Diff for /imach/src/imach.c between versions 1.45 and 1.116

version 1.45, 2002/05/24 16:34:18 version 1.116, 2006/03/06 10:29:27
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.116  2006/03/06 10:29:27  brouard
      (Module): Variance-covariance wrong links and
   This program computes Healthy Life Expectancies from    varian-covariance of ej. is needed (Saito).
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.115  2006/02/27 12:17:45  brouard
   interviewed on their health status or degree of disability (in the    (Module): One freematrix added in mlikeli! 0.98c
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.114  2006/02/26 12:57:58  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Some improvements in processing parameter
   computed from the time spent in each health state according to a    filename with strsep.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.113  2006/02/24 14:20:24  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): Memory leaks checks with valgrind and:
   probability to be observed in state j at the second wave    datafile was not closed, some imatrix were not freed and on matrix
   conditional to be observed in state i at the first wave. Therefore    allocation too.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.112  2006/01/30 09:55:26  brouard
   complex model than "constant and age", you should modify the program    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.111  2006/01/25 20:38:18  brouard
   convergence.    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
   The advantage of this computer programme, compared to a simple    can be a simple dot '.'.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.110  2006/01/25 00:51:50  brouard
   intermediate interview, the information is lost, but taken into    (Module): Lots of cleaning and bugs added (Gompertz)
   account using an interpolation or extrapolation.    
     Revision 1.109  2006/01/24 19:37:15  brouard
   hPijx is the probability to be observed in state i at age x+h    (Module): Comments (lines starting with a #) are allowed in data.
   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 1.108  2006/01/19 18:05:42  lievre
   states. This elementary transition (by month or quarter trimester,    Gnuplot problem appeared...
   semester or year) is model as a multinomial logistic.  The hPx    To be fixed
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.107  2006/01/19 16:20:37  brouard
   hPijx.    Test existence of gnuplot in imach path
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.106  2006/01/19 13:24:36  brouard
   of the life expectancies. It also computes the prevalence limits.    Some cleaning and links added in html output
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.105  2006/01/05 20:23:19  lievre
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.104  2005/09/30 16:11:43  lievre
   It is copyrighted identically to a GNU software product, ie programme and    (Module): sump fixed, loop imx fixed, and simplifications.
   software can be distributed freely for non commercial use. Latest version    (Module): If the status is missing at the last wave but we know
   can be accessed at http://euroreves.ined.fr/imach .    that the person is alive, then we can code his/her status as -2
   **********************************************************************/    (instead of missing=-1 in earlier versions) and his/her
      contributions to the likelihood is 1 - Prob of dying from last
 #include <math.h>    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #include <stdio.h>    the healthy state at last known wave). Version is 0.98
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "gnuplot"    Revision 1.102  2004/09/15 17:31:30  brouard
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Add the possibility to read data file including tab characters.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.101  2004/09/15 10:38:38  brouard
 #define windows    Fix on curr_time
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.98  2004/05/16 15:05:56  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    New version 0.97 . First attempt to estimate force of mortality
 #define NCOVMAX 8 /* Maximum number of covariates */    directly from the data i.e. without the need of knowing the health
 #define MAXN 20000    state at each age, but using a Gompertz model: log u =a + b*age .
 #define YEARM 12. /* Number of months per year */    This is the basic analysis of mortality and should be done before any
 #define AGESUP 130    other analysis, in order to test if the mortality estimated from the
 #define AGEBASE 40    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
   
 int erreur; /* Error number */    The same imach parameter file can be used but the option for mle should be -3.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Agnès, who wrote this part of the code, tried to keep most of the
 int npar=NPARMAX;    former routines in order to include the new code within the former code.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    The output is very simple: only an estimate of the intercept and of
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    the slope with 95% confident intervals.
 int popbased=0;  
     Current limitations:
 int *wav; /* Number of waves for this individuual 0 is possible */    A) Even if you enter covariates, i.e. with the
 int maxwav; /* Maxim number of waves */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int jmin, jmax; /* min, max spacing between 2 waves */    B) There is no computation of Life Expectancy nor Life Table.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.97  2004/02/20 13:25:42  lievre
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Version 0.96d. Population forecasting command line is (temporarily)
 double jmean; /* Mean space between 2 waves */    suppressed.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.96  2003/07/15 15:38:55  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 FILE *ficgp,*ficresprob,*ficpop;    rewritten within the same printf. Workaround: many printfs.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.95  2003/07/08 07:54:34  brouard
  FILE  *ficresvij;    * imach.c (Repository):
   char fileresv[FILENAMELENGTH];    (Repository): Using imachwizard code to output a more meaningful covariance
  FILE  *ficresvpl;    matrix (cov(a12,c31) instead of numbers.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.94  2003/06/27 13:00:02  brouard
 #define NR_END 1    Just cleaning
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define NRANSI    exist so I changed back to asctime which exists.
 #define ITMAX 200    (Module): Version 0.96b
   
 #define TOL 2.0e-4    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define CGOLD 0.3819660    exist so I changed back to asctime which exists.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 #define GOLD 1.618034    (Repository): Elapsed time after each iteration is now output. It
 #define GLIMIT 100.0    helps to forecast when convergence will be reached. Elapsed time
 #define TINY 1.0e-20    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.90  2003/06/24 12:34:15  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    of the covariance matrix to be input.
 #define rint(a) floor(a+0.5)  
     Revision 1.89  2003/06/24 12:30:52  brouard
 static double sqrarg;    (Module): Some bugs corrected for windows. Also, when
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    mle=-1 a template is output in file "or"mypar.txt with the design
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    of the covariance matrix to be input.
   
 int imx;    Revision 1.88  2003/06/23 17:54:56  brouard
 int stepm;    * 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.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.87  2003/06/18 12:26:01  brouard
 int estepm;    Version 0.96
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.86  2003/06/17 20:04:08  brouard
 int m,nb;    (Module): Change position of html and gnuplot routines and added
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    routine fileappend.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.85  2003/06/17 13:12:43  brouard
 double dateintmean=0;    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 double *weight;    prior to the death. In this case, dh was negative and likelihood
 int **s; /* Status */    was wrong (infinity). We still send an "Error" but patch by
 double *agedc, **covar, idx;    assuming that the date of death was just one stepm after the
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    interview.
     (Repository): Because some people have very long ID (first column)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    we changed int to long in num[] and we added a new lvector for
 double ftolhess; /* Tolerance for computing hessian */    memory allocation. But we also truncated to 8 characters (left
     truncation)
 /**************** split *************************/    (Repository): No more line truncation errors.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
    char *s;                             /* pointer */    * imach.c (Repository): Replace "freqsummary" at a correct
    int  l1, l2;                         /* length counters */    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
    l1 = strlen( path );                 /* length of path */    parcimony.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.83  2003/06/10 13:39:11  lievre
 #else    *** empty log message ***
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.82  2003/06/05 15:57:20  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    Add log in  imach.c and  fullversion number is now printed.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  */
   /*
       if ( getwd( dirc ) == NULL ) {     Interpolated Markov Chain
 #else  
       extern char       *getcwd( );    Short summary of the programme:
     
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    This program computes Healthy Life Expectancies from
 #endif    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
          return( GLOCK_ERROR_GETCWD );    first survey ("cross") where individuals from different ages are
       }    interviewed on their health status or degree of disability (in the
       strcpy( name, path );             /* we've got it */    case of a health survey which is our main interest) -2- at least a
    } else {                             /* strip direcotry from path */    second wave of interviews ("longitudinal") which measure each change
       s++;                              /* after this, the filename */    (if any) in individual health status.  Health expectancies are
       l2 = strlen( s );                 /* length of filename */    computed from the time spent in each health state according to a
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    model. More health states you consider, more time is necessary to reach the
       strcpy( name, s );                /* save file name */    Maximum Likelihood of the parameters involved in the model.  The
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    simplest model is the multinomial logistic model where pij is the
       dirc[l1-l2] = 0;                  /* add zero */    probability to be observed in state j at the second wave
    }    conditional to be observed in state i at the first wave. Therefore
    l1 = strlen( dirc );                 /* length of directory */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #ifdef windows    'age' is age and 'sex' is a covariate. If you want to have a more
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    complex model than "constant and age", you should modify the program
 #else    where the markup *Covariates have to be included here again* invites
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    you to do it.  More covariates you add, slower the
 #endif    convergence.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    The advantage of this computer programme, compared to a simple
    strcpy(ext,s);                       /* save extension */    multinomial logistic model, is clear when the delay between waves is not
    l1= strlen( name);    identical for each individual. Also, if a individual missed an
    l2= strlen( s)+1;    intermediate interview, the information is lost, but taken into
    strncpy( finame, name, l1-l2);    account using an interpolation or extrapolation.  
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    hPijx is the probability to be observed in state i at age x+h
 }    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 /******************************************/    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 void replace(char *s, char*t)    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   int i;  
   int lg=20;    Also this programme outputs the covariance matrix of the parameters but also
   i=0;    of the life expectancies. It also computes the stable prevalence. 
   lg=strlen(t);    
   for(i=0; i<= lg; i++) {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     (s[i] = t[i]);             Institut national d'études démographiques, Paris.
     if (t[i]== '\\') s[i]='/';    This software have been partly granted by Euro-REVES, a concerted action
   }    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 int nbocc(char *s, char occ)    can be accessed at http://euroreves.ined.fr/imach .
 {  
   int i,j=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int lg=20;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   i=0;    
   lg=strlen(s);    **********************************************************************/
   for(i=0; i<= lg; i++) {  /*
   if  (s[i] == occ ) j++;    main
   }    read parameterfile
   return j;    read datafile
 }    concatwav
     freqsummary
 void cutv(char *u,char *v, char*t, char occ)    if (mle >= 1)
 {      mlikeli
   int i,lg,j,p=0;    print results files
   i=0;    if mle==1 
   for(j=0; j<=strlen(t)-1; j++) {       computes hessian
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    read end of parameter file: agemin, agemax, bage, fage, estepm
   }        begin-prev-date,...
     open gnuplot file
   lg=strlen(t);    open html file
   for(j=0; j<p; j++) {    stable prevalence
     (u[j] = t[j]);     for age prevalim()
   }    h Pij x
      u[p]='\0';    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
    for(j=0; j<= lg; j++) {    health expectancies
     if (j>=(p+1))(v[j-p-1] = t[j]);    Variance-covariance of DFLE
   }    prevalence()
 }     movingaverage()
     varevsij() 
 /********************** nrerror ********************/    if popbased==1 varevsij(,popbased)
     total life expectancies
 void nrerror(char error_text[])    Variance of stable prevalence
 {   end
   fprintf(stderr,"ERREUR ...\n");  */
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  
 }  
 /*********************** vector *******************/   
 double *vector(int nl, int nh)  #include <math.h>
 {  #include <stdio.h>
   double *v;  #include <stdlib.h>
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #include <string.h>
   if (!v) nrerror("allocation failure in vector");  #include <unistd.h>
   return v-nl+NR_END;  
 }  #include <limits.h>
   #include <sys/types.h>
 /************************ free vector ******************/  #include <sys/stat.h>
 void free_vector(double*v, int nl, int nh)  #include <errno.h>
 {  extern int errno;
   free((FREE_ARG)(v+nl-NR_END));  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /************************ivector *******************************/  #include "timeval.h"
 int *ivector(long nl,long nh)  
 {  /* #include <libintl.h> */
   int *v;  /* #define _(String) gettext (String) */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  #define MAXLINE 256
   return v-nl+NR_END;  
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /******************free ivector **************************/  #define FILENAMELENGTH 132
 void free_ivector(int *v, long nl, long nh)  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   free((FREE_ARG)(v+nl-NR_END));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 /******************* imatrix *******************************/  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   int **m;  #define NCOVMAX 8 /* Maximum number of covariates */
    #define MAXN 20000
   /* allocate pointers to rows */  #define YEARM 12. /* Number of months per year */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define AGESUP 130
   if (!m) nrerror("allocation failure 1 in matrix()");  #define AGEBASE 40
   m += NR_END;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m -= nrl;  #ifdef UNIX
    #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)));  #else
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define DIRSEPARATOR '\\'
   m[nrl] += NR_END;  #define CHARSEPARATOR "\\"
   m[nrl] -= ncl;  #define ODIRSEPARATOR '/'
    #endif
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /* $Id$ */
   /* return pointer to array of pointers to rows */  /* $State$ */
   return m;  
 }  char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 /****************** free_imatrix *************************/  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 void free_imatrix(m,nrl,nrh,ncl,nch)  int nvar;
       int **m;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
       long nch,ncl,nrh,nrl;  int npar=NPARMAX;
      /* free an int matrix allocated by imatrix() */  int nlstate=2; /* Number of live states */
 {  int ndeath=1; /* Number of dead states */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   free((FREE_ARG) (m+nrl-NR_END));  int popbased=0;
 }  
   int *wav; /* Number of waves for this individuual 0 is possible */
 /******************* matrix *******************************/  int maxwav; /* Maxim number of waves */
 double **matrix(long nrl, long nrh, long ncl, long nch)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int gipmx, gsw; /* Global variables on the number of contributions 
   double **m;                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   if (!m) nrerror("allocation failure 1 in matrix()");  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   m += NR_END;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   m -= nrl;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double **oldm, **newm, **savm; /* Working pointers to matrices */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m[nrl] += NR_END;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m[nrl] -= ncl;  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double fretone; /* Only one call to likelihood */
   return m;  long ipmx; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /*************************free matrix ************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  FILE *ficresilk;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *ficresprobmorprev;
   free((FREE_ARG)(m+nrl-NR_END));  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 /******************* ma3x *******************************/  FILE  *ficresvij;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char fileresvpl[FILENAMELENGTH];
   double ***m;  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m += NR_END;  char command[FILENAMELENGTH];
   m -= nrl;  int  outcmd=0;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  char filelog[FILENAMELENGTH]; /* Log file */
   m[nrl] -= ncl;  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char popfile[FILENAMELENGTH];
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m[nrl][ncl] -= nll;  struct timezone tzp;
   for (j=ncl+1; j<=nch; j++)  extern int gettimeofday();
     m[nrl][j]=m[nrl][j-1]+nlay;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
   for (i=nrl+1; i<=nrh; i++) {  extern long time();
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char strcurr[80], strfor[80];
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  char *endptr;
   }  long lval;
   return m;  
 }  #define NR_END 1
   #define FREE_ARG char*
 /*************************free ma3x ************************/  #define FTOL 1.0e-10
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #define NRANSI 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define ITMAX 200 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #define TOL 2.0e-4 
 }  
   #define CGOLD 0.3819660 
 /***************** f1dim *************************/  #define ZEPS 1.0e-10 
 extern int ncom;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  #define GOLD 1.618034 
    #define GLIMIT 100.0 
 double f1dim(double x)  #define TINY 1.0e-20 
 {  
   int j;  static double maxarg1,maxarg2;
   double f;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double *xt;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
   xt=vector(1,ncom);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define rint(a) floor(a+0.5)
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  static double sqrarg;
   return f;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int imx; 
 {  int stepm=1;
   int iter;  /* Stepm, step in month: minimum step interpolation*/
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  int estepm;
   double ftemp;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  int m,nb;
    long *num;
   a=(ax < cx ? ax : cx);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   b=(ax > cx ? ax : cx);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   x=w=v=bx;  double **pmmij, ***probs;
   fw=fv=fx=(*f)(x);  double *ageexmed,*agecens;
   for (iter=1;iter<=ITMAX;iter++) {  double dateintmean=0;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double *weight;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int **s; /* Status */
     printf(".");fflush(stdout);  double *agedc, **covar, idx;
 #ifdef DEBUG  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     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);  double *lsurv, *lpop, *tpop;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double ftolhess; /* Tolerance for computing hessian */
       *xmin=x;  
       return fx;  /**************** split *************************/
     }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     ftemp=fu;  {
     if (fabs(e) > tol1) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       r=(x-w)*(fx-fv);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       q=(x-v)*(fx-fw);    */ 
       p=(x-v)*q-(x-w)*r;    char  *ss;                            /* pointer */
       q=2.0*(q-r);    int   l1, l2;                         /* length counters */
       if (q > 0.0) p = -p;  
       q=fabs(q);    l1 = strlen(path );                   /* length of path */
       etemp=e;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       e=d;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    if ( ss == NULL ) {                   /* no directory, so determine current directory */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      strcpy( name, path );               /* we got the fullname name because no directory */
       else {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         d=p/q;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         u=x+d;      /* get current working directory */
         if (u-a < tol2 || b-u < tol2)      /*    extern  char* getcwd ( char *buf , int len);*/
           d=SIGN(tol1,xm-x);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       }        return( GLOCK_ERROR_GETCWD );
     } else {      }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      /* got dirc from getcwd*/
     }      printf(" DIRC = %s \n",dirc);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    } else {                              /* strip direcotry from path */
     fu=(*f)(u);      ss++;                               /* after this, the filename */
     if (fu <= fx) {      l2 = strlen( ss );                  /* length of filename */
       if (u >= x) a=x; else b=x;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       SHFT(v,w,x,u)      strcpy( name, ss );         /* save file name */
         SHFT(fv,fw,fx,fu)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         } else {      dirc[l1-l2] = 0;                    /* add zero */
           if (u < x) a=u; else b=u;      printf(" DIRC2 = %s \n",dirc);
           if (fu <= fw || w == x) {    }
             v=w;    /* We add a separator at the end of dirc if not exists */
             w=u;    l1 = strlen( dirc );                  /* length of directory */
             fv=fw;    if( dirc[l1-1] != DIRSEPARATOR ){
             fw=fu;      dirc[l1] =  DIRSEPARATOR;
           } else if (fu <= fv || v == x || v == w) {      dirc[l1+1] = 0; 
             v=u;      printf(" DIRC3 = %s \n",dirc);
             fv=fu;    }
           }    ss = strrchr( name, '.' );            /* find last / */
         }    if (ss >0){
   }      ss++;
   nrerror("Too many iterations in brent");      strcpy(ext,ss);                     /* save extension */
   *xmin=x;      l1= strlen( name);
   return fx;      l2= strlen(ss)+1;
 }      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
 /****************** mnbrak ***********************/    }
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    return( 0 );                          /* we're done */
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  
   double fu;  /******************************************/
    
   *fa=(*func)(*ax);  void replace_back_to_slash(char *s, char*t)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    int i;
     SHFT(dum,*ax,*bx,dum)    int lg=0;
       SHFT(dum,*fb,*fa,dum)    i=0;
       }    lg=strlen(t);
   *cx=(*bx)+GOLD*(*bx-*ax);    for(i=0; i<= lg; i++) {
   *fc=(*func)(*cx);      (s[i] = t[i]);
   while (*fb > *fc) {      if (t[i]== '\\') s[i]='/';
     r=(*bx-*ax)*(*fb-*fc);    }
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int nbocc(char *s, char occ)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    int i,j=0;
       fu=(*func)(u);    int lg=20;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    i=0;
       fu=(*func)(u);    lg=strlen(s);
       if (fu < *fc) {    for(i=0; i<= lg; i++) {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    if  (s[i] == occ ) j++;
           SHFT(*fb,*fc,fu,(*func)(u))    }
           }    return j;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  void cutv(char *u,char *v, char*t, char occ)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       fu=(*func)(u);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     }       gives u="abcedf" and v="ghi2j" */
     SHFT(*ax,*bx,*cx,u)    int i,lg,j,p=0;
       SHFT(*fa,*fb,*fc,fu)    i=0;
       }    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /*************** linmin ************************/  
     lg=strlen(t);
 int ncom;    for(j=0; j<p; j++) {
 double *pcom,*xicom;      (u[j] = t[j]);
 double (*nrfunc)(double []);    }
         u[p]='\0';
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {     for(j=0; j<= lg; j++) {
   double brent(double ax, double bx, double cx,      if (j>=(p+1))(v[j-p-1] = t[j]);
                double (*f)(double), double tol, double *xmin);    }
   double f1dim(double x);  }
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  /********************** nrerror ********************/
   int j;  
   double xx,xmin,bx,ax;  void nrerror(char error_text[])
   double fx,fb,fa;  {
      fprintf(stderr,"ERREUR ...\n");
   ncom=n;    fprintf(stderr,"%s\n",error_text);
   pcom=vector(1,n);    exit(EXIT_FAILURE);
   xicom=vector(1,n);  }
   nrfunc=func;  /*********************** vector *******************/
   for (j=1;j<=n;j++) {  double *vector(int nl, int nh)
     pcom[j]=p[j];  {
     xicom[j]=xi[j];    double *v;
   }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   ax=0.0;    if (!v) nrerror("allocation failure in vector");
   xx=1.0;    return v-nl+NR_END;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /************************ free vector ******************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  void free_vector(double*v, int nl, int nh)
 #endif  {
   for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  /************************ivector *******************************/
   free_vector(xicom,1,n);  int *ivector(long nl,long nh)
   free_vector(pcom,1,n);  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /*************** powell ************************/    if (!v) nrerror("allocation failure in ivector");
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    return v-nl+NR_END;
             double (*func)(double []))  }
 {  
   void linmin(double p[], double xi[], int n, double *fret,  /******************free ivector **************************/
               double (*func)(double []));  void free_ivector(int *v, long nl, long nh)
   int i,ibig,j;  {
   double del,t,*pt,*ptt,*xit;    free((FREE_ARG)(v+nl-NR_END));
   double fp,fptt;  }
   double *xits;  
   pt=vector(1,n);  /************************lvector *******************************/
   ptt=vector(1,n);  long *lvector(long nl,long nh)
   xit=vector(1,n);  {
   xits=vector(1,n);    long *v;
   *fret=(*func)(p);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for (j=1;j<=n;j++) pt[j]=p[j];    if (!v) nrerror("allocation failure in ivector");
   for (*iter=1;;++(*iter)) {    return v-nl+NR_END;
     fp=(*fret);  }
     ibig=0;  
     del=0.0;  /******************free lvector **************************/
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  void free_lvector(long *v, long nl, long nh)
     for (i=1;i<=n;i++)  {
       printf(" %d %.12f",i, p[i]);    free((FREE_ARG)(v+nl-NR_END));
     printf("\n");  }
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /******************* imatrix *******************************/
       fptt=(*fret);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 #ifdef DEBUG       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       printf("fret=%lf \n",*fret);  { 
 #endif    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       printf("%d",i);fflush(stdout);    int **m; 
       linmin(p,xit,n,fret,func);    
       if (fabs(fptt-(*fret)) > del) {    /* allocate pointers to rows */ 
         del=fabs(fptt-(*fret));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         ibig=i;    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
 #ifdef DEBUG    m -= nrl; 
       printf("%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {    
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    /* allocate rows and set pointers to them */ 
         printf(" x(%d)=%.12e",j,xit[j]);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for(j=1;j<=n;j++)    m[nrl] += NR_END; 
         printf(" p=%.12e",p[j]);    m[nrl] -= ncl; 
       printf("\n");    
 #endif    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     }    
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    /* return pointer to array of pointers to rows */ 
 #ifdef DEBUG    return m; 
       int k[2],l;  } 
       k[0]=1;  
       k[1]=-1;  /****************** free_imatrix *************************/
       printf("Max: %.12e",(*func)(p));  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (j=1;j<=n;j++)        int **m;
         printf(" %.12e",p[j]);        long nch,ncl,nrh,nrl; 
       printf("\n");       /* free an int matrix allocated by imatrix() */ 
       for(l=0;l<=1;l++) {  { 
         for (j=1;j<=n;j++) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free((FREE_ARG) (m+nrl-NR_END)); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  } 
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
 #endif  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
       free_vector(xit,1,n);  
       free_vector(xits,1,n);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       free_vector(ptt,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
       free_vector(pt,1,n);    m += NR_END;
       return;    m -= nrl;
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       ptt[j]=2.0*p[j]-pt[j];    m[nrl] += NR_END;
       xit[j]=p[j]-pt[j];    m[nrl] -= ncl;
       pt[j]=p[j];  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     fptt=(*func)(ptt);    return m;
     if (fptt < fp) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);     */
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /*************************free matrix ************************/
           xi[j][ibig]=xi[j][n];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
           xi[j][n]=xit[j];  {
         }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #ifdef DEBUG    free((FREE_ARG)(m+nrl-NR_END));
         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++)  
           printf(" %.12e",xit[j]);  /******************* ma3x *******************************/
         printf("\n");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 #endif  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
   }  
 }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /**** Prevalence limit ****************/    m += NR_END;
     m -= nrl;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      matrix by transitions matrix until convergence is reached */    m[nrl] += NR_END;
     m[nrl] -= ncl;
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double **newm;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double agefin, delaymax=50 ; /* Max number of years to converge */    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=nlstate+ndeath;j++){      m[nrl][j]=m[nrl][j-1]+nlay;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    
     }    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
    cov[1]=1.;      for (j=ncl+1; j<=nch; j++) 
          m[i][j]=m[i][j-1]+nlay;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    return m; 
     newm=savm;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /* Covariates have to be included here again */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      cov[2]=agefin;    */
    }
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*************************free ma3x ************************/
         /*      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]]);*/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       }  {
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for (k=1; k<=cptcovprod;k++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    free((FREE_ARG)(m+nrl-NR_END));
   }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /*************** function subdirf ***********/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  char *subdirf(char fileres[])
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  {
     /* Caution optionfilefiname is hidden */
     savm=oldm;    strcpy(tmpout,optionfilefiname);
     oldm=newm;    strcat(tmpout,"/"); /* Add to the right */
     maxmax=0.;    strcat(tmpout,fileres);
     for(j=1;j<=nlstate;j++){    return tmpout;
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /*************** function subdirf2 ***********/
         sumnew=0;  char *subdirf2(char fileres[], char *preop)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  {
         prlim[i][j]= newm[i][j]/(1-sumnew);    
         max=FMAX(max,prlim[i][j]);    /* Caution optionfilefiname is hidden */
         min=FMIN(min,prlim[i][j]);    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
       maxmin=max-min;    strcat(tmpout,preop);
       maxmax=FMAX(maxmax,maxmin);    strcat(tmpout,fileres);
     }    return tmpout;
     if(maxmax < ftolpl){  }
       return prlim;  
     }  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 /*************** transition probabilities ***************/    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   double s1, s2;    strcat(tmpout,preop2);
   /*double t34;*/    strcat(tmpout,fileres);
   int i,j,j1, nc, ii, jj;    return tmpout;
   }
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  /***************** f1dim *************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  extern int ncom; 
         /*s2 += param[i][j][nc]*cov[nc];*/  extern double *pcom,*xicom;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  extern double (*nrfunc)(double []); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/   
       }  double f1dim(double x) 
       ps[i][j]=s2;  { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    int j; 
     }    double f;
     for(j=i+1; j<=nlstate+ndeath;j++){    double *xt; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){   
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    xt=vector(1,ncom); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
       ps[i][j]=s2;    free_vector(xt,1,ncom); 
     }    return f; 
   }  } 
     /*ps[3][2]=1;*/  
   /*****************brent *************************/
   for(i=1; i<= nlstate; i++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
      s1=0;  { 
     for(j=1; j<i; j++)    int iter; 
       s1+=exp(ps[i][j]);    double a,b,d,etemp;
     for(j=i+1; j<=nlstate+ndeath; j++)    double fu,fv,fw,fx;
       s1+=exp(ps[i][j]);    double ftemp;
     ps[i][i]=1./(s1+1.);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for(j=1; j<i; j++)    double e=0.0; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     for(j=i+1; j<=nlstate+ndeath; j++)    a=(ax < cx ? ax : cx); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    b=(ax > cx ? ax : cx); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    x=w=v=bx; 
   } /* end i */    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      xm=0.5*(a+b); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       ps[ii][jj]=0;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       ps[ii][ii]=1;      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(jj=1; jj<= nlstate+ndeath; jj++){  #endif
      printf("%lf ",ps[ii][jj]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
    }        *xmin=x; 
     printf("\n ");        return fx; 
     }      } 
     printf("\n ");printf("%lf ",cov[2]);*/      ftemp=fu;
 /*      if (fabs(e) > tol1) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        r=(x-w)*(fx-fv); 
   goto end;*/        q=(x-v)*(fx-fw); 
     return ps;        p=(x-v)*q-(x-w)*r; 
 }        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
 /**************** Product of 2 matrices ******************/        q=fabs(q); 
         etemp=e; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        e=d; 
 {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        else { 
   /* in, b, out are matrice of pointers which should have been initialized          d=p/q; 
      before: only the contents of out is modified. The function returns          u=x+d; 
      a pointer to pointers identical to out */          if (u-a < tol2 || b-u < tol2) 
   long i, j, k;            d=SIGN(tol1,xm-x); 
   for(i=nrl; i<= nrh; i++)        } 
     for(k=ncolol; k<=ncoloh; k++)      } else { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         out[i][k] +=in[i][j]*b[j][k];      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   return out;      fu=(*f)(u); 
 }      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
 /************* Higher Matrix Product ***************/          SHFT(fv,fw,fx,fu) 
           } else { 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            if (u < x) a=u; else b=u; 
 {            if (fu <= fw || w == x) { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month              v=w; 
      duration (i.e. until              w=u; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.              fv=fw; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step              fw=fu; 
      (typically every 2 years instead of every month which is too big).            } else if (fu <= fv || v == x || v == w) { 
      Model is determined by parameters x and covariates have to be              v=u; 
      included manually here.              fv=fu; 
             } 
      */          } 
     } 
   int i, j, d, h, k;    nrerror("Too many iterations in brent"); 
   double **out, cov[NCOVMAX];    *xmin=x; 
   double **newm;    return fx; 
   } 
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /****************** mnbrak ***********************/
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       po[i][j][0]=(i==j ? 1.0 : 0.0);              double (*func)(double)) 
     }  { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double ulim,u,r,q, dum;
   for(h=1; h <=nhstepm; h++){    double fu; 
     for(d=1; d <=hstepm; d++){   
       newm=savm;    *fa=(*func)(*ax); 
       /* Covariates have to be included here again */    *fb=(*func)(*bx); 
       cov[1]=1.;    if (*fb > *fa) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      SHFT(dum,*ax,*bx,dum) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        SHFT(dum,*fb,*fa,dum) 
       for (k=1; k<=cptcovage;k++)        } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    *cx=(*bx)+GOLD*(*bx-*ax); 
       for (k=1; k<=cptcovprod;k++)    *fc=(*func)(*cx); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      ulim=(*bx)+GLIMIT*(*cx-*bx); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      if ((*bx-u)*(u-*cx) > 0.0) { 
       savm=oldm;        fu=(*func)(u); 
       oldm=newm;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     }        fu=(*func)(u); 
     for(i=1; i<=nlstate+ndeath; i++)        if (fu < *fc) { 
       for(j=1;j<=nlstate+ndeath;j++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         po[i][j][h]=newm[i][j];            SHFT(*fb,*fc,fu,(*func)(u)) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);            } 
          */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       }        u=ulim; 
   } /* end h */        fu=(*func)(u); 
   return po;      } else { 
 }        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
       } 
 /*************** log-likelihood *************/      SHFT(*ax,*bx,*cx,u) 
 double func( double *x)        SHFT(*fa,*fb,*fc,fu) 
 {        } 
   int i, ii, j, k, mi, d, kk;  } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  /*************** linmin ************************/
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  int ncom; 
   long ipmx;  double *pcom,*xicom;
   /*extern weight */  double (*nrfunc)(double []); 
   /* We are differentiating ll according to initial status */   
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   /*for(i=1;i<imx;i++)  { 
     printf(" %d\n",s[4][i]);    double brent(double ax, double bx, double cx, 
   */                 double (*f)(double), double tol, double *xmin); 
   cov[1]=1.;    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   for(k=1; k<=nlstate; k++) ll[k]=0.;                double *fc, double (*func)(double)); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    int j; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    double xx,xmin,bx,ax; 
     for(mi=1; mi<= wav[i]-1; mi++){    double fx,fb,fa;
       for (ii=1;ii<=nlstate+ndeath;ii++)   
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    ncom=n; 
       for(d=0; d<dh[mi][i]; d++){    pcom=vector(1,n); 
         newm=savm;    xicom=vector(1,n); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    nrfunc=func; 
         for (kk=1; kk<=cptcovage;kk++) {    for (j=1;j<=n;j++) { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      pcom[j]=p[j]; 
         }      xicom[j]=xi[j]; 
            } 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    ax=0.0; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    xx=1.0; 
         savm=oldm;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         oldm=newm;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
          #ifdef DEBUG
            printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       } /* end mult */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
        #endif
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    for (j=1;j<=n;j++) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      xi[j] *= xmin; 
       ipmx +=1;      p[j] += xi[j]; 
       sw += weight[i];    } 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    free_vector(xicom,1,n); 
     } /* end of wave */    free_vector(pcom,1,n); 
   } /* end of individual */  } 
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  char *asc_diff_time(long time_sec, char ascdiff[])
   /* 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 */    long sec_left, days, hours, minutes;
   return -l;    days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
 /*********** Maximum Likelihood Estimation ***************/    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 {    return ascdiff;
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  /*************** powell ************************/
   xi=matrix(1,npar,1,npar);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (i=1;i<=npar;i++)              double (*func)(double [])) 
     for (j=1;j<=npar;j++)  { 
       xi[i][j]=(i==j ? 1.0 : 0.0);    void linmin(double p[], double xi[], int n, double *fret, 
   printf("Powell\n");                double (*func)(double [])); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double fp,fptt;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double *xits;
     int niterf, itmp;
 }  
     pt=vector(1,n); 
 /**** Computes Hessian and covariance matrix ***/    ptt=vector(1,n); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    xit=vector(1,n); 
 {    xits=vector(1,n); 
   double  **a,**y,*x,pd;    *fret=(*func)(p); 
   double **hess;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   int i, j,jk;    for (*iter=1;;++(*iter)) { 
   int *indx;      fp=(*fret); 
       ibig=0; 
   double hessii(double p[], double delta, int theta, double delti[]);      del=0.0; 
   double hessij(double p[], double delti[], int i, int j);      last_time=curr_time;
   void lubksb(double **a, int npar, int *indx, double b[]) ;      (void) gettimeofday(&curr_time,&tzp);
   void ludcmp(double **a, int npar, int *indx, double *d) ;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   hess=matrix(1,npar,1,npar);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
   printf("\nCalculation of the hessian matrix. Wait...\n");     for (i=1;i<=n;i++) {
   for (i=1;i<=npar;i++){        printf(" %d %.12f",i, p[i]);
     printf("%d",i);fflush(stdout);        fprintf(ficlog," %d %.12lf",i, p[i]);
     hess[i][i]=hessii(p,ftolhess,i,delti);        fprintf(ficrespow," %.12lf", p[i]);
     /*printf(" %f ",p[i]);*/      }
     /*printf(" %lf ",hess[i][i]);*/      printf("\n");
   }      fprintf(ficlog,"\n");
        fprintf(ficrespow,"\n");fflush(ficrespow);
   for (i=1;i<=npar;i++) {      if(*iter <=3){
     for (j=1;j<=npar;j++)  {        tm = *localtime(&curr_time.tv_sec);
       if (j>i) {        strcpy(strcurr,asctime(&tm));
         printf(".%d%d",i,j);fflush(stdout);  /*       asctime_r(&tm,strcurr); */
         hess[i][j]=hessij(p,delti,i,j);        forecast_time=curr_time; 
         hess[j][i]=hess[i][j];            itmp = strlen(strcurr);
         /*printf(" %lf ",hess[i][j]);*/        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       }          strcurr[itmp-1]='\0';
     }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   printf("\n");        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);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          tmf = *localtime(&forecast_time.tv_sec);
    /*      asctime_r(&tmf,strfor); */
   a=matrix(1,npar,1,npar);          strcpy(strfor,asctime(&tmf));
   y=matrix(1,npar,1,npar);          itmp = strlen(strfor);
   x=vector(1,npar);          if(strfor[itmp-1]=='\n')
   indx=ivector(1,npar);          strfor[itmp-1]='\0';
   for (i=1;i<=npar;i++)          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);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          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);
   ludcmp(a,npar,indx,&pd);        }
       }
   for (j=1;j<=npar;j++) {      for (i=1;i<=n;i++) { 
     for (i=1;i<=npar;i++) x[i]=0;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     x[j]=1;        fptt=(*fret); 
     lubksb(a,npar,indx,x);  #ifdef DEBUG
     for (i=1;i<=npar;i++){        printf("fret=%lf \n",*fret);
       matcov[i][j]=x[i];        fprintf(ficlog,"fret=%lf \n",*fret);
     }  #endif
   }        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   printf("\n#Hessian matrix#\n");        linmin(p,xit,n,fret,func); 
   for (i=1;i<=npar;i++) {        if (fabs(fptt-(*fret)) > del) { 
     for (j=1;j<=npar;j++) {          del=fabs(fptt-(*fret)); 
       printf("%.3e ",hess[i][j]);          ibig=i; 
     }        } 
     printf("\n");  #ifdef DEBUG
   }        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   /* Recompute Inverse */        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          printf(" x(%d)=%.12e",j,xit[j]);
   ludcmp(a,npar,indx,&pd);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   /*  printf("\n#Hessian matrix recomputed#\n");        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   for (j=1;j<=npar;j++) {          fprintf(ficlog," p=%.12e",p[j]);
     for (i=1;i<=npar;i++) x[i]=0;        }
     x[j]=1;        printf("\n");
     lubksb(a,npar,indx,x);        fprintf(ficlog,"\n");
     for (i=1;i<=npar;i++){  #endif
       y[i][j]=x[i];      } 
       printf("%.3e ",y[i][j]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
     printf("\n");        int k[2],l;
   }        k[0]=1;
   */        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
   free_matrix(a,1,npar,1,npar);        fprintf(ficlog,"Max: %.12e",(*func)(p));
   free_matrix(y,1,npar,1,npar);        for (j=1;j<=n;j++) {
   free_vector(x,1,npar);          printf(" %.12e",p[j]);
   free_ivector(indx,1,npar);          fprintf(ficlog," %.12e",p[j]);
   free_matrix(hess,1,npar,1,npar);        }
         printf("\n");
         fprintf(ficlog,"\n");
 }        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 /*************** hessian matrix ****************/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 double hessii( double x[], double delta, int theta, double delti[])            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]);
   int i;          }
   int l=1, lmax=20;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double k1,k2;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double p2[NPARMAX+1];        }
   double res;  #endif
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;  
   int k=0,kmax=10;        free_vector(xit,1,n); 
   double l1;        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   fx=func(x);        free_vector(pt,1,n); 
   for (i=1;i<=npar;i++) p2[i]=x[i];        return; 
   for(l=0 ; l <=lmax; l++){      } 
     l1=pow(10,l);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     delts=delt;      for (j=1;j<=n;j++) { 
     for(k=1 ; k <kmax; k=k+1){        ptt[j]=2.0*p[j]-pt[j]; 
       delt = delta*(l1*k);        xit[j]=p[j]-pt[j]; 
       p2[theta]=x[theta] +delt;        pt[j]=p[j]; 
       k1=func(p2)-fx;      } 
       p2[theta]=x[theta]-delt;      fptt=(*func)(ptt); 
       k2=func(p2)-fx;      if (fptt < fp) { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        if (t < 0.0) { 
                linmin(p,xit,n,fret,func); 
 #ifdef DEBUG          for (j=1;j<=n;j++) { 
       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);            xi[j][ibig]=xi[j][n]; 
 #endif            xi[j][n]=xit[j]; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  #ifdef DEBUG
         k=kmax;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          for(j=1;j<=n;j++){
         k=kmax; l=lmax*10.;            printf(" %.12e",xit[j]);
       }            fprintf(ficlog," %.12e",xit[j]);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          }
         delts=delt;          printf("\n");
       }          fprintf(ficlog,"\n");
     }  #endif
   }        }
   delti[theta]=delts;      } 
   return res;    } 
    } 
 }  
   /**** Prevalence limit (stable prevalence)  ****************/
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int i;  {
   int l=1, l1, lmax=20;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   double k1,k2,k3,k4,res,fx;       matrix by transitions matrix until convergence is reached */
   double p2[NPARMAX+1];  
   int k;    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   fx=func(x);    double **matprod2();
   for (k=1; k<=2; k++) {    double **out, cov[NCOVMAX], **pmij();
     for (i=1;i<=npar;i++) p2[i]=x[i];    double **newm;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double agefin, delaymax=50 ; /* Max number of years to converge */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    for (ii=1;ii<=nlstate+ndeath;ii++)
        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;      }
     k2=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 */
     k3=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;
     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<=cptcovn;k++) {
 #ifdef DEBUG          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[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);          /*      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]]);*/
 #endif        }
   }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   return res;        for (k=1; k<=cptcovprod;k++)
 }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 /************** Inverse of matrix **************/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 void ludcmp(double **a, int n, int *indx, double *d)        /*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]);*/
   int i,imax,j,k;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double big,dum,sum,temp;  
   double *vv;      savm=oldm;
        oldm=newm;
   vv=vector(1,n);      maxmax=0.;
   *d=1.0;      for(j=1;j<=nlstate;j++){
   for (i=1;i<=n;i++) {        min=1.;
     big=0.0;        max=0.;
     for (j=1;j<=n;j++)        for(i=1; i<=nlstate; i++) {
       if ((temp=fabs(a[i][j])) > big) big=temp;          sumnew=0;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     vv[i]=1.0/big;          prlim[i][j]= newm[i][j]/(1-sumnew);
   }          max=FMAX(max,prlim[i][j]);
   for (j=1;j<=n;j++) {          min=FMIN(min,prlim[i][j]);
     for (i=1;i<j;i++) {        }
       sum=a[i][j];        maxmin=max-min;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        maxmax=FMAX(maxmax,maxmin);
       a[i][j]=sum;      }
     }      if(maxmax < ftolpl){
     big=0.0;        return prlim;
     for (i=j;i<=n;i++) {      }
       sum=a[i][j];    }
       for (k=1;k<j;k++)  }
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /*************** transition probabilities ***************/ 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         imax=i;  {
       }    double s1, s2;
     }    /*double t34;*/
     if (j != imax) {    int i,j,j1, nc, ii, jj;
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];      for(i=1; i<= nlstate; i++){
         a[imax][k]=a[j][k];        for(j=1; j<i;j++){
         a[j][k]=dum;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       }            /*s2 += param[i][j][nc]*cov[nc];*/
       *d = -(*d);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       vv[imax]=vv[j];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     }          }
     indx[j]=imax;          ps[i][j]=s2;
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     if (j != n) {        }
       dum=1.0/(a[j][j]);        for(j=i+1; j<=nlstate+ndeath;j++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   free_vector(vv,1,n);  /* Doesn't work */          }
 ;          ps[i][j]=s2;
 }        }
       }
 void lubksb(double **a, int n, int *indx, double b[])      /*ps[3][2]=1;*/
 {      
   int i,ii=0,ip,j;      for(i=1; i<= nlstate; i++){
   double sum;        s1=0;
          for(j=1; j<i; j++)
   for (i=1;i<=n;i++) {          s1+=exp(ps[i][j]);
     ip=indx[i];        for(j=i+1; j<=nlstate+ndeath; j++)
     sum=b[ip];          s1+=exp(ps[i][j]);
     b[ip]=b[i];        ps[i][i]=1./(s1+1.);
     if (ii)        for(j=1; j<i; j++)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     else if (sum) ii=i;        for(j=i+1; j<=nlstate+ndeath; j++)
     b[i]=sum;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for (i=n;i>=1;i--) {      } /* end i */
     sum=b[i];      
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     b[i]=sum/a[i][i];        for(jj=1; jj<= nlstate+ndeath; jj++){
   }          ps[ii][jj]=0;
 }          ps[ii][ii]=1;
         }
 /************ Frequencies ********************/      }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)      
 {  /* Some frequencies */  
    /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   double ***freq; /* Frequencies */  /*         printf("ddd %lf ",ps[ii][jj]); */
   double *pp;  /*       } */
   double pos, k2, dateintsum=0,k2cpt=0;  /*       printf("\n "); */
   FILE *ficresp;  /*        } */
   char fileresp[FILENAMELENGTH];  /*        printf("\n ");printf("%lf ",cov[2]); */
           /*
   pp=vector(1,nlstate);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        goto end;*/
   strcpy(fileresp,"p");      return ps;
   strcat(fileresp,fileres);  }
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);  /**************** Product of 2 matrices ******************/
     exit(0);  
   }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  {
   j1=0;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   j=cptcoveff;    /* in, b, out are matrice of pointers which should have been initialized 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
   for(k1=1; k1<=j;k1++){    long i, j, k;
     for(i1=1; i1<=ncodemax[k1];i1++){    for(i=nrl; i<= nrh; i++)
       j1++;      for(k=ncolol; k<=ncoloh; k++)
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         scanf("%d", i);*/          out[i][k] +=in[i][j]*b[j][k];
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      return out;
           for(m=agemin; m <= agemax+3; m++)  }
             freq[i][jk][m]=0;  
        
       dateintsum=0;  /************* Higher Matrix Product ***************/
       k2cpt=0;  
       for (i=1; i<=imx; i++) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         bool=1;  {
         if  (cptcovn>0) {    /* Computes the transition matrix starting at age 'age' over 
           for (z1=1; z1<=cptcoveff; z1++)       'nhstepm*hstepm*stepm' months (i.e. until
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
               bool=0;       nhstepm*hstepm matrices. 
         }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         if (bool==1) {       (typically every 2 years instead of every month which is too big 
           for(m=firstpass; m<=lastpass; m++){       for the memory).
             k2=anint[m][i]+(mint[m][i]/12.);       Model is determined by parameters x and covariates have to be 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {       included manually here. 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;       */
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    int i, j, d, h, k;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double **out, cov[NCOVMAX];
               }    double **newm;
                
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    /* Hstepm could be zero and should return the unit matrix */
                 dateintsum=dateintsum+k2;    for (i=1;i<=nlstate+ndeath;i++)
                 k2cpt++;      for (j=1;j<=nlstate+ndeath;j++){
               }        oldm[i][j]=(i==j ? 1.0 : 0.0);
             }        po[i][j][0]=(i==j ? 1.0 : 0.0);
           }      }
         }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       }    for(h=1; h <=nhstepm; h++){
              for(d=1; d <=hstepm; d++){
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        newm=savm;
         /* Covariates have to be included here again */
       if  (cptcovn>0) {        cov[1]=1.;
         fprintf(ficresp, "\n#********** Variable ");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         fprintf(ficresp, "**********\n#");        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++)
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          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=(int)agemin; i <= (int)agemax+3; i++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         if(i==(int)agemax+3)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           printf("Total");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         else                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           printf("Age %d", i);        savm=oldm;
         for(jk=1; jk <=nlstate ; jk++){        oldm=newm;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
             pp[jk] += freq[jk][m][i];      for(i=1; i<=nlstate+ndeath; i++)
         }        for(j=1;j<=nlstate+ndeath;j++) {
         for(jk=1; jk <=nlstate ; jk++){          po[i][j][h]=newm[i][j];
           for(m=-1, pos=0; m <=0 ; m++)          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
             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]);    } /* end h */
           else    return po;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  }
         }  
   
         for(jk=1; jk <=nlstate ; jk++){  /*************** log-likelihood *************/
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  double func( double *x)
             pp[jk] += freq[jk][m][i];  {
         }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double **out;
           pos += pp[jk];    double sw; /* Sum of weights */
         for(jk=1; jk <=nlstate ; jk++){    double lli; /* Individual log likelihood */
           if(pos>=1.e-5)    int s1, s2;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double bbh, survp;
           else    long ipmx;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /*extern weight */
           if( i <= (int) agemax){    /* We are differentiating ll according to initial status */
             if(pos>=1.e-5){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    /*for(i=1;i<imx;i++) 
               probs[i][jk][j1]= pp[jk]/pos;      printf(" %d\n",s[4][i]);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    */
             }    cov[1]=1.;
             else  
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    for(k=1; k<=nlstate; k++) ll[k]=0.;
           }  
         }    if(mle==1){
              for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=-1; jk <=nlstate+ndeath; jk++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(m=-1; m <=nlstate+ndeath; m++)        for(mi=1; mi<= wav[i]-1; mi++){
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(i <= (int) agemax)            for (j=1;j<=nlstate+ndeath;j++){
           fprintf(ficresp,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf("\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     }          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   dateintmean=dateintsum/k2cpt;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   fclose(ficresp);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            }
   free_vector(pp,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* End of Freq */            savm=oldm;
 }            oldm=newm;
           } /* end mult */
 /************ Prevalence ********************/        
 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)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 {  /* Some frequencies */          /* 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 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double ***freq; /* Frequencies */           * the nearest (and in case of equal distance, to the lowest) interval but now
   double *pp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double pos, k2;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
   pp=vector(1,nlstate);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * For stepm > 1 the results are less biased than in previous versions. 
   j1=0;           */
            s1=s[mw[mi][i]][i];
   j=cptcoveff;          s2=s[mw[mi+1][i]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias bh is positive if real duration
   for(k1=1; k1<=j;k1++){           * is higher than the multiple of stepm and negative otherwise.
     for(i1=1; i1<=ncodemax[k1];i1++){           */
       j1++;          /* 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 (i=-1; i<=nlstate+ndeath; i++)              /* i.e. if s2 is a death state and if the date of death is known 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                 then the contribution to the likelihood is the probability to 
           for(m=agemin; m <= agemax+3; m++)               die between last step unit time and current  step unit time, 
             freq[i][jk][m]=0;               which is also equal to probability to die before dh 
                     minus probability to die before dh-stepm . 
       for (i=1; i<=imx; i++) {               In version up to 0.92 likelihood was computed
         bool=1;          as if date of death was unknown. Death was treated as any other
         if  (cptcovn>0) {          health state: the date of the interview describes the actual state
           for (z1=1; z1<=cptcoveff; z1++)          and not the date of a change in health state. The former idea was
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          to consider that at each interview the state was recorded
               bool=0;          (healthy, disable or death) and IMaCh was corrected; but when we
         }          introduced the exact date of death then we should have modified
         if (bool==1) {          the contribution of an exact death to the likelihood. This new
           for(m=firstpass; m<=lastpass; m++){          contribution is smaller and very dependent of the step unit
             k2=anint[m][i]+(mint[m][i]/12.);          stepm. It is no more the probability to die between last interview
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          and month of death but the probability to survive from last
               if(agev[m][i]==0) agev[m][i]=agemax+1;          interview up to one month before death multiplied by the
               if(agev[m][i]==1) agev[m][i]=agemax+2;          probability to die within a month. Thanks to Chris
               if (m<lastpass) {          Jackson for correcting this bug.  Former versions increased
                 if (calagedate>0)          mortality artificially. The bad side is that we add another loop
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          which slows down the processing. The difference can be up to 10%
                 else          lower mortality.
                   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];            lli=log(out[s1][s2] - savm[s1][s2]);
               }  
             }  
           }          } else if  (s2==-2) {
         }            for (j=1,survp=0. ; j<=nlstate; j++) 
       }              survp += out[s1][j];
       for(i=(int)agemin; i <= (int)agemax+3; i++){            lli= survp;
         for(jk=1; jk <=nlstate ; jk++){          }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          
             pp[jk] += freq[jk][m][i];          else if  (s2==-4) {
         }            for (j=3,survp=0. ; j<=nlstate; j++) 
         for(jk=1; jk <=nlstate ; jk++){              survp += out[s1][j];
           for(m=-1, pos=0; m <=0 ; m++)            lli= survp;
             pos += freq[jk][m][i];          }
         }          
                  else if  (s2==-5) {
         for(jk=1; jk <=nlstate ; jk++){            for (j=1,survp=0. ; j<=2; j++) 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              survp += out[s1][j];
             pp[jk] += freq[jk][m][i];            lli= survp;
         }          }
          
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
                  else{
         for(jk=1; jk <=nlstate ; jk++){                lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           if( i <= (int) agemax){            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
             if(pos>=1.e-5){          } 
               probs[i][jk][j1]= pp[jk]/pos;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
             }          /*if(lli ==000.0)*/
           }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         }          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++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_vector(pp,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
 }  /* End of Freq */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************* Waves Concatenation ***************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          for(d=0; d<=dh[mi][i]; d++){
 {            newm=savm;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      Death is a valid wave (if date is known).            for (kk=1; kk<=cptcovage;kk++) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            }
      and mw[mi+1][i]. dh depends on stepm.            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   int i, mi, m;            oldm=newm;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          } /* end mult */
      double sum=0., jmean=0.;*/        
           s1=s[mw[mi][i]][i];
   int j, k=0,jk, ju, jl;          s2=s[mw[mi+1][i]][i];
   double sum=0.;          bbh=(double)bh[mi][i]/(double)stepm; 
   jmin=1e+5;          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 */
   jmax=-1;          ipmx +=1;
   jmean=0.;          sw += weight[i];
   for(i=1; i<=imx; i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     mi=0;        } /* end of wave */
     m=firstpass;      } /* end of individual */
     while(s[m][i] <= nlstate){    }  else if(mle==3){  /* exponential inter-extrapolation */
       if(s[m][i]>=1)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         mw[++mi][i]=m;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if(m >=lastpass)        for(mi=1; mi<= wav[i]-1; mi++){
         break;          for (ii=1;ii<=nlstate+ndeath;ii++)
       else            for (j=1;j<=nlstate+ndeath;j++){
         m++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }/* end while */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (s[m][i] > nlstate){            }
       mi++;     /* Death is another wave */          for(d=0; d<dh[mi][i]; d++){
       /* if(mi==0)  never been interviewed correctly before death */            newm=savm;
          /* Only death is a correct wave */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       mw[mi][i]=m;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
     wav[i]=mi;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if(mi==0)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            savm=oldm;
   }            oldm=newm;
           } /* end mult */
   for(i=1; i<=imx; i++){        
     for(mi=1; mi<wav[i];mi++){          s1=s[mw[mi][i]][i];
       if (stepm <=0)          s2=s[mw[mi+1][i]][i];
         dh[mi][i]=1;          bbh=(double)bh[mi][i]/(double)stepm; 
       else{          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 */
         if (s[mw[mi+1][i]][i] > nlstate) {          ipmx +=1;
           if (agedc[i] < 2*AGESUP) {          sw += weight[i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if(j==0) j=1;  /* Survives at least one month after exam */        } /* end of wave */
           k=k+1;      } /* end of individual */
           if (j >= jmax) jmax=j;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           if (j <= jmin) jmin=j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           sum=sum+j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(mi=1; mi<= wav[i]-1; mi++){
           }          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
         else{              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;            }
           if (j >= jmax) jmax=j;          for(d=0; d<dh[mi][i]; d++){
           else if (j <= jmin)jmin=j;            newm=savm;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           sum=sum+j;            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         jk= j/stepm;            }
         jl= j -jk*stepm;          
         ju= j -(jk+1)*stepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if(jl <= -ju)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           dh[mi][i]=jk;            savm=oldm;
         else            oldm=newm;
           dh[mi][i]=jk+1;          } /* end mult */
         if(dh[mi][i]==0)        
           dh[mi][i]=1; /* At least one step */          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
     }          if( s2 > nlstate){ 
   }            lli=log(out[s1][s2] - savm[s1][s2]);
   jmean=sum/k;          }else{
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
  }          }
 /*********** Tricode ****************************/          ipmx +=1;
 void tricode(int *Tvar, int **nbcode, int imx)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int Ndum[20],ij=1, k, j, i;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   int cptcode=0;        } /* end of wave */
   cptcoveff=0;      } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   for (k=0; k<19; k++) Ndum[k]=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (k=1; k<=7; k++) ncodemax[k]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1; i<=imx; i++) {            for (j=1;j<=nlstate+ndeath;j++){
       ij=(int)(covar[Tvar[j]][i]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       Ndum[ij]++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            }
       if (ij > cptcode) cptcode=ij;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for (i=0; i<=cptcode; i++) {            for (kk=1; kk<=cptcovage;kk++) {
       if(Ndum[i]!=0) ncodemax[j]++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     ij=1;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1; i<=ncodemax[j]; i++) {            savm=oldm;
       for (k=0; k<=19; k++) {            oldm=newm;
         if (Ndum[k] != 0) {          } /* end mult */
           nbcode[Tvar[j]][ij]=k;        
                    s1=s[mw[mi][i]][i];
           ij++;          s2=s[mw[mi+1][i]][i];
         }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         if (ij > ncodemax[j]) break;          ipmx +=1;
       }            sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }            /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
  for (k=0; k<19; k++) Ndum[k]=0;      } /* end of individual */
     } /* End of if */
  for (i=1; i<=ncovmodel-2; i++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       ij=Tvar[i];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       Ndum[ij]++;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
   }
  ij=1;  
  for (i=1; i<=10; i++) {  /*************** log-likelihood *************/
    if((Ndum[i]!=0) && (i<=ncovcol)){  double funcone( double *x)
      Tvaraff[ij]=i;  {
      ij++;    /* Same as likeli but slower because of a lot of printf and if */
    }    int i, ii, j, k, mi, d, kk;
  }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
     cptcoveff=ij-1;    double lli; /* Individual log likelihood */
 }    double llt;
     int s1, s2;
 /*********** Health Expectancies ****************/    double bbh, survp;
     /*extern weight */
 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 )    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 {    /*for(i=1;i<imx;i++) 
   /* Health expectancies */      printf(" %d\n",s[4][i]);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    */
   double age, agelim, hf;    cov[1]=1.;
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double *xp;  
   double **gp, **gm;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double ***gradg, ***trgradg;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int theta;      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          for (j=1;j<=nlstate+ndeath;j++){
   xp=vector(1,npar);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewm=matrix(1,nlstate*2,1,npar);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate*2,1,nlstate*2);          }
          for(d=0; d<dh[mi][i]; d++){
   fprintf(ficreseij,"# Health expectancies\n");          newm=savm;
   fprintf(ficreseij,"# Age");          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=nlstate;i++)          for (kk=1; kk<=cptcovage;kk++) {
     for(j=1; j<=nlstate;j++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          }
   fprintf(ficreseij,"\n");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if(estepm < stepm){          savm=oldm;
     printf ("Problem %d lower than %d\n",estepm, stepm);          oldm=newm;
   }        } /* end mult */
   else  hstepm=estepm;          
   /* We compute the life expectancy from trapezoids spaced every estepm months        s1=s[mw[mi][i]][i];
    * This is mainly to measure the difference between two models: for example        s2=s[mw[mi+1][i]][i];
    * if stepm=24 months pijx are given only every 2 years and by summing them        bbh=(double)bh[mi][i]/(double)stepm; 
    * we are calculating an estimate of the Life Expectancy assuming a linear        /* bias is positive if real duration
    * progression inbetween and thus overestimating or underestimating according         * is higher than the multiple of stepm and negative otherwise.
    * to the curvature of the survival function. If, for the same date, we         */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        if( s2 > nlstate && (mle <5) ){  /* Jackson */
    * to compare the new estimate of Life expectancy with the same linear          lli=log(out[s1][s2] - savm[s1][s2]);
    * hypothesis. A more precise result, taking into account a more precise        } else if (mle==1){
    * curvature will be obtained if estepm is as small as stepm. */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
   /* For example we decided to compute the life expectancy with the smallest unit */          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 */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        } else if(mle==3){  /* exponential inter-extrapolation */
      nhstepm is the number of hstepm from age to agelim          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 */
      nstepm is the number of stepm from age to agelin.        } else if (mle==4){  /* mle=4 no inter-extrapolation */
      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 */        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          lli=log(out[s1][s2]); /* Original formula */
      survival function given by stepm (the optimization length). Unfortunately it        } /* End of if */
      means that if the survival funtion is printed only each two years of age and if        ipmx +=1;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        sw += weight[i];
      results. So we changed our mind and took the option of the best precision.        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]); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        if(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   agelim=AGESUP;   %10.6f %10.6f %10.6f ", \
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     /* nhstepm age range expressed in number of stepm */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            llt +=ll[k]*gipmx/gsw;
     /* if (stepm >= YEARM) hstepm=1;*/            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresilk," %10.6f\n", -llt);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        }
     gp=matrix(0,nhstepm,1,nlstate*2);      } /* end of wave */
     gm=matrix(0,nhstepm,1,nlstate*2);    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      if(globpr==0){ /* First time we count the contributions and weights */
        gipmx=ipmx;
       gsw=sw;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    }
     return -l;
     /* Computing Variances of health expectancies */  }
   
      for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){  /*************** function likelione ***********/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       }  {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* This routine should help understanding what is done with 
         the selection of individuals/waves and
       cptj=0;       to check the exact contribution to the likelihood.
       for(j=1; j<= nlstate; j++){       Plotting could be done.
         for(i=1; i<=nlstate; i++){     */
           cptj=cptj+1;    int k;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    if(*globpri !=0){ /* Just counts and sums, no printings */
           }      strcpy(fileresilk,"ilk"); 
         }      strcat(fileresilk,fileres);
       }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", fileresilk);
              fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       for(i=1; i<=npar; i++)      }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      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");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
            /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       cptj=0;      for(k=1; k<=nlstate; k++) 
       for(j=1; j<= nlstate; j++){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         for(i=1;i<=nlstate;i++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           cptj=cptj+1;    }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    *fretone=(*funcone)(p);
           }    if(*globpri !=0){
         }      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++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }  /*********** Maximum Likelihood Estimation ***************/
   
      }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
      {
 /* End theta */    int i,j, iter;
     double **xi;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    double fret;
     double fretone; /* Only one call to likelihood */
      for(h=0; h<=nhstepm-1; h++)    /*  char filerespow[FILENAMELENGTH];*/
       for(j=1; j<=nlstate*2;j++)    xi=matrix(1,npar,1,npar);
         for(theta=1; theta <=npar; theta++)    for (i=1;i<=npar;i++)
         trgradg[h][j][theta]=gradg[h][theta][j];      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
      for(i=1;i<=nlstate*2;i++)    strcpy(filerespow,"pow"); 
       for(j=1;j<=nlstate*2;j++)    strcat(filerespow,fileres);
         varhe[i][j][(int)age] =0.;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
      printf("%d|",(int)age);fflush(stdout);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(h=0;h<=nhstepm-1;h++){    }
       for(k=0;k<=nhstepm-1;k++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    for (i=1;i<=nlstate;i++)
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      for(j=1;j<=nlstate+ndeath;j++)
         for(i=1;i<=nlstate*2;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           for(j=1;j<=nlstate*2;j++)    fprintf(ficrespow,"\n");
             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);
     /* Computing expectancies */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(j=1; j<=nlstate;j++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  }
            
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         }  {
     double  **a,**y,*x,pd;
     fprintf(ficreseij,"%3.0f",age );    double **hess;
     cptj=0;    int i, j,jk;
     for(i=1; i<=nlstate;i++)    int *indx;
       for(j=1; j<=nlstate;j++){  
         cptj++;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     fprintf(ficreseij,"\n");    void ludcmp(double **a, int npar, int *indx, double *d) ;
        double gompertz(double p[]);
     free_matrix(gm,0,nhstepm,1,nlstate*2);    hess=matrix(1,npar,1,npar);
     free_matrix(gp,0,nhstepm,1,nlstate*2);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    printf("\nCalculation of the hessian matrix. Wait...\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++){
   }      printf("%d",i);fflush(stdout);
   free_vector(xp,1,npar);      fprintf(ficlog,"%d",i);fflush(ficlog);
   free_matrix(dnewm,1,nlstate*2,1,npar);     
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   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++) {
   /* Variance of health expectancies */      for (j=1;j<=npar;j++)  {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        if (j>i) { 
   double **newm;          printf(".%d%d",i,j);fflush(stdout);
   double **dnewm,**doldm;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   int i, j, nhstepm, hstepm, h, nstepm ;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   int k, cptcode;          
   double *xp;          hess[j][i]=hess[i][j];    
   double **gp, **gm;          /*printf(" %lf ",hess[i][j]);*/
   double ***gradg, ***trgradg;        }
   double ***p3mat;      }
   double age,agelim, hf;    }
   int theta;    printf("\n");
     fprintf(ficlog,"\n");
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  
   fprintf(ficresvij,"# Age");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(j=1; j<=nlstate;j++)    
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    a=matrix(1,npar,1,npar);
   fprintf(ficresvij,"\n");    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
   xp=vector(1,npar);    indx=ivector(1,npar);
   dnewm=matrix(1,nlstate,1,npar);    for (i=1;i<=npar;i++)
   doldm=matrix(1,nlstate,1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
      ludcmp(a,npar,indx,&pd);
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   else  hstepm=estepm;        x[j]=1;
   /* For example we decided to compute the life expectancy with the smallest unit */      lubksb(a,npar,indx,x);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1;i<=npar;i++){ 
      nhstepm is the number of hstepm from age to agelim        matcov[i][j]=x[i];
      nstepm is the number of stepm from age to agelin.      }
      Look at hpijx to understand the reason of that which relies in memory size    }
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    printf("\n#Hessian matrix#\n");
      survival function given by stepm (the optimization length). Unfortunately it    fprintf(ficlog,"\n#Hessian matrix#\n");
      means that if the survival funtion is printed only each two years of age and if    for (i=1;i<=npar;i++) { 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      for (j=1;j<=npar;j++) { 
      results. So we changed our mind and took the option of the best precision.        printf("%.3e ",hess[i][j]);
   */        fprintf(ficlog,"%.3e ",hess[i][j]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      }
   agelim = AGESUP;      printf("\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficlog,"\n");
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* Recompute Inverse */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    for (i=1;i<=npar;i++)
     gp=matrix(0,nhstepm,1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     gm=matrix(0,nhstepm,1,nlstate);    ludcmp(a,npar,indx,&pd);
   
     for(theta=1; theta <=npar; theta++){    /*  printf("\n#Hessian matrix recomputed#\n");
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        x[j]=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
       if (popbased==1) {        y[i][j]=x[i];
         for(i=1; i<=nlstate;i++)        printf("%.3e ",y[i][j]);
           prlim[i][i]=probs[(int)age][i][ij];        fprintf(ficlog,"%.3e ",y[i][j]);
       }      }
        printf("\n");
       for(j=1; j<= nlstate; j++){      fprintf(ficlog,"\n");
         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);
       for(i=1; i<=npar; i++) /* Computes gradient */    free_ivector(indx,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    free_matrix(hess,1,npar,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
    }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  /*************** hessian matrix ****************/
           prlim[i][i]=probs[(int)age][i][ij];  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       }  {
     int i;
       for(j=1; j<= nlstate; j++){    int l=1, lmax=20;
         for(h=0; h<=nhstepm; h++){    double k1,k2;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    double p2[NPARMAX+1];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double res;
         }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       }    double fx;
     int k=0,kmax=10;
       for(j=1; j<= nlstate; j++)    double l1;
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
     } /* End theta */    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
     for(h=0; h<=nhstepm; h++)        delt = delta*(l1*k);
       for(j=1; j<=nlstate;j++)        p2[theta]=x[theta] +delt;
         for(theta=1; theta <=npar; theta++)        k1=func(p2)-fx;
           trgradg[h][j][theta]=gradg[h][theta][j];        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(i=1;i<=nlstate;i++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       for(j=1;j<=nlstate;j++)        
         vareij[i][j][(int)age] =0.;  #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);
     for(h=0;h<=nhstepm;h++){        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(k=0;k<=nhstepm;k++){  #endif
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(i=1;i<=nlstate;i++)          k=kmax;
           for(j=1;j<=nlstate;j++)        }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       }          k=kmax; l=lmax*10.;
     }        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     fprintf(ficresvij,"%.0f ",age );          delts=delt;
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++){      }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    }
       }    delti[theta]=delts;
     fprintf(ficresvij,"\n");    return res; 
     free_matrix(gp,0,nhstepm,1,nlstate);    
     free_matrix(gm,0,nhstepm,1,nlstate);  }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
   } /* End age */    int i;
      int l=1, l1, lmax=20;
   free_vector(xp,1,npar);    double k1,k2,k3,k4,res,fx;
   free_matrix(doldm,1,nlstate,1,npar);    double p2[NPARMAX+1];
   free_matrix(dnewm,1,nlstate,1,nlstate);    int k;
   
 }    fx=func(x);
     for (k=1; k<=2; k++) {
 /************ Variance of prevlim ******************/      for (i=1;i<=npar;i++) p2[i]=x[i];
 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[thetai]=x[thetai]+delti[thetai]/k;
 {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   /* Variance of prevalence limit */      k1=func(p2)-fx;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    
   double **newm;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double **dnewm,**doldm;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   int i, j, nhstepm, hstepm;      k2=func(p2)-fx;
   int k, cptcode;    
   double *xp;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double *gp, *gm;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **gradg, **trgradg;      k3=func(p2)-fx;
   double age,agelim;    
   int theta;      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      k4=func(p2)-fx;
   fprintf(ficresvpl,"# Age");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   for(i=1; i<=nlstate;i++)  #ifdef DEBUG
       fprintf(ficresvpl," %1d-%1d",i,i);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   fprintf(ficresvpl,"\n");      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);    return res;
   doldm=matrix(1,nlstate,1,nlstate);  }
    
   hstepm=1*YEARM; /* Every year of age */  /************** Inverse of matrix **************/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  void ludcmp(double **a, int n, int *indx, double *d) 
   agelim = AGESUP;  { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i,imax,j,k; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double big,dum,sum,temp; 
     if (stepm >= YEARM) hstepm=1;    double *vv; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   
     gradg=matrix(1,npar,1,nlstate);    vv=vector(1,n); 
     gp=vector(1,nlstate);    *d=1.0; 
     gm=vector(1,nlstate);    for (i=1;i<=n;i++) { 
       big=0.0; 
     for(theta=1; theta <=npar; theta++){      for (j=1;j<=n;j++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */        if ((temp=fabs(a[i][j])) > big) big=temp; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       }      vv[i]=1.0/big; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } 
       for(i=1;i<=nlstate;i++)    for (j=1;j<=n;j++) { 
         gp[i] = prlim[i][i];      for (i=1;i<j;i++) { 
            sum=a[i][j]; 
       for(i=1; i<=npar; i++) /* Computes gradient */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        a[i][j]=sum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } 
       for(i=1;i<=nlstate;i++)      big=0.0; 
         gm[i] = prlim[i][i];      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
       for(i=1;i<=nlstate;i++)        for (k=1;k<j;k++) 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          sum -= a[i][k]*a[k][j]; 
     } /* End theta */        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     trgradg =matrix(1,nlstate,1,npar);          big=dum; 
           imax=i; 
     for(j=1; j<=nlstate;j++)        } 
       for(theta=1; theta <=npar; theta++)      } 
         trgradg[j][theta]=gradg[theta][j];      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     for(i=1;i<=nlstate;i++)          dum=a[imax][k]; 
       varpl[i][(int)age] =0.;          a[imax][k]=a[j][k]; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          a[j][k]=dum; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        } 
     for(i=1;i<=nlstate;i++)        *d = -(*d); 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        vv[imax]=vv[j]; 
       } 
     fprintf(ficresvpl,"%.0f ",age );      indx[j]=imax; 
     for(i=1; i<=nlstate;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      if (j != n) { 
     fprintf(ficresvpl,"\n");        dum=1.0/(a[j][j]); 
     free_vector(gp,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_vector(gm,1,nlstate);      } 
     free_matrix(gradg,1,npar,1,nlstate);    } 
     free_matrix(trgradg,1,nlstate,1,npar);    free_vector(vv,1,n);  /* Doesn't work */
   } /* End age */  ;
   } 
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
   free_matrix(dnewm,1,nlstate,1,nlstate);  { 
     int i,ii=0,ip,j; 
 }    double sum; 
    
 /************ Variance of one-step probabilities  ******************/    for (i=1;i<=n;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)      ip=indx[i]; 
 {      sum=b[ip]; 
   int i, j, i1, k1, j1, z1;      b[ip]=b[i]; 
   int k=0, cptcode;      if (ii) 
   double **dnewm,**doldm;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double *xp;      else if (sum) ii=i; 
   double *gp, *gm;      b[i]=sum; 
   double **gradg, **trgradg;    } 
   double age,agelim, cov[NCOVMAX];    for (i=n;i>=1;i--) { 
   int theta;      sum=b[i]; 
   char fileresprob[FILENAMELENGTH];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
   strcpy(fileresprob,"prob");    } 
   strcat(fileresprob,fileres);  } 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);  /************ Frequencies ********************/
   }  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[])
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  {  /* Some frequencies */
      
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   fprintf(ficresprob,"# Age");    int first;
   for(i=1; i<=nlstate;i++)    double ***freq; /* Frequencies */
     for(j=1; j<=(nlstate+ndeath);j++)    double *pp, **prop;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
     char fileresp[FILENAMELENGTH];
   fprintf(ficresprob,"\n");    
     pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
   xp=vector(1,npar);    strcpy(fileresp,"p");
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    strcat(fileresp,fileres);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    if((ficresp=fopen(fileresp,"w"))==NULL) {
        printf("Problem with prevalence resultfile: %s\n", fileresp);
   cov[1]=1;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   j=cptcoveff;      exit(0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    }
   j1=0;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   for(k1=1; k1<=1;k1++){    j1=0;
     for(i1=1; i1<=ncodemax[k1];i1++){    
     j1++;    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     if  (cptcovn>0) {  
       fprintf(ficresprob, "\n#********** Variable ");    first=1;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficresprob, "**********\n#");    for(k1=1; k1<=j;k1++){
     }      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
       for (age=bage; age<=fage; age ++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         cov[2]=age;          scanf("%d", i);*/
         for (k=1; k<=cptcovn;k++) {        for (i=-5; i<=nlstate+ndeath; i++)  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                      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 (k=1; k<=cptcovprod;k++)      for (i=1; i<=nlstate; i++)  
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for(m=iagemin; m <= iagemax+3; m++)
                  prop[i][m]=0;
         gradg=matrix(1,npar,1,9);        
         trgradg=matrix(1,9,1,npar);        dateintsum=0;
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        k2cpt=0;
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        for (i=1; i<=imx; i++) {
              bool=1;
         for(theta=1; theta <=npar; theta++){          if  (cptcovn>0) {
           for(i=1; i<=npar; i++)            for (z1=1; z1<=cptcoveff; z1++) 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                          bool=0;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          }
                    if (bool==1){
           k=0;            for(m=firstpass; m<=lastpass; m++){
           for(i=1; i<= (nlstate+ndeath); i++){              k2=anint[m][i]+(mint[m][i]/12.);
             for(j=1; j<=(nlstate+ndeath);j++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
               k=k+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               gp[k]=pmmij[i][j];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
           }                if (m<lastpass) {
                            freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           for(i=1; i<=npar; i++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
             xp[i] = x[i] - (i==theta ?delti[theta]:0);                }
                    
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           k=0;                  dateintsum=dateintsum+k2;
           for(i=1; i<=(nlstate+ndeath); i++){                  k2cpt++;
             for(j=1; j<=(nlstate+ndeath);j++){                }
               k=k+1;                /*}*/
               gm[k]=pmmij[i][j];            }
             }          }
           }        }
               
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    fprintf(ficresp, "#Local time at start: %s", strstart);
         }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(theta=1; theta <=npar; theta++)          fprintf(ficresp, "**********\n#");
             trgradg[j][theta]=gradg[theta][j];        }
                for(i=1; i<=nlstate;i++) 
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        fprintf(ficresp, "\n");
                
         pmij(pmmij,cov,ncovmodel,x,nlstate);        for(i=iagemin; i <= iagemax+3; i++){
                  if(i==iagemax+3){
         k=0;            fprintf(ficlog,"Total");
         for(i=1; i<=(nlstate+ndeath); i++){          }else{
           for(j=1; j<=(nlstate+ndeath);j++){            if(first==1){
             k=k+1;              first=0;
             gm[k]=pmmij[i][j];              printf("See log file for details...\n");
           }            }
         }            fprintf(ficlog,"Age %d", i);
                }
      /*printf("\n%d ",(int)age);          for(jk=1; jk <=nlstate ; jk++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              pp[jk] += freq[jk][m][i]; 
      }*/          }
           for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficresprob,"\n%d ",(int)age);            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)            if(pp[jk]>=1.e-10){
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));              if(first==1){
                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]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            }else{
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              if(first==1)
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }            }
   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){
                   double jprev1, double mprev1,double anprev1, \              if(first==1)
                   double jprev2, double mprev2,double anprev2){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int jj1, k1, i1, cpt;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   FILE *fichtm;            }else{
   /*char optionfilehtm[FILENAMELENGTH];*/              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   strcpy(optionfilehtm,optionfile);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   strcat(optionfilehtm,".htm");            }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            if( i <= iagemax){
     printf("Problem with %s \n",optionfilehtm), exit(0);              if(pos>=1.e-5){
   }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \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]);*/
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n              }
 \n              else
 Total number of observations=%d <br>\n                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            }
 <hr  size=\"2\" color=\"#EC5E5E\">          }
  <ul><li>Parameter files<br>\n          
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          for(jk=-1; jk <=nlstate+ndeath; jk++)
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n              if(first==1)
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n              }
  - Life expectancies by age and initial health status (estepm=%2d months):          if(i <= iagemax)
    <a href=\"e%s\">e%s</a> <br>\n</li>", \            fprintf(ficresp,"\n");
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          if(first==1)
             printf("Others in log...\n");
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n          fprintf(ficlog,"\n");
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n        }
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      }
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    }
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    dateintmean=dateintsum/k2cpt; 
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);   
     fclose(ficresp);
  if(popforecast==1) fprintf(fichtm,"\n    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    free_vector(pp,1,nlstate);
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         <br>",fileres,fileres,fileres,fileres);    /* End of Freq */
  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);  
 fprintf(fichtm," <li>Graphs</li><p>");  /************ Prevalence ********************/
   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)
  m=cptcoveff;  {  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
  jj1=0;       We still use firstpass and lastpass as another selection.
  for(k1=1; k1<=m;k1++){    */
    for(i1=1; i1<=ncodemax[k1];i1++){   
      jj1++;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
      if (cptcovn > 0) {    double ***freq; /* Frequencies */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double *pp, **prop;
        for (cpt=1; cpt<=cptcoveff;cpt++)    double pos,posprop; 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double  y2; /* in fractional years */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    int iagemin, iagemax;
      }  
      /* Pij */    iagemin= (int) agemin;
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    iagemax= (int) agemax;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        /*pp=vector(1,nlstate);*/
      /* Quasi-incidences */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    j1=0;
        /* Stable prevalence in each health state */    
        for(cpt=1; cpt<nlstate;cpt++){    j=cptcoveff;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
        }    for(k1=1; k1<=j;k1++){
     for(cpt=1; cpt<=nlstate;cpt++) {      for(i1=1; i1<=ncodemax[k1];i1++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        j1++;
 interval) in state (%d): v%s%d%d.png <br>        
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for (i=1; i<=nlstate; i++)  
      }          for(m=iagemin; m <= iagemax+3; m++)
      for(cpt=1; cpt<=nlstate;cpt++) {            prop[i][m]=0.0;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>       
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for (i=1; i<=imx; i++) { /* Each individual */
      }          bool=1;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          if  (cptcovn>0) {
 health expectancies in states (1) and (2): e%s%d.png<br>            for (z1=1; z1<=cptcoveff; z1++) 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 fprintf(fichtm,"\n</body>");                bool=0;
    }          } 
  }          if (bool==1) { 
 fclose(fichtm);            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) */
 /******************* Gnuplot file **************/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   int ng;                  /*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]]);*/
   strcpy(optionfilegnuplot,optionfilefiname);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   strcat(optionfilegnuplot,".gp.txt");                  prop[s[m][i]][iagemax+3] += weight[i]; 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                } 
     printf("Problem with file %s",optionfilegnuplot);              }
   }            } /* end selection of waves */
           }
 #ifdef windows        }
     fprintf(ficgp,"cd \"%s\" \n",pathc);        for(i=iagemin; i <= iagemax+3; i++){  
 #endif          
 m=pow(2,cptcoveff);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
              posprop += prop[jk][i]; 
  /* 1eme*/          } 
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
 #ifdef windows              if(posprop>=1.e-5){ 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                probs[i][jk][j1]= prop[jk][i]/posprop;
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);              } 
 #endif            } 
 #ifdef unix          }/* end jk */ 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }/* end i */ 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      } /* end i1 */
 #endif    } /* end k1 */
     
 for (i=1; i<= nlstate ; i ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*free_vector(pp,1,nlstate);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 }  }  /* End of prevalence */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {  /************* Waves Concatenation ***************/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 }  {
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      for (i=1; i<= nlstate ; i ++) {       Death is a valid wave (if date is known).
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   else fprintf(ficgp," \%%*lf (\%%*lf)");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 }         and mw[mi+1][i]. dh depends on stepm.
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       */
 #ifdef unix  
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    int i, mi, m;
 #endif    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
    }       double sum=0., jmean=0.;*/
   }    int first;
   /*2 eme*/    int j, k=0,jk, ju, jl;
     double sum=0.;
   for (k1=1; k1<= m ; k1 ++) {    first=0;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    jmin=1e+5;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    jmax=-1;
        jmean=0.;
     for (i=1; i<= nlstate+1 ; i ++) {    for(i=1; i<=imx; i++){
       k=2*i;      mi=0;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%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== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          break;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        else
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          m++;
       for (j=1; j<= nlstate+1 ; j ++) {      }/* end while */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      if (s[m][i] > nlstate){
         else fprintf(ficgp," \%%*lf (\%%*lf)");        mi++;     /* Death is another wave */
 }          /* if(mi==0)  never been interviewed correctly before death */
       fprintf(ficgp,"\" t\"\" w l 0,");           /* Only death is a correct wave */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        mw[mi][i]=m;
       for (j=1; j<= nlstate+1 ; j ++) {      }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      wav[i]=mi;
 }        if(mi==0){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        nbwarn++;
       else fprintf(ficgp,"\" t\"\" w l 0,");        if(first==0){
     }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   }          first=1;
          }
   /*3eme*/        if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<= nlstate ; cpt ++) {      } /* end mi==0 */
       k=2+nlstate*(2*cpt-2);    } /* End individuals */
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    for(i=1; i<=imx; i++){
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      for(mi=1; mi<wav[i];mi++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        if (stepm <=0)
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          dh[mi][i]=1;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        else{
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 */              if(j==0) j=1;  /* Survives at least one month after exam */
       for (i=1; i< nlstate ; i ++) {              else if(j<0){
         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);                nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       }                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);
   }                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(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);
   /* CV preval stat */              }
     for (k1=1; k1<= m ; k1 ++) {              k=k+1;
     for (cpt=1; cpt<nlstate ; cpt ++) {              if (j >= jmax){
       k=3;                jmax=j;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                ijmax=i;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              }
               if (j <= jmin){
       for (i=1; i< nlstate ; i ++)                jmin=j;
         fprintf(ficgp,"+$%d",k+i+1);                ijmin=i;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              }
                    sum=sum+j;
       l=3+(nlstate+ndeath)*cpt;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for (i=1; i< nlstate ; i ++) {            }
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    /*        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) {
   /* proba elementaires */              jmax=j;
    for(i=1,jk=1; i <=nlstate; i++){              ijmax=i;
     for(k=1; k <=(nlstate+ndeath); k++){            }
       if (k != i) {            else if (j <= jmin){
         for(j=1; j <=ncovmodel; j++){              jmin=j;
                      ijmin=i;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            }
           jk++;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           fprintf(ficgp,"\n");            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         }            if(j<0){
       }              nberr++;
     }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    }              fprintf(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]);
             }
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/            sum=sum+j;
      for(jk=1; jk <=m; jk++) {          }
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          jk= j/stepm;
        if (ng==2)          jl= j -jk*stepm;
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          ju= j -(jk+1)*stepm;
        else          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
          fprintf(ficgp,"\nset title \"Probability\"\n");            if(jl==0){
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);              dh[mi][i]=jk;
        i=1;              bh[mi][i]=0;
        for(k2=1; k2<=nlstate; k2++) {            }else{ /* We want a negative bias in order to only have interpolation ie
          k3=i;                    * at the price of an extra matrix product in likelihood */
          for(k=1; k<=(nlstate+ndeath); k++) {              dh[mi][i]=jk+1;
            if (k != k2){              bh[mi][i]=ju;
              if(ng==2)            }
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);          }else{
              else            if(jl <= -ju){
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              dh[mi][i]=jk;
              ij=1;              bh[mi][i]=jl;       /* bias is positive if real duration
              for(j=3; j <=ncovmodel; j++) {                                   * is higher than the multiple of stepm and negative otherwise.
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                                   */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
                  ij++;            else{
                }              dh[mi][i]=jk+1;
                else              bh[mi][i]=ju;
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            }
              }            if(dh[mi][i]==0){
              fprintf(ficgp,")/(1");              dh[mi][i]=1; /* At least one step */
                            bh[mi][i]=ju; /* At least one step */
              for(k1=1; k1 <=nlstate; k1++){                /*  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);*/
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            }
                ij=1;          } /* end if mle */
                for(j=3; j <=ncovmodel; j++){        }
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      } /* end wave */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }
                    ij++;    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);
                  else    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);   }
                }  
                fprintf(ficgp,")");  /*********** Tricode ****************************/
              }  void tricode(int *Tvar, int **nbcode, int imx)
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  {
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    
              i=i+ncovmodel;    int Ndum[20],ij=1, k, j, i, maxncov=19;
            }    int cptcode=0;
          }    cptcoveff=0; 
        }   
      }    for (k=0; k<maxncov; k++) Ndum[k]=0;
    }    for (k=1; k<=7; k++) ncodemax[k]=0;
    fclose(ficgp);  
 }  /* end gnuplot */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
 /*************** Moving average **************/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   int i, cpt, cptcod;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                                         Tvar[j]. If V=sex and male is 0 and 
       for (i=1; i<=nlstate;i++)                                         female is 1, then  cptcode=1.*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
          for (i=0; i<=cptcode; i++) {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        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 */
       for (i=1; i<=nlstate;i++){      }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){      ij=1; 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      for (i=1; i<=ncodemax[j]; i++) {
           }        for (k=0; k<= maxncov; k++) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          if (Ndum[k] != 0) {
         }            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; */
     }            
                ij++;
 }          }
           if (ij > ncodemax[j]) break; 
         }  
 /************** Forecasting ******************/      } 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    }  
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   for (i=1; i<=ncovmodel-2; i++) { 
   double *popeffectif,*popcount;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   double ***p3mat;     ij=Tvar[i];
   char fileresf[FILENAMELENGTH];     Ndum[ij]++;
    }
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;   ij=1;
    for (i=1; i<= maxncov; i++) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
         ij++;
   strcpy(fileresf,"f");     }
   strcat(fileresf,fileres);   }
   if((ficresf=fopen(fileresf,"w"))==NULL) {   
     printf("Problem with forecast resultfile: %s\n", fileresf);   cptcoveff=ij-1; /*Number of simple covariates*/
   }  }
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   /*********** Health Expectancies ****************/
   if (cptcoveff==0) ncodemax[cptcoveff]=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[] )
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /* Health expectancies */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double ***p3mat,***varhe;
   if (stepm<=12) stepsize=1;    double **dnewm,**doldm;
      double *xp;
   agelim=AGESUP;    double **gp, **gm;
      double ***gradg, ***trgradg;
   hstepm=1;    int theta;
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   anprojmean=yp;    xp=vector(1,npar);
   yp2=modf((yp1*12),&yp);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   mprojmean=yp;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   yp1=modf((yp2*30.5),&yp);    
   jprojmean=yp;    fprintf(ficreseij,"# Local time at start: %s", strstart);
   if(jprojmean==0) jprojmean=1;    fprintf(ficreseij,"# Health expectancies\n");
   if(mprojmean==0) jprojmean=1;    fprintf(ficreseij,"# Age");
      for(i=1; i<=nlstate;i++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      for(j=1; j<=nlstate;j++)
          fprintf(ficreseij," %1d-%1d (SE)",i,j);
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficreseij,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;    if(estepm < stepm){
       fprintf(ficresf,"\n#******");      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    else  hstepm=estepm;   
       }    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficresf,"******\n");     * This is mainly to measure the difference between two models: for example
       fprintf(ficresf,"# StartingAge FinalAge");     * if stepm=24 months pijx are given only every 2 years and by summing them
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           * progression in between and thus overestimating or underestimating according
           * to the curvature of the survival function. If, for the same date, we 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficresf,"\n");     * to compare the new estimate of Life expectancy with the same linear 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);       * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* For example we decided to compute the life expectancy with the smallest unit */
           nhstepm = nhstepm/hstepm;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                 nhstepm is the number of hstepm from age to agelim 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       nstepm is the number of stepm from age to agelin. 
           oldm=oldms;savm=savms;       Look at hpijx to understand the reason of that which relies in memory size
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         and note for a fixed period like estepm months */
            /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           for (h=0; h<=nhstepm; h++){       survival function given by stepm (the optimization length). Unfortunately it
             if (h==(int) (calagedate+YEARM*cpt)) {       means that if the survival funtion is printed only each two years of age and if
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       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.
             for(j=1; j<=nlstate+ndeath;j++) {    */
               kk1=0.;kk2=0;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)    agelim=AGESUP;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                 else {      /* nhstepm age range expressed in number of stepm */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
                 }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                      /* if (stepm >= YEARM) hstepm=1;*/
               }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               if (h==(int)(calagedate+12*cpt)){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 fprintf(ficresf," %.3f", kk1);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                              gp=matrix(0,nhstepm,1,nlstate*nlstate);
               }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
             }  
           }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       }   
     }  
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* Computing  Variances of health expectancies */
   
   fclose(ficresf);       for(theta=1; theta <=npar; theta++){
 }        for(i=1; i<=npar; i++){ 
 /************** Forecasting ******************/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 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){        }
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    
   int *popage;        cptj=0;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        for(j=1; j<= nlstate; j++){
   double *popeffectif,*popcount;          for(i=1; i<=nlstate; i++){
   double ***p3mat,***tabpop,***tabpopprev;            cptj=cptj+1;
   char filerespop[FILENAMELENGTH];            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   agelim=AGESUP;        }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       
         
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(i=1; i<=npar; i++) 
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcpy(filerespop,"pop");        
   strcat(filerespop,fileres);        cptj=0;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        for(j=1; j<= nlstate; j++){
     printf("Problem with forecast resultfile: %s\n", filerespop);          for(i=1;i<=nlstate;i++){
   }            cptj=cptj+1;
   printf("Computing forecasting: result on file '%s' \n", filerespop);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   if (mobilav==1) {          }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
     movingaverage(agedeb, fage, ageminpar, mobaverage);        for(j=1; j<= nlstate*nlstate; j++)
   }          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;       } 
       
   agelim=AGESUP;  /* End theta */
    
   hstepm=1;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   hstepm=hstepm/stepm;  
         for(h=0; h<=nhstepm-1; h++)
   if (popforecast==1) {        for(j=1; j<=nlstate*nlstate;j++)
     if((ficpop=fopen(popfile,"r"))==NULL) {          for(theta=1; theta <=npar; theta++)
       printf("Problem with population file : %s\n",popfile);exit(0);            trgradg[h][j][theta]=gradg[h][theta][j];
     }       
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);       for(i=1;i<=nlstate*nlstate;i++)
     popcount=vector(0,AGESUP);        for(j=1;j<=nlstate*nlstate;j++)
              varhe[i][j][(int)age] =0.;
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;       printf("%d|",(int)age);fflush(stdout);
           fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     imx=i;       for(h=0;h<=nhstepm-1;h++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(k=0;k<=nhstepm-1;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   for(cptcov=1;cptcov<=i2;cptcov++){          for(i=1;i<=nlstate*nlstate;i++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(j=1;j<=nlstate*nlstate;j++)
       k=k+1;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficrespop,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {      }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      /* Computing expectancies */
       }      for(i=1; i<=nlstate;i++)
       fprintf(ficrespop,"******\n");        for(j=1; j<=nlstate;j++)
       fprintf(ficrespop,"# Age");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       if (popforecast==1)  fprintf(ficrespop," [Population]");            
        /* 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]);*/
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            }
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      fprintf(ficreseij,"%3.0f",age );
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      cptj=0;
           nhstepm = nhstepm/hstepm;      for(i=1; i<=nlstate;i++)
                  for(j=1; j<=nlstate;j++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          cptj++;
           oldm=oldms;savm=savms;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
              fprintf(ficreseij,"\n");
           for (h=0; h<=nhstepm; h++){     
             if (h==(int) (calagedate+YEARM*cpt)) {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
               kk1=0.;kk2=0;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               for(i=1; i<=nlstate;i++) {                  }
                 if (mobilav==1)    printf("\n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(ficlog,"\n");
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    free_vector(xp,1,npar);
                 }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
               }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
               if (h==(int)(calagedate+12*cpt)){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  }
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  /************ Variance ******************/
               }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
             }  {
             for(i=1; i<=nlstate;i++){    /* Variance of health expectancies */
               kk1=0.;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                 for(j=1; j<=nlstate;j++){    /* double **newm;*/
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double **dnewm,**doldm;
                 }    double **dnewmp,**doldmp;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    int i, j, nhstepm, hstepm, h, nstepm ;
             }    int k, cptcode;
     double *xp;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    double **gp, **gm;  /* for var eij */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    double ***gradg, ***trgradg; /*for var eij */
           }    double **gradgp, **trgradgp; /* for var p point j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *gpp, *gmp; /* for var p point j */
         }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       }    double ***p3mat;
      double age,agelim, hf;
   /******/    double ***mobaverage;
     int theta;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    char digit[4];
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      char digitp[25];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    char fileresprobmorprev[FILENAMELENGTH];
           nhstepm = nhstepm/hstepm;  
              if(popbased==1){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if(mobilav!=0)
           oldm=oldms;savm=savms;        strcpy(digitp,"-populbased-mobilav-");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        else strcpy(digitp,"-populbased-nomobil-");
           for (h=0; h<=nhstepm; h++){    }
             if (h==(int) (calagedate+YEARM*cpt)) {    else 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      strcpy(digitp,"-stablbased-");
             }  
             for(j=1; j<=nlstate+ndeath;j++) {    if (mobilav!=0) {
               kk1=0.;kk2=0;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               for(i=1; i<=nlstate;i++) {                    if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      }
             }    }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcpy(fileresprobmorprev,"prmorprev"); 
         }    sprintf(digit,"%-d",ij);
       }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
    }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(fileresprobmorprev,fileres);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   if (popforecast==1) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     free_vector(popcount,0,AGESUP);   
   }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    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);
   fclose(ficrespop);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
 /***********************************************/      for(i=1; i<=nlstate;i++)
 /**************** Main Program *****************/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 /***********************************************/    }  
     fprintf(ficresprobmorprev,"\n");
 int main(int argc, char *argv[])    fprintf(ficgp,"\n# Routine varevsij");
 {    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   double agedeb, agefin,hf;  /*   } */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    fprintf(ficresvij, "#Local time at start: %s", strstart);
   double fret;    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");
   double **xi,tmp,delta;    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   double dum; /* Dummy variable */      for(j=1; j<=nlstate;j++)
   double ***p3mat;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   int *indx;    fprintf(ficresvij,"\n");
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];    xp=vector(1,npar);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    dnewm=matrix(1,nlstate,1,npar);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   char filerest[FILENAMELENGTH];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   char fileregp[FILENAMELENGTH];    gpp=vector(nlstate+1,nlstate+ndeath);
   char popfile[FILENAMELENGTH];    gmp=vector(nlstate+1,nlstate+ndeath);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   int firstobs=1, lastobs=10;    
   int sdeb, sfin; /* Status at beginning and end */    if(estepm < stepm){
   int c,  h , cpt,l;      printf ("Problem %d lower than %d\n",estepm, stepm);
   int ju,jl, mi;    }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    else  hstepm=estepm;   
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /* For example we decided to compute the life expectancy with the smallest unit */
   int mobilav=0,popforecast=0;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int hstepm, nhstepm;       nhstepm is the number of hstepm from age to agelim 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   double bage, fage, age, agelim, agebase;       and note for a fixed period like k years */
   double ftolpl=FTOL;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double **prlim;       survival function given by stepm (the optimization length). Unfortunately it
   double *severity;       means that if the survival funtion is printed every two years of age and if
   double ***param; /* Matrix of parameters */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double  *p;       results. So we changed our mind and took the option of the best precision.
   double **matcov; /* Matrix of covariance */    */
   double ***delti3; /* Scale */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double *delti; /* Scale */    agelim = AGESUP;
   double ***eij, ***vareij;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double **varpl; /* Variances of prevalence limits by age */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double *epj, vepp;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double kk1, kk2;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   char version[80]="Imach version 0.8f, May 2002, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   char z[1]="c", occ;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #include <sys/time.h>        }
 #include <time.h>        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   /* long total_usecs;        if (popbased==1) {
   struct timeval start_time, end_time;          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              prlim[i][i]=probs[(int)age][i][ij];
   getcwd(pathcd, size);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   printf("\n%s",version);              prlim[i][i]=mobaverage[(int)age][i][ij];
   if(argc <=1){          }
     printf("\nEnter the parameter file name: ");        }
     scanf("%s",pathtot);    
   }        for(j=1; j<= nlstate; j++){
   else{          for(h=0; h<=nhstepm; h++){
     strcpy(pathtot,argv[1]);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          }
   /*cygwin_split_path(pathtot,path,optionfile);        }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        /* This for computing probability of death (h=1 means
   /* cutv(path,optionfile,pathtot,'\\');*/           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   chdir(path);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   replace(pathc,path);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
 /*-------- arguments in the command line --------*/        /* end probability of death */
   
   strcpy(fileres,"r");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   strcat(fileres, optionfilefiname);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   strcat(fileres,".txt");    /* Other files have txt extension */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*---------arguments file --------*/   
         if (popbased==1) {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          if(mobilav ==0){
     printf("Problem with optionfile %s\n",optionfile);            for(i=1; i<=nlstate;i++)
     goto end;              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   strcpy(filereso,"o");              prlim[i][i]=mobaverage[(int)age][i][ij];
   strcat(filereso,fileres);          }
   if((ficparo=fopen(filereso,"w"))==NULL) {        }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   /* Reads comments: lines beginning with '#' */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        /* This for computing probability of death (h=1 means
     fputs(line,ficparo);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   ungetc(c,ficpar);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   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);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   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);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   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);        }    
 while((c=getc(ficpar))=='#' && c!= EOF){        /* end probability of death */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(j=1; j<= nlstate; j++) /* vareij */
     puts(line);          for(h=0; h<=nhstepm; h++){
     fputs(line,ficparo);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   ungetc(c,ficpar);  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   covar=matrix(0,NCOVMAX,1,n);        }
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      } /* End theta */
   
   ncovmodel=2+cptcovn;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
        for(h=0; h<=nhstepm; h++) /* veij */
   /* Read guess parameters */        for(j=1; j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          for(theta=1; theta <=npar; theta++)
   while((c=getc(ficpar))=='#' && c!= EOF){            trgradg[h][j][theta]=gradg[h][theta][j];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     puts(line);        for(theta=1; theta <=npar; theta++)
     fputs(line,ficparo);          trgradgp[j][theta]=gradgp[theta][j];
   }    
   ungetc(c,ficpar);  
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(i=1;i<=nlstate;i++)
     for(i=1; i <=nlstate; i++)        for(j=1;j<=nlstate;j++)
     for(j=1; j <=nlstate+ndeath-1; j++){          vareij[i][j][(int)age] =0.;
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);      for(h=0;h<=nhstepm;h++){
       printf("%1d%1d",i,j);        for(k=0;k<=nhstepm;k++){
       for(k=1; k<=ncovmodel;k++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         fscanf(ficpar," %lf",&param[i][j][k]);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         printf(" %lf",param[i][j][k]);          for(i=1;i<=nlstate;i++)
         fprintf(ficparo," %lf",param[i][j][k]);            for(j=1;j<=nlstate;j++)
       }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fscanf(ficpar,"\n");        }
       printf("\n");      }
       fprintf(ficparo,"\n");    
     }      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
   p=param[1][1];        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
   /* Reads comments: lines beginning with '#' */      /* end ppptj */
   while((c=getc(ficpar))=='#' && c!= EOF){      /*  x centered again */
     ungetc(c,ficpar);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     fgets(line, MAXLINE, ficpar);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     puts(line);   
     fputs(line,ficparo);      if (popbased==1) {
   }        if(mobilav ==0){
   ungetc(c,ficpar);          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }else{ /* mobilav */ 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          for(i=1; i<=nlstate;i++)
   for(i=1; i <=nlstate; i++){            prlim[i][i]=mobaverage[(int)age][i][ij];
     for(j=1; j <=nlstate+ndeath-1; j++){        }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      }
       printf("%1d%1d",i,j);               
       fprintf(ficparo,"%1d%1d",i1,j1);      /* This for computing probability of death (h=1 means
       for(k=1; k<=ncovmodel;k++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fscanf(ficpar,"%le",&delti3[i][j][k]);         as a weighted average of prlim.
         printf(" %le",delti3[i][j][k]);      */
         fprintf(ficparo," %le",delti3[i][j][k]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fscanf(ficpar,"\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       printf("\n");      }    
       fprintf(ficparo,"\n");      /* end probability of death */
     }  
   }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   delti=delti3[1][1];      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   /* Reads comments: lines beginning with '#' */        for(i=1; i<=nlstate;i++){
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      } 
     puts(line);      fprintf(ficresprobmorprev,"\n");
     fputs(line,ficparo);  
   }      fprintf(ficresvij,"%.0f ",age );
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   matcov=matrix(1,npar,1,npar);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   for(i=1; i <=npar; i++){        }
     fscanf(ficpar,"%s",&str);      fprintf(ficresvij,"\n");
     printf("%s",str);      free_matrix(gp,0,nhstepm,1,nlstate);
     fprintf(ficparo,"%s",str);      free_matrix(gm,0,nhstepm,1,nlstate);
     for(j=1; j <=i; j++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fscanf(ficpar," %le",&matcov[i][j]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       printf(" %.5le",matcov[i][j]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo," %.5le",matcov[i][j]);    } /* End age */
     }    free_vector(gpp,nlstate+1,nlstate+ndeath);
     fscanf(ficpar,"\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
     printf("\n");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     fprintf(ficparo,"\n");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   for(i=1; i <=npar; i++)    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     for(j=i+1;j<=npar;j++)    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       matcov[i][j]=matcov[j][i];  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   printf("\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     /*-------- Rewriting paramater file ----------*/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
      strcpy(rfileres,"r");    /* "Rparameterfile */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    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);
      strcat(rfileres,".");    /* */    /*  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);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  */
     if((ficres =fopen(rfileres,"w"))==NULL) {  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     }  
     fprintf(ficres,"#%s\n",version);    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,nlstate);
     /*-------- data file ----------*/    free_matrix(dnewm,1,nlstate,1,npar);
     if((fic=fopen(datafile,"r"))==NULL)    {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       printf("Problem with datafile: %s\n", datafile);goto end;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     n= lastobs;    fclose(ficresprobmorprev);
     severity = vector(1,maxwav);    fflush(ficgp);
     outcome=imatrix(1,maxwav+1,1,n);    fflush(fichtm); 
     num=ivector(1,n);  }  /* end varevsij */
     moisnais=vector(1,n);  
     annais=vector(1,n);  /************ Variance of prevlim ******************/
     moisdc=vector(1,n);  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[])
     andc=vector(1,n);  {
     agedc=vector(1,n);    /* Variance of prevalence limit */
     cod=ivector(1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     weight=vector(1,n);    double **newm;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **dnewm,**doldm;
     mint=matrix(1,maxwav,1,n);    int i, j, nhstepm, hstepm;
     anint=matrix(1,maxwav,1,n);    int k, cptcode;
     s=imatrix(1,maxwav+1,1,n);    double *xp;
     adl=imatrix(1,maxwav+1,1,n);        double *gp, *gm;
     tab=ivector(1,NCOVMAX);    double **gradg, **trgradg;
     ncodemax=ivector(1,8);    double age,agelim;
     int theta;
     i=1;    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     while (fgets(line, MAXLINE, fic) != NULL)    {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       if ((i >= firstobs) && (i <=lastobs)) {    fprintf(ficresvpl,"# Age");
            for(i=1; i<=nlstate;i++)
         for (j=maxwav;j>=1;j--){        fprintf(ficresvpl," %1d-%1d",i,i);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficresvpl,"\n");
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    xp=vector(1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate,1,npar);
         }    doldm=matrix(1,nlstate,1,nlstate);
            
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=1*YEARM; /* Every year of age */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         for (j=ncovcol;j>=1;j--){      gradg=matrix(1,npar,1,nlstate);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      gp=vector(1,nlstate);
         }      gm=vector(1,nlstate);
         num[i]=atol(stra);  
              for(theta=1; theta <=npar; theta++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        for(i=1; i<=npar; i++){ /* Computes gradient */
           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;}*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         i=i+1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }        for(i=1;i<=nlstate;i++)
     }          gp[i] = prlim[i][i];
     /* printf("ii=%d", ij);      
        scanf("%d",i);*/        for(i=1; i<=npar; i++) /* Computes gradient */
   imx=i-1; /* Number of individuals */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* for (i=1; i<=imx; i++){        for(i=1;i<=nlstate;i++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          gm[i] = prlim[i][i];
     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<=nlstate;i++)
     }*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
    /*  for (i=1; i<=imx; i++){      } /* End theta */
      if (s[4][i]==9)  s[4][i]=-1;  
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/      trgradg =matrix(1,nlstate,1,npar);
    
        for(j=1; j<=nlstate;j++)
   /* Calculation of the number of parameter from char model*/        for(theta=1; theta <=npar; theta++)
   Tvar=ivector(1,15);          trgradg[j][theta]=gradg[theta][j];
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);      for(i=1;i<=nlstate;i++)
   Tvard=imatrix(1,15,1,2);        varpl[i][(int)age] =0.;
   Tage=ivector(1,15);            matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   if (strlen(model) >1){      for(i=1;i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');      fprintf(ficresvpl,"%.0f ",age );
     cptcovn=j+1;      for(i=1; i<=nlstate;i++)
     cptcovprod=j1;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
          fprintf(ficresvpl,"\n");
     strcpy(modelsav,model);      free_vector(gp,1,nlstate);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      free_vector(gm,1,nlstate);
       printf("Error. Non available option model=%s ",model);      free_matrix(gradg,1,npar,1,nlstate);
       goto end;      free_matrix(trgradg,1,nlstate,1,npar);
     }    } /* End age */
      
     for(i=(j+1); i>=1;i--){    free_vector(xp,1,npar);
       cutv(stra,strb,modelsav,'+');    free_matrix(doldm,1,nlstate,1,npar);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    free_matrix(dnewm,1,nlstate,1,nlstate);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/  }
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');  /************ Variance of one-step probabilities  ******************/
         if (strcmp(strc,"age")==0) {  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[])
           cptcovprod--;  {
           cutv(strb,stre,strd,'V');    int i, j=0,  i1, k1, l1, t, tj;
           Tvar[i]=atoi(stre);    int k2, l2, j1,  z1;
           cptcovage++;    int k=0,l, cptcode;
             Tage[cptcovage]=i;    int first=1, first1;
             /*printf("stre=%s ", stre);*/    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         }    double **dnewm,**doldm;
         else if (strcmp(strd,"age")==0) {    double *xp;
           cptcovprod--;    double *gp, *gm;
           cutv(strb,stre,strc,'V');    double **gradg, **trgradg;
           Tvar[i]=atoi(stre);    double **mu;
           cptcovage++;    double age,agelim, cov[NCOVMAX];
           Tage[cptcovage]=i;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         }    int theta;
         else {    char fileresprob[FILENAMELENGTH];
           cutv(strb,stre,strc,'V');    char fileresprobcov[FILENAMELENGTH];
           Tvar[i]=ncovcol+k1;    char fileresprobcor[FILENAMELENGTH];
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;    double ***varpij;
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);    strcpy(fileresprob,"prob"); 
           Tvar[cptcovn+k2]=Tvard[k1][1];    strcat(fileresprob,fileres);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           for (k=1; k<=lastobs;k++)      printf("Problem with resultfile: %s\n", fileresprob);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           k1++;    }
           k2=k2+2;    strcpy(fileresprobcov,"probcov"); 
         }    strcat(fileresprobcov,fileres);
       }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       else {      printf("Problem with resultfile: %s\n", fileresprobcov);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
        /*  scanf("%d",i);*/    }
       cutv(strd,strc,strb,'V');    strcpy(fileresprobcor,"probcor"); 
       Tvar[i]=atoi(strc);    strcat(fileresprobcor,fileres);
       }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       strcpy(modelsav,stra);        printf("Problem with resultfile: %s\n", fileresprobcor);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         scanf("%d",i);*/    }
     }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("cptcovprod=%d ", cptcovprod);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   scanf("%d ",i);*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fclose(fic);    fprintf(ficresprob, "#Local time at start: %s", strstart);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     /*  if(mle==1){*/    fprintf(ficresprob,"# Age");
     if (weightopt != 1) { /* Maximisation without weights*/    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     }    fprintf(ficresprobcov,"# Age");
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     agev=matrix(1,maxwav,1,imx);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    for(i=1; i<=nlstate;i++)
          anint[m][i]=9999;      for(j=1; j<=(nlstate+ndeath);j++){
          s[m][i]=-1;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }      }  
     }   /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     for (i=1; i<=imx; i++)  {    fprintf(ficresprobcor,"\n");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   */
       for(m=1; (m<= maxwav); m++){   xp=vector(1,npar);
         if(s[m][i] >0){    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           if (s[m][i] >= nlstate+1) {    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             if(agedc[i]>0)    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               if(moisdc[i]!=99 && andc[i]!=9999)    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
                 agev[m][i]=agedc[i];    first=1;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    fprintf(ficgp,"\n# Routine varprob");
            else {    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
               if (andc[i]!=9999){    fprintf(fichtm,"\n");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               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);
               }    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 if(s[m][i] !=9){ /* Should no more exist */  and drawn. It helps understanding how is the covariance between two incidences.\
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
             if(mint[m][i]==99 || anint[m][i]==9999)    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. \
               agev[m][i]=1;  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
             else if(agev[m][i] <agemin){  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
               agemin=agev[m][i];  standard deviations wide on each axis. <br>\
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
             }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
             else if(agev[m][i] >agemax){  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    cov[1]=1;
             }    tj=cptcoveff;
             /*agev[m][i]=anint[m][i]-annais[i];*/    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
             /*   agev[m][i] = age[i]+2*m;*/    j1=0;
           }    for(t=1; t<=tj;t++){
           else { /* =9 */      for(i1=1; i1<=ncodemax[t];i1++){ 
             agev[m][i]=1;        j1++;
             s[m][i]=-1;        if  (cptcovn>0) {
           }          fprintf(ficresprob, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         else /*= 0 Unknown */          fprintf(ficresprob, "**********\n#\n");
           agev[m][i]=1;          fprintf(ficresprobcov, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresprobcov, "**********\n#\n");
     }          
     for (i=1; i<=imx; i++)  {          fprintf(ficgp, "\n#********** Variable "); 
       for(m=1; (m<= maxwav); m++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(ficgp, "**********\n#\n");
           printf("Error: Wrong value in nlstate or ndeath\n");            
           goto end;          
         }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(severity,1,maxwav);          fprintf(ficresprobcor, "**********\n#");    
     free_imatrix(outcome,1,maxwav+1,1,n);        }
     free_vector(moisnais,1,n);        
     free_vector(annais,1,n);        for (age=bage; age<=fage; age ++){ 
     /* free_matrix(mint,1,maxwav,1,n);          cov[2]=age;
        free_matrix(anint,1,maxwav,1,n);*/          for (k=1; k<=cptcovn;k++) {
     free_vector(moisdc,1,n);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     free_vector(andc,1,n);          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              for (k=1; k<=cptcovprod;k++)
     wav=ivector(1,imx);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
              trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     /* Concatenates waves */          gp=vector(1,(nlstate)*(nlstate+ndeath));
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
       Tcode=ivector(1,100);            for(i=1; i<=npar; i++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       ncodemax[1]=1;            
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                  
    codtab=imatrix(1,100,1,10);            k=0;
    h=0;            for(i=1; i<= (nlstate); i++){
    m=pow(2,cptcoveff);              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
    for(k=1;k<=cptcoveff; k++){                gp[k]=pmmij[i][j];
      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++;            for(i=1; i<=npar; i++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      
          }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
        }            k=0;
      }            for(i=1; i<=(nlstate); i++){
    }              for(j=1; j<=(nlstate+ndeath);j++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                k=k+1;
       codtab[1][2]=1;codtab[2][2]=2; */                gm[k]=pmmij[i][j];
    /* 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);       
       }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       printf("\n");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       }          }
       scanf("%d",i);*/  
              for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
    /* Calculates basic frequencies. Computes observed prevalence at single age            for(theta=1; theta <=npar; theta++)
        and prints on file fileres'p'. */              trgradg[j][theta]=gradg[theta][j];
           
              matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
              matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
                pmij(pmmij,cov,ncovmodel,x,nlstate);
     /* 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] */          k=0;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
     if(mle==1){              k=k+1;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              mu[k][(int) age]=pmmij[i][j];
     }            }
              }
     /*--------- results files --------------*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     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(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                varpij[i][j][(int)age] = doldm[i][j];
   
    jk=1;          /*printf("\n%d ",(int)age);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    for(i=1,jk=1; i <=nlstate; i++){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      for(k=1; k <=(nlstate+ndeath); k++){            }*/
        if (k != i)  
          {          fprintf(ficresprob,"\n%d ",(int)age);
            printf("%d%d ",i,k);          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficres,"%1d%1d ",i,k);          fprintf(ficresprobcor,"\n%d ",(int)age);
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              fprintf(ficres,"%f ",p[jk]);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
              jk++;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
            printf("\n");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            fprintf(ficres,"\n");          }
          }          i=0;
      }          for (k=1; k<=(nlstate);k++){
    }            for (l=1; l<=(nlstate+ndeath);l++){ 
  if(mle==1){              i=i++;
     /* Computing hessian and covariance matrix */              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     ftolhess=ftol; /* Usually correct */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     hesscov(matcov, p, npar, delti, ftolhess, func);              for (j=1; j<=i;j++){
  }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     printf("# Scales (for hessian or gradient estimation)\n");              }
      for(i=1,jk=1; i <=nlstate; i++){            }
       for(j=1; j <=nlstate+ndeath; j++){          }/* end of loop for state */
         if (j!=i) {        } /* end of loop for age */
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);        /* Confidence intervalle of pij  */
           for(k=1; k<=ncovmodel;k++){        /*
             printf(" %.5e",delti[jk]);          fprintf(ficgp,"\nset noparametric;unset label");
             fprintf(ficres," %.5e",delti[jk]);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
             jk++;          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);
           printf("\n");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficres,"\n");          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       }        */
      }  
            /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     k=1;        first1=1;
     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");        for (k2=1; k2<=(nlstate);k2++){
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     for(i=1;i<=npar;i++){            if(l2==k2) continue;
       /*  if (k>nlstate) k=1;            j=(k2-1)*(nlstate+ndeath)+l2;
       i1=(i-1)/(ncovmodel*nlstate)+1;            for (k1=1; k1<=(nlstate);k1++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       printf("%s%d%d",alph[k],i1,tab[i]);*/                if(l1==k1) continue;
       fprintf(ficres,"%3d",i);                i=(k1-1)*(nlstate+ndeath)+l1;
       printf("%3d",i);                if(i<=j) continue;
       for(j=1; j<=i;j++){                for (age=bage; age<=fage; age ++){ 
         fprintf(ficres," %.5e",matcov[i][j]);                  if ((int)age %5==0){
         printf(" %.5e",matcov[i][j]);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficres,"\n");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       printf("\n");                    mu1=mu[i][(int) age]/stepm*YEARM ;
       k++;                    mu2=mu[j][(int) age]/stepm*YEARM;
     }                    c12=cv12/sqrt(v1*v2);
                        /* Computing eigen value of matrix of covariance */
     while((c=getc(ficpar))=='#' && c!= EOF){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       ungetc(c,ficpar);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fgets(line, MAXLINE, ficpar);                    /* Eigen vectors */
       puts(line);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       fputs(line,ficparo);                    /*v21=sqrt(1.-v11*v11); *//* error */
     }                    v21=(lc1-v1)/cv12*v11;
     ungetc(c,ficpar);                    v12=-v21;
     estepm=0;                    v22=v11;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    tnalp=v21/v11;
     if (estepm==0 || estepm < stepm) estepm=stepm;                    if(first1==1){
     if (fage <= 2) {                      first1=0;
       bage = ageminpar;                      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);
       fage = agemaxpar;                    }
     }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                        /*printf(fignu*/
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    if(first==1){
                        first=0;
     while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\nset parametric;unset label");
     ungetc(c,ficpar);                      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);
     fgets(line, MAXLINE, ficpar);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     puts(line);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     fputs(line,ficparo);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   }  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   ungetc(c,ficpar);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                            fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     ungetc(c,ficpar);                      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",\
     fgets(line, MAXLINE, ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     puts(line);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     fputs(line,ficparo);                    }else{
   }                      first=0;
   ungetc(c,ficpar);                      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);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                      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",\
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fscanf(ficpar,"pop_based=%d\n",&popbased);                    }/* if first */
   fprintf(ficparo,"pop_based=%d\n",popbased);                    } /* age mod 5 */
   fprintf(ficres,"pop_based=%d\n",popbased);                  } /* end loop age */
                  fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   while((c=getc(ficpar))=='#' && c!= EOF){                first=1;
     ungetc(c,ficpar);              } /*l12 */
     fgets(line, MAXLINE, ficpar);            } /* k12 */
     puts(line);          } /*l1 */
     fputs(line,ficparo);        }/* k1 */
   }      } /* loop covariates */
   ungetc(c,ficpar);    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   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);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
 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);    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 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);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
 while((c=getc(ficpar))=='#' && c!= EOF){    fclose(ficresprobcov);
     ungetc(c,ficpar);    fclose(ficresprobcor);
     fgets(line, MAXLINE, ficpar);    fflush(ficgp);
     puts(line);    fflush(fichtmcov);
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  
   /******************* Printing html file ***********/
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                    int lastpass, int stepm, int weightopt, char model[],\
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
 /*------------ gnuplot -------------*/    int jj1, k1, i1, cpt;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  
       fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
 /*------------ free_vector  -------------*/     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  chdir(path);  </ul>");
       fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
  free_ivector(wav,1,imx);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       fprintf(fichtm,"\
  free_ivector(num,1,n);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
  free_vector(agedc,1,n);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
  /*free_matrix(covar,1,NCOVMAX,1,n);*/     fprintf(fichtm,"\
  fclose(ficparo);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
  fclose(ficres);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
 /*--------- index.htm --------*/   - Life expectancies by age and initial health status (estepm=%2d months) WRONG LINK (to be made): \
      <a href=\"%s\">%s</a> <br>\n</li>",
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);             estepm,subdirf2(fileres,"le"),subdirf2(fileres,"le"));
      fprintf(fichtm,"\
     - Health expectancies by age and initial health status with standard errors (estepm=%2d months): \
   /*--------------- Prevalence limit --------------*/     <a href=\"%s\">%s</a> <br>\n</li>",
               estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   strcpy(filerespl,"pl");     fprintf(fichtm,"\
   strcat(filerespl,fileres);   - Variances and covariances of health expectancies by age and initial health status (estepm=%2d months) TO BE MADE: \
   if((ficrespl=fopen(filerespl,"w"))==NULL) {     <a href=\"%s\">%s</a> <br>\n</li>",
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;             estepm,subdirf2(fileres,"vch"),subdirf2(fileres,"vch"));
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);   m=cptcoveff;
   fprintf(ficrespl,"\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   prlim=matrix(1,nlstate,1,nlstate);   jj1=0;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   for(k1=1; k1<=m;k1++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     for(i1=1; i1<=ncodemax[k1];i1++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       jj1++;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       if (cptcovn > 0) {
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   k=0;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   agebase=ageminpar;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   agelim=agemaxpar;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   ftolpl=1.e-10;       }
   i1=cptcoveff;       /* Pij */
   if (cptcovn < 1){i1=1;}       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> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   for(cptcov=1;cptcov<=i1;cptcov++){       /* Quasi-incidences */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
         k=k+1;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
         fprintf(ficrespl,"\n#******");         /* Stable prevalence in each health state */
         for(j=1;j<=cptcoveff;j++)         for(cpt=1; cpt<nlstate;cpt++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         fprintf(ficrespl,"******\n");  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
                 }
         for (age=agebase; age<=agelim; age++){       for(cpt=1; cpt<=nlstate;cpt++) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
           fprintf(ficrespl,"%.0f",age );  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           for(i=1; i<=nlstate;i++)       }
           fprintf(ficrespl," %.5f", prlim[i][i]);     } /* end i1 */
           fprintf(ficrespl,"\n");   }/* End k1 */
         }   fprintf(fichtm,"</ul>");
       }  
     }  
   fclose(ficrespl);   fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   /*------------- h Pij x at various ages ------------*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   if((ficrespij=fopen(filerespij,"w"))==NULL) {           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   fprintf(fichtm,"\
   }   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   printf("Computing pij: result on file '%s' \n", filerespij);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;   fprintf(fichtm,"\
   /*if (stepm<=24) stepsize=2;*/   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   agelim=AGESUP;   fprintf(fichtm,"\
   hstepm=stepsize*YEARM; /* Every year of age */   - Variances and covariances of health expectancies by age (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     fprintf(fichtm,"\
   k=0;   - Life and health expectancies with their standard errors: <a href=\"%s\">%s</a> <br>\n",
   for(cptcov=1;cptcov<=i1;cptcov++){           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   fprintf(fichtm,"\
       k=k+1;   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
         fprintf(ficrespij,"\n#****** ");           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*  if(popforecast==1) fprintf(fichtm,"\n */
         fprintf(ficrespij,"******\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 */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  /*      <br>",fileres,fileres,fileres,fileres); */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /*  else  */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  /*    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); */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   fflush(fichtm);
           oldm=oldms;savm=savms;   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");   m=cptcoveff;
           for(i=1; i<=nlstate;i++)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);   jj1=0;
           fprintf(ficrespij,"\n");   for(k1=1; k1<=m;k1++){
            for (h=0; h<=nhstepm; h++){     for(i1=1; i1<=ncodemax[k1];i1++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       jj1++;
             for(i=1; i<=nlstate;i++)       if (cptcovn > 0) {
               for(j=1; j<=nlstate+ndeath;j++)         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(ficrespij,"\n");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
              }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       }
           fprintf(ficrespij,"\n");       for(cpt=1; cpt<=nlstate;cpt++) {
         }         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
     }  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   fclose(ficrespij);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
   /*---------- Forecasting ------------------*/   fprintf(fichtm,"</ul>");
   if((stepm == 1) && (strcmp(model,".")==0)){   fflush(fichtm);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  }
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
   }  /******************* Gnuplot file **************/
   else{  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     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);    char dirfileres[132],optfileres[132];
   }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*---------- Health expectancies and variances ------------*/  /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   strcpy(filerest,"t");  /*   } */
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    /*#ifdef windows */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    fprintf(ficgp,"cd \"%s\" \n",pathc);
   }      /*#endif */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
   strcpy(filerese,"e");    strcpy(optfileres,"vpl");
   strcat(filerese,fileres);   /* 1eme*/
   if((ficreseij=fopen(filerese,"w"))==NULL) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);     for (k1=1; k1<= m ; k1 ++) {
   }       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
  strcpy(fileresv,"v");  set ylabel \"Probability\" \n\
   strcat(fileresv,fileres);  set ter png small\n\
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  set size 0.65,0.65\n\
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       for (i=1; i<= nlstate ; i ++) {
   calagedate=-1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
   k=0;       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);
   for(cptcov=1;cptcov<=i1;cptcov++){       for (i=1; i<= nlstate ; i ++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       k=k+1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficrest,"\n#****** ");       } 
       for(j=1;j<=cptcoveff;j++)       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       for (i=1; i<= nlstate ; i ++) {
       fprintf(ficrest,"******\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficreseij,"\n#****** ");       }  
       for(j=1;j<=cptcoveff;j++)       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     }
       fprintf(ficreseij,"******\n");    }
     /*2 eme*/
       fprintf(ficresvij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    for (k1=1; k1<= m ; k1 ++) { 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficresvij,"******\n");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for (i=1; i<= nlstate+1 ; i ++) {
       oldm=oldms;savm=savms;        k=2*i;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       oldm=oldms;savm=savms;          else fprintf(ficgp," \%%*lf (\%%*lf)");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        }   
            if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        for (j=1; j<= nlstate+1 ; j ++) {
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficrest,"\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
       epj=vector(1,nlstate+1);        fprintf(ficgp,"\" t\"\" w l 0,");
       for(age=bage; age <=fage ;age++){        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for (j=1; j<= nlstate+1 ; j ++) {
         if (popbased==1) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           for(i=1; i<=nlstate;i++)          else fprintf(ficgp," \%%*lf (\%%*lf)");
             prlim[i][i]=probs[(int)age][i][k];        }   
         }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
                else fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficrest," %4.0f",age);      }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    /*3eme*/
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    
           }    for (k1=1; k1<= m ; k1 ++) { 
           epj[nlstate+1] +=epj[j];      for (cpt=1; cpt<= nlstate ; cpt ++) {
         }        k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         for(i=1, vepp=0.;i <=nlstate;i++)        fprintf(ficgp,"set ter png small\n\
           for(j=1;j <=nlstate;j++)  set size 0.65,0.65\n\
             vepp += vareij[i][j][(int)age];  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for(j=1;j <=nlstate;j++){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         fprintf(ficrest,"\n");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     }          
   }        */
 free_matrix(mint,1,maxwav,1,n);        for (i=1; i< nlstate ; i ++) {
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          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);
     free_vector(weight,1,n);          
   fclose(ficreseij);        } 
   fclose(ficresvij);      }
   fclose(ficrest);    }
   fclose(ficpar);    
   free_vector(epj,1,nlstate+1);    /* CV preval stable (period) */
      for (k1=1; k1<= m ; k1 ++) { 
   /*------- Variance limit prevalence------*/        for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
   strcpy(fileresvpl,"vpl");        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   strcat(fileresvpl,fileres);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  set ter png small\nset size 0.65,0.65\n\
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  unset log y\n\
     exit(0);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   }        
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
   k=0;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   for(cptcov=1;cptcov<=i1;cptcov++){        
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        l=3+(nlstate+ndeath)*cpt;
       k=k+1;        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
       fprintf(ficresvpl,"\n#****** ");        for (i=1; i< nlstate ; i ++) {
       for(j=1;j<=cptcoveff;j++)          l=3+(nlstate+ndeath)*cpt;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"+$%d",l+i+1);
       fprintf(ficresvpl,"******\n");        }
              fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       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);    
     }    /* proba elementaires */
  }    for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
   fclose(ficresvpl);        if (k != i) {
           for(j=1; j <=ncovmodel; j++){
   /*---------- End : free ----------------*/            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            jk++; 
              fprintf(ficgp,"\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
        }
       }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       for(jk=1; jk <=m; jk++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
           if (ng==2)
   free_matrix(matcov,1,npar,1,npar);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   free_vector(delti,1,npar);         else
   free_matrix(agev,1,maxwav,1,imx);           fprintf(ficgp,"\nset title \"Probability\"\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
   if(erreur >0)         for(k2=1; k2<=nlstate; k2++) {
     printf("End of Imach with error or warning %d\n",erreur);           k3=i;
   else   printf("End of Imach\n");           for(k=1; k<=(nlstate+ndeath); k++) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */             if (k != k2){
                 if(ng==2)
   /* 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);*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   /*printf("Total time was %d uSec.\n", total_usecs);*/               else
   /*------ End -----------*/                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
  end:                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
 #ifdef windows                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   /* chdir(pathcd);*/                   ij++;
 #endif                 }
  /*system("wgnuplot graph.plt");*/                 else
  /*system("../gp37mgw/wgnuplot graph.plt");*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  /*system("cd ../gp37mgw");*/               }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/               fprintf(ficgp,")/(1");
  strcpy(plotcmd,GNUPLOTPROGRAM);               
  strcat(plotcmd," ");               for(k1=1; k1 <=nlstate; k1++){   
  strcat(plotcmd,optionfilegnuplot);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  system(plotcmd);                 ij=1;
                  for(j=3; j <=ncovmodel; j++){
 #ifdef windows                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   while (z[0] != 'q') {                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     /* chdir(path); */                     ij++;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                   }
     scanf("%s",z);                   else
     if (z[0] == 'c') system("./imach");                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     else if (z[0] == 'e') system(optionfilehtm);                 }
     else if (z[0] == 'g') system(plotcmd);                 fprintf(ficgp,")");
     else if (z[0] == 'q') exit(0);               }
   }               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 #endif               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.1.45  
changed lines
  Added in v.1.116


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