector(epj,1,nlstate+1);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   /*------- Variance limit prevalence------*/            
         */
   strcpy(fileresvpl,"vpl");        for (i=1; i< nlstate ; i ++) {
   strcat(fileresvpl,fileres);          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);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        } 
     exit(0);      }
   }    }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    
     /* CV preval stable (period) */
   k=0;    for (k1=1; k1<= m ; k1 ++) { 
   for(cptcov=1;cptcov<=i1;cptcov++){      for (cpt=1; cpt<=nlstate ; cpt ++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        k=3;
       k=k+1;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
       fprintf(ficresvpl,"\n#****** ");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
       for(j=1;j<=cptcoveff;j++)  set ter png small\nset size 0.65,0.65\n\
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  unset log y\n\
       fprintf(ficresvpl,"******\n");  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
              
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        for (i=1; i< nlstate ; i ++)
       oldm=oldms;savm=savms;          fprintf(ficgp,"+$%d",k+i+1);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        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/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   fclose(ficresvpl);        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
   /*---------- End : free ----------------*/          fprintf(ficgp,"+$%d",l+i+1);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        }
          fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      } 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }  
      
      /* proba elementaires */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    for(i=1,jk=1; i <=nlstate; i++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      for(k=1; k <=(nlstate+ndeath); k++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        if (k != i) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(j=1; j <=ncovmodel; j++){
              fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   free_matrix(matcov,1,npar,1,npar);            jk++; 
   free_vector(delti,1,npar);            fprintf(ficgp,"\n");
   free_matrix(agev,1,maxwav,1,imx);          }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        }
       }
   if(erreur >0)     }
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       for(jk=1; jk <=m; jk++) {
           fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   /* 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);*/         if (ng==2)
   /*printf("Total time was %d uSec.\n", total_usecs);*/           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   /*------ End -----------*/         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);
  end:         i=1;
 #ifdef windows         for(k2=1; k2<=nlstate; k2++) {
   /* chdir(pathcd);*/           k3=i;
 #endif           for(k=1; k<=(nlstate+ndeath); k++) {
  /*system("wgnuplot graph.plt");*/             if (k != k2){
  /*system("../gp37mgw/wgnuplot graph.plt");*/               if(ng==2)
  /*system("cd ../gp37mgw");*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/               else
  strcpy(plotcmd,GNUPLOTPROGRAM);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
  strcat(plotcmd," ");               ij=1;
  strcat(plotcmd,optionfilegnuplot);               for(j=3; j <=ncovmodel; j++) {
  system(plotcmd);                 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]]]);
 #ifdef windows                   ij++;
   while (z[0] != 'q') {                 }
     /* chdir(path); */                 else
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     scanf("%s",z);               }
     if (z[0] == 'c') system("./imach");               fprintf(ficgp,")/(1");
     else if (z[0] == 'e') system(optionfilehtm);               
     else if (z[0] == 'g') system(plotcmd);               for(k1=1; k1 <=nlstate; k1++){   
     else if (z[0] == 'q') exit(0);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   }                 ij=1;
 #endif                 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 strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - 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,\
             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  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#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*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       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 LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: 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(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#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\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, 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);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: 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(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of 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.1.41  
changed lines
  Added in v.1.115


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