Diff for /imach/src/imach.c between versions 1.24 and 1.113

version 1.24, 2002/02/22 18:10:15 version 1.113, 2006/02/24 14:20:24
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.113  2006/02/24 14:20:24  brouard
      (Module): Memory leaks checks with valgrind and:
   This program computes Healthy Life Expectancies from    datafile was not closed, some imatrix were not freed and on matrix
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    allocation too.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.112  2006/01/30 09:55:26  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.111  2006/01/25 20:38:18  brouard
   computed from the time spent in each health state according to a    (Module): Lots of cleaning and bugs added (Gompertz)
   model. More health states you consider, more time is necessary to reach the    (Module): Comments can be added in data file. Missing date values
   Maximum Likelihood of the parameters involved in the model.  The    can be a simple dot '.'.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.110  2006/01/25 00:51:50  brouard
   conditional to be observed in state i at the first wave. Therefore    (Module): Lots of cleaning and bugs added (Gompertz)
   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 1.109  2006/01/24 19:37:15  brouard
   complex model than "constant and age", you should modify the program    (Module): Comments (lines starting with a #) are allowed in data.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.108  2006/01/19 18:05:42  lievre
   convergence.    Gnuplot problem appeared...
     To be fixed
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.107  2006/01/19 16:20:37  brouard
   identical for each individual. Also, if a individual missed an    Test existence of gnuplot in imach path
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
   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    Revision 1.105  2006/01/05 20:23:19  lievre
   split into an exact number (nh*stepm) of unobserved intermediate    *** empty log message ***
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.104  2005/09/30 16:11:43  lievre
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): sump fixed, loop imx fixed, and simplifications.
   and the contribution of each individual to the likelihood is simply    (Module): If the status is missing at the last wave but we know
   hPijx.    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
   Also this programme outputs the covariance matrix of the parameters but also    contributions to the likelihood is 1 - Prob of dying from last
   of the life expectancies. It also computes the prevalence limits.    health status (= 1-p13= p11+p12 in the easiest case of somebody in
      the healthy state at last known wave). Version is 0.98
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.103  2005/09/30 15:54:49  lievre
   This software have been partly granted by Euro-REVES, a concerted action    (Module): sump fixed, loop imx fixed, and simplifications.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.102  2004/09/15 17:31:30  brouard
   software can be distributed freely for non commercial use. Latest version    Add the possibility to read data file including tab characters.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
 #include <math.h>  
 #include <stdio.h>    Revision 1.100  2004/07/12 18:29:06  brouard
 #include <stdlib.h>    Add version for Mac OS X. Just define UNIX in Makefile
 #include <unistd.h>  
     Revision 1.99  2004/06/05 08:57:40  brouard
 #define MAXLINE 256    *** empty log message ***
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    Revision 1.98  2004/05/16 15:05:56  brouard
 /*#define DEBUG*/    New version 0.97 . First attempt to estimate force of mortality
 #define windows    directly from the data i.e. without the need of knowing the health
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    state at each age, but using a Gompertz model: log u =a + b*age .
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    cross-longitudinal survey is different from the mortality estimated
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    from other sources like vital statistic data.
   
 #define NINTERVMAX 8    The same imach parameter file can be used but the option for mle should be -3.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Agnès, who wrote this part of the code, tried to keep most of the
 #define NCOVMAX 8 /* Maximum number of covariates */    former routines in order to include the new code within the former code.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    The output is very simple: only an estimate of the intercept and of
 #define AGESUP 130    the slope with 95% confident intervals.
 #define AGEBASE 40  
     Current limitations:
     A) Even if you enter covariates, i.e. with the
 int erreur; /* Error number */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int nvar;    B) There is no computation of Life Expectancy nor Life Table.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.97  2004/02/20 13:25:42  lievre
 int nlstate=2; /* Number of live states */    Version 0.96d. Population forecasting command line is (temporarily)
 int ndeath=1; /* Number of dead states */    suppressed.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 int *wav; /* Number of waves for this individuual 0 is possible */    rewritten within the same printf. Workaround: many printfs.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.95  2003/07/08 07:54:34  brouard
 int mle, weightopt;    * imach.c (Repository):
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Repository): Using imachwizard code to output a more meaningful covariance
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    matrix (cov(a12,c31) instead of numbers.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.94  2003/06/27 13:00:02  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Just cleaning
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    Revision 1.93  2003/06/25 16:33:55  brouard
 FILE *ficreseij;    (Module): On windows (cygwin) function asctime_r doesn't
   char filerese[FILENAMELENGTH];    exist so I changed back to asctime which exists.
  FILE  *ficresvij;    (Module): Version 0.96b
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.92  2003/06/25 16:30:45  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.91  2003/06/25 15:30:29  brouard
 #define FTOL 1.0e-10    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 #define NRANSI    helps to forecast when convergence will be reached. Elapsed time
 #define ITMAX 200    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 #define TOL 2.0e-4  
     Revision 1.90  2003/06/24 12:34:15  brouard
 #define CGOLD 0.3819660    (Module): Some bugs corrected for windows. Also, when
 #define ZEPS 1.0e-10    mle=-1 a template is output in file "or"mypar.txt with the design
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    of the covariance matrix to be input.
   
 #define GOLD 1.618034    Revision 1.89  2003/06/24 12:30:52  brouard
 #define GLIMIT 100.0    (Module): Some bugs corrected for windows. Also, when
 #define TINY 1.0e-20    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.88  2003/06/23 17:54:56  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.87  2003/06/18 12:26:01  brouard
 #define rint(a) floor(a+0.5)    Version 0.96
   
 static double sqrarg;    Revision 1.86  2003/06/17 20:04:08  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Change position of html and gnuplot routines and added
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    routine fileappend.
   
 int imx;    Revision 1.85  2003/06/17 13:12:43  brouard
 int stepm;    * imach.c (Repository): Check when date of death was earlier that
 /* Stepm, step in month: minimum step interpolation*/    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 int m,nb;    was wrong (infinity). We still send an "Error" but patch by
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    assuming that the date of death was just one stepm after the
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    interview.
 double **pmmij, ***probs, ***mobaverage;    (Repository): Because some people have very long ID (first column)
 double dateintmean=0;    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 double *weight;    truncation)
 int **s; /* Status */    (Repository): No more line truncation errors.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    place. It differs from routine "prevalence" which may be called
 double ftolhess; /* Tolerance for computing hessian */    many times. Probs is memory consuming and must be used with
     parcimony.
 /**************** split *************************/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.83  2003/06/10 13:39:11  lievre
    char *s;                             /* pointer */    *** empty log message ***
    int  l1, l2;                         /* length counters */  
     Revision 1.82  2003/06/05 15:57:20  brouard
    l1 = strlen( path );                 /* length of path */    Add log in  imach.c and  fullversion number is now printed.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  */
    s = strrchr( path, '\\' );           /* find last / */  /*
 #else     Interpolated Markov Chain
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Short summary of the programme:
    if ( s == NULL ) {                   /* no directory, so use current */    
 #if     defined(__bsd__)                /* get current working directory */    This program computes Healthy Life Expectancies from
       extern char       *getwd( );    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
       if ( getwd( dirc ) == NULL ) {    interviewed on their health status or degree of disability (in the
 #else    case of a health survey which is our main interest) -2- at least a
       extern char       *getcwd( );    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    computed from the time spent in each health state according to a
 #endif    model. More health states you consider, more time is necessary to reach the
          return( GLOCK_ERROR_GETCWD );    Maximum Likelihood of the parameters involved in the model.  The
       }    simplest model is the multinomial logistic model where pij is the
       strcpy( name, path );             /* we've got it */    probability to be observed in state j at the second wave
    } else {                             /* strip direcotry from path */    conditional to be observed in state i at the first wave. Therefore
       s++;                              /* after this, the filename */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       l2 = strlen( s );                 /* length of filename */    'age' is age and 'sex' is a covariate. If you want to have a more
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    complex model than "constant and age", you should modify the program
       strcpy( name, s );                /* save file name */    where the markup *Covariates have to be included here again* invites
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    you to do it.  More covariates you add, slower the
       dirc[l1-l2] = 0;                  /* add zero */    convergence.
    }  
    l1 = strlen( dirc );                 /* length of directory */    The advantage of this computer programme, compared to a simple
 #ifdef windows    multinomial logistic model, is clear when the delay between waves is not
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    identical for each individual. Also, if a individual missed an
 #else    intermediate interview, the information is lost, but taken into
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    account using an interpolation or extrapolation.  
 #endif  
    s = strrchr( name, '.' );            /* find last / */    hPijx is the probability to be observed in state i at age x+h
    s++;    conditional to the observed state i at age x. The delay 'h' can be
    strcpy(ext,s);                       /* save extension */    split into an exact number (nh*stepm) of unobserved intermediate
    l1= strlen( name);    states. This elementary transition (by month, quarter,
    l2= strlen( s)+1;    semester or year) is modelled as a multinomial logistic.  The hPx
    strncpy( finame, name, l1-l2);    matrix is simply the matrix product of nh*stepm elementary matrices
    finame[l1-l2]= 0;    and the contribution of each individual to the likelihood is simply
    return( 0 );                         /* we're done */    hPijx.
 }  
     Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 /******************************************/    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 void replace(char *s, char*t)             Institut national d'études démographiques, Paris.
 {    This software have been partly granted by Euro-REVES, a concerted action
   int i;    from the European Union.
   int lg=20;    It is copyrighted identically to a GNU software product, ie programme and
   i=0;    software can be distributed freely for non commercial use. Latest version
   lg=strlen(t);    can be accessed at http://euroreves.ined.fr/imach .
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     if (t[i]== '\\') s[i]='/';    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   }    
 }    **********************************************************************/
   /*
 int nbocc(char *s, char occ)    main
 {    read parameterfile
   int i,j=0;    read datafile
   int lg=20;    concatwav
   i=0;    freqsummary
   lg=strlen(s);    if (mle >= 1)
   for(i=0; i<= lg; i++) {      mlikeli
   if  (s[i] == occ ) j++;    print results files
   }    if mle==1 
   return j;       computes hessian
 }    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 void cutv(char *u,char *v, char*t, char occ)    open gnuplot file
 {    open html file
   int i,lg,j,p=0;    stable prevalence
   i=0;     for age prevalim()
   for(j=0; j<=strlen(t)-1; j++) {    h Pij x
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    variance of p varprob
   }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
   lg=strlen(t);    Variance-covariance of DFLE
   for(j=0; j<p; j++) {    prevalence()
     (u[j] = t[j]);     movingaverage()
   }    varevsij() 
      u[p]='\0';    if popbased==1 varevsij(,popbased)
     total life expectancies
    for(j=0; j<= lg; j++) {    Variance of stable prevalence
     if (j>=(p+1))(v[j-p-1] = t[j]);   end
   }  */
 }  
   
 /********************** nrerror ********************/  
    
 void nrerror(char error_text[])  #include <math.h>
 {  #include <stdio.h>
   fprintf(stderr,"ERREUR ...\n");  #include <stdlib.h>
   fprintf(stderr,"%s\n",error_text);  #include <string.h>
   exit(1);  #include <unistd.h>
 }  
 /*********************** vector *******************/  #include <limits.h>
 double *vector(int nl, int nh)  #include <sys/types.h>
 {  #include <sys/stat.h>
   double *v;  #include <errno.h>
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  extern int errno;
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define MAXLINE 256
   
 /************************ivector *******************************/  #define GNUPLOTPROGRAM "gnuplot"
 int *ivector(long nl,long nh)  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 {  #define FILENAMELENGTH 132
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   if (!v) nrerror("allocation failure in ivector");  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   return v-nl+NR_END;  
 }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   free((FREE_ARG)(v+nl-NR_END));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 }  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 /******************* imatrix *******************************/  #define YEARM 12. /* Number of months per year */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define AGESUP 130
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define AGEBASE 40
 {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #ifdef UNIX
   int **m;  #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
   /* allocate pointers to rows */  #define ODIRSEPARATOR '\\'
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #else
   if (!m) nrerror("allocation failure 1 in matrix()");  #define DIRSEPARATOR '\\'
   m += NR_END;  #define CHARSEPARATOR "\\"
   m -= nrl;  #define ODIRSEPARATOR '/'
    #endif
    
   /* allocate rows and set pointers to them */  /* $Id$ */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /* $State$ */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
   m[nrl] -= ncl;  char fullversion[]="$Revision$ $Date$"; 
    int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int nvar;
    int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   /* return pointer to array of pointers to rows */  int npar=NPARMAX;
   return m;  int nlstate=2; /* Number of live states */
 }  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 /****************** free_imatrix *************************/  int popbased=0;
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  int *wav; /* Number of waves for this individuual 0 is possible */
       long nch,ncl,nrh,nrl;  int maxwav; /* Maxim number of waves */
      /* free an int matrix allocated by imatrix() */  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int gipmx, gsw; /* Global variables on the number of contributions 
   free((FREE_ARG) (m+nrl-NR_END));                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /******************* matrix *******************************/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 double **matrix(long nrl, long nrh, long ncl, long nch)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  double jmean; /* Mean space between 2 waves */
   double **m;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *ficlog, *ficrespow;
   m += NR_END;  int globpr; /* Global variable for printing or not */
   m -= nrl;  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double sw; /* Sum of weights */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char filerespow[FILENAMELENGTH];
   m[nrl] += NR_END;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   m[nrl] -= ncl;  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE *ficresprobmorprev;
   return m;  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 /*************************free matrix ************************/  FILE  *ficresvij;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char fileresvpl[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char title[MAXLINE];
 }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 /******************* ma3x *******************************/  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char command[FILENAMELENGTH];
 {  int  outcmd=0;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char filelog[FILENAMELENGTH]; /* Log file */
   if (!m) nrerror("allocation failure 1 in matrix()");  char filerest[FILENAMELENGTH];
   m += NR_END;  char fileregp[FILENAMELENGTH];
   m -= nrl;  char popfile[FILENAMELENGTH];
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m[nrl] -= ncl;  struct timezone tzp;
   extern int gettimeofday();
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  extern long time();
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char strcurr[80], strfor[80];
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  char *endptr;
   for (j=ncl+1; j<=nch; j++)  long lval;
     m[nrl][j]=m[nrl][j-1]+nlay;  
    #define NR_END 1
   for (i=nrl+1; i<=nrh; i++) {  #define FREE_ARG char*
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define FTOL 1.0e-10
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define NRANSI 
   }  #define ITMAX 200 
   return m;  
 }  #define TOL 2.0e-4 
   
 /*************************free ma3x ************************/  #define CGOLD 0.3819660 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define GOLD 1.618034 
   free((FREE_ARG)(m+nrl-NR_END));  #define GLIMIT 100.0 
 }  #define TINY 1.0e-20 
   
 /***************** f1dim *************************/  static double maxarg1,maxarg2;
 extern int ncom;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 extern double *pcom,*xicom;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 extern double (*nrfunc)(double []);    
    #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double f1dim(double x)  #define rint(a) floor(a+0.5)
 {  
   int j;  static double sqrarg;
   double f;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double *xt;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    int agegomp= AGEGOMP;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int imx; 
   f=(*nrfunc)(xt);  int stepm=1;
   free_vector(xt,1,ncom);  /* Stepm, step in month: minimum step interpolation*/
   return f;  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int m,nb;
 {  long *num;
   int iter;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double a,b,d,etemp;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double fu,fv,fw,fx;  double **pmmij, ***probs;
   double ftemp;  double *ageexmed,*agecens;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double dateintmean=0;
   double e=0.0;  
    double *weight;
   a=(ax < cx ? ax : cx);  int **s; /* Status */
   b=(ax > cx ? ax : cx);  double *agedc, **covar, idx;
   x=w=v=bx;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   fw=fv=fx=(*f)(x);  double *lsurv, *lpop, *tpop;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double ftolhess; /* Tolerance for computing hessian */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /**************** split *************************/
 #ifdef DEBUG  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 #endif       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    */ 
       *xmin=x;    char  *ss;                            /* pointer */
       return fx;    int   l1, l2;                         /* length counters */
     }  
     ftemp=fu;    l1 = strlen(path );                   /* length of path */
     if (fabs(e) > tol1) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       r=(x-w)*(fx-fv);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       q=(x-v)*(fx-fw);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       p=(x-v)*q-(x-w)*r;      strcpy( name, path );               /* we got the fullname name because no directory */
       q=2.0*(q-r);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       if (q > 0.0) p = -p;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       q=fabs(q);      /* get current working directory */
       etemp=e;      /*    extern  char* getcwd ( char *buf , int len);*/
       e=d;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))        return( GLOCK_ERROR_GETCWD );
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      }
       else {      /* got dirc from getcwd*/
         d=p/q;      printf(" DIRC = %s \n",dirc);
         u=x+d;    } else {                              /* strip direcotry from path */
         if (u-a < tol2 || b-u < tol2)      ss++;                               /* after this, the filename */
           d=SIGN(tol1,xm-x);      l2 = strlen( ss );                  /* length of filename */
       }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     } else {      strcpy( name, ss );         /* save file name */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     }      dirc[l1-l2] = 0;                    /* add zero */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      printf(" DIRC2 = %s \n",dirc);
     fu=(*f)(u);    }
     if (fu <= fx) {    /* We add a separator at the end of dirc if not exists */
       if (u >= x) a=x; else b=x;    l1 = strlen( dirc );                  /* length of directory */
       SHFT(v,w,x,u)    if( dirc[l1-1] != DIRSEPARATOR ){
         SHFT(fv,fw,fx,fu)      dirc[l1] =  DIRSEPARATOR;
         } else {      dirc[l1+1] = 0; 
           if (u < x) a=u; else b=u;      printf(" DIRC3 = %s \n",dirc);
           if (fu <= fw || w == x) {    }
             v=w;    ss = strrchr( name, '.' );            /* find last / */
             w=u;    if (ss >0){
             fv=fw;      ss++;
             fw=fu;      strcpy(ext,ss);                     /* save extension */
           } else if (fu <= fv || v == x || v == w) {      l1= strlen( name);
             v=u;      l2= strlen(ss)+1;
             fv=fu;      strncpy( finame, name, l1-l2);
           }      finame[l1-l2]= 0;
         }    }
   }  
   nrerror("Too many iterations in brent");    return( 0 );                          /* we're done */
   *xmin=x;  }
   return fx;  
 }  
   /******************************************/
 /****************** mnbrak ***********************/  
   void replace_back_to_slash(char *s, char*t)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  {
             double (*func)(double))    int i;
 {    int lg=0;
   double ulim,u,r,q, dum;    i=0;
   double fu;    lg=strlen(t);
      for(i=0; i<= lg; i++) {
   *fa=(*func)(*ax);      (s[i] = t[i]);
   *fb=(*func)(*bx);      if (t[i]== '\\') s[i]='/';
   if (*fb > *fa) {    }
     SHFT(dum,*ax,*bx,dum)  }
       SHFT(dum,*fb,*fa,dum)  
       }  int nbocc(char *s, char occ)
   *cx=(*bx)+GOLD*(*bx-*ax);  {
   *fc=(*func)(*cx);    int i,j=0;
   while (*fb > *fc) {    int lg=20;
     r=(*bx-*ax)*(*fb-*fc);    i=0;
     q=(*bx-*cx)*(*fb-*fa);    lg=strlen(s);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    for(i=0; i<= lg; i++) {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    if  (s[i] == occ ) j++;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    }
     if ((*bx-u)*(u-*cx) > 0.0) {    return j;
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  void cutv(char *u,char *v, char*t, char occ)
       if (fu < *fc) {  {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
           SHFT(*fb,*fc,fu,(*func)(u))       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
           }       gives u="abcedf" and v="ghi2j" */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    int i,lg,j,p=0;
       u=ulim;    i=0;
       fu=(*func)(u);    for(j=0; j<=strlen(t)-1; j++) {
     } else {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       u=(*cx)+GOLD*(*cx-*bx);    }
       fu=(*func)(u);  
     }    lg=strlen(t);
     SHFT(*ax,*bx,*cx,u)    for(j=0; j<p; j++) {
       SHFT(*fa,*fb,*fc,fu)      (u[j] = t[j]);
       }    }
 }       u[p]='\0';
   
 /*************** linmin ************************/     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 int ncom;    }
 double *pcom,*xicom;  }
 double (*nrfunc)(double []);  
    /********************** nrerror ********************/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  void nrerror(char error_text[])
   double brent(double ax, double bx, double cx,  {
                double (*f)(double), double tol, double *xmin);    fprintf(stderr,"ERREUR ...\n");
   double f1dim(double x);    fprintf(stderr,"%s\n",error_text);
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    exit(EXIT_FAILURE);
               double *fc, double (*func)(double));  }
   int j;  /*********************** vector *******************/
   double xx,xmin,bx,ax;  double *vector(int nl, int nh)
   double fx,fb,fa;  {
      double *v;
   ncom=n;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   pcom=vector(1,n);    if (!v) nrerror("allocation failure in vector");
   xicom=vector(1,n);    return v-nl+NR_END;
   nrfunc=func;  }
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /************************ free vector ******************/
     xicom[j]=xi[j];  void free_vector(double*v, int nl, int nh)
   }  {
   ax=0.0;    free((FREE_ARG)(v+nl-NR_END));
   xx=1.0;  }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /************************ivector *******************************/
 #ifdef DEBUG  int *ivector(long nl,long nh)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  {
 #endif    int *v;
   for (j=1;j<=n;j++) {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     xi[j] *= xmin;    if (!v) nrerror("allocation failure in ivector");
     p[j] += xi[j];    return v-nl+NR_END;
   }  }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 /*************** powell ************************/    free((FREE_ARG)(v+nl-NR_END));
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  
 {  /************************lvector *******************************/
   void linmin(double p[], double xi[], int n, double *fret,  long *lvector(long nl,long nh)
               double (*func)(double []));  {
   int i,ibig,j;    long *v;
   double del,t,*pt,*ptt,*xit;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double fp,fptt;    if (!v) nrerror("allocation failure in ivector");
   double *xits;    return v-nl+NR_END;
   pt=vector(1,n);  }
   ptt=vector(1,n);  
   xit=vector(1,n);  /******************free lvector **************************/
   xits=vector(1,n);  void free_lvector(long *v, long nl, long nh)
   *fret=(*func)(p);  {
   for (j=1;j<=n;j++) pt[j]=p[j];    free((FREE_ARG)(v+nl-NR_END));
   for (*iter=1;;++(*iter)) {  }
     fp=(*fret);  
     ibig=0;  /******************* imatrix *******************************/
     del=0.0;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for (i=1;i<=n;i++)  { 
       printf(" %d %.12f",i, p[i]);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     printf("\n");    int **m; 
     for (i=1;i<=n;i++) {    
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    /* allocate pointers to rows */ 
       fptt=(*fret);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()"); 
       printf("fret=%lf \n",*fret);    m += NR_END; 
 #endif    m -= nrl; 
       printf("%d",i);fflush(stdout);    
       linmin(p,xit,n,fret,func);    
       if (fabs(fptt-(*fret)) > del) {    /* allocate rows and set pointers to them */ 
         del=fabs(fptt-(*fret));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         ibig=i;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       }    m[nrl] += NR_END; 
 #ifdef DEBUG    m[nrl] -= ncl; 
       printf("%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    
         printf(" x(%d)=%.12e",j,xit[j]);    /* return pointer to array of pointers to rows */ 
       }    return m; 
       for(j=1;j<=n;j++)  } 
         printf(" p=%.12e",p[j]);  
       printf("\n");  /****************** free_imatrix *************************/
 #endif  void free_imatrix(m,nrl,nrh,ncl,nch)
     }        int **m;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        long nch,ncl,nrh,nrl; 
 #ifdef DEBUG       /* free an int matrix allocated by imatrix() */ 
       int k[2],l;  { 
       k[0]=1;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       k[1]=-1;    free((FREE_ARG) (m+nrl-NR_END)); 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /******************* matrix *******************************/
       printf("\n");  double **matrix(long nrl, long nrh, long ncl, long nch)
       for(l=0;l<=1;l++) {  {
         for (j=1;j<=n;j++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double **m;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
 #endif    m -= nrl;
   
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       free_vector(xit,1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       free_vector(xits,1,n);    m[nrl] += NR_END;
       free_vector(ptt,1,n);    m[nrl] -= ncl;
       free_vector(pt,1,n);  
       return;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     for (j=1;j<=n;j++) {     */
       ptt[j]=2.0*p[j]-pt[j];  }
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     fptt=(*func)(ptt);  {
     if (fptt < fp) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    free((FREE_ARG)(m+nrl-NR_END));
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /******************* ma3x *******************************/
           xi[j][ibig]=xi[j][n];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           xi[j][n]=xit[j];  {
         }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 #ifdef DEBUG    double ***m;
         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++)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           printf(" %.12e",xit[j]);    if (!m) nrerror("allocation failure 1 in matrix()");
         printf("\n");    m += NR_END;
 #endif    m -= nrl;
       }  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /**** Prevalence limit ****************/  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      matrix by transitions matrix until convergence is reached */    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   int i, ii,j,k;    for (j=ncl+1; j<=nch; j++) 
   double min, max, maxmin, maxmax,sumnew=0.;      m[nrl][j]=m[nrl][j-1]+nlay;
   double **matprod2();    
   double **out, cov[NCOVMAX], **pmij();    for (i=nrl+1; i<=nrh; i++) {
   double **newm;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double agefin, delaymax=50 ; /* Max number of years to converge */      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
   for (ii=1;ii<=nlstate+ndeath;ii++)    }
     for (j=1;j<=nlstate+ndeath;j++){    return m; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
    cov[1]=1.;  }
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*************************free ma3x ************************/
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     newm=savm;  {
     /* Covariates have to be included here again */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
      cov[2]=agefin;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
       for (k=1; k<=cptcovn;k++) {  }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  /*************** function subdirf ***********/
       }  char *subdirf(char fileres[])
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovprod;k++)    strcpy(tmpout,optionfilefiname);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    return tmpout;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  }
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
     savm=oldm;  {
     oldm=newm;    
     maxmax=0.;    /* Caution optionfilefiname is hidden */
     for(j=1;j<=nlstate;j++){    strcpy(tmpout,optionfilefiname);
       min=1.;    strcat(tmpout,"/");
       max=0.;    strcat(tmpout,preop);
       for(i=1; i<=nlstate; i++) {    strcat(tmpout,fileres);
         sumnew=0;    return tmpout;
         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]);  /*************** function subdirf3 ***********/
         min=FMIN(min,prlim[i][j]);  char *subdirf3(char fileres[], char *preop, char *preop2)
       }  {
       maxmin=max-min;    
       maxmax=FMAX(maxmax,maxmin);    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     if(maxmax < ftolpl){    strcat(tmpout,"/");
       return prlim;    strcat(tmpout,preop);
     }    strcat(tmpout,preop2);
   }    strcat(tmpout,fileres);
 }    return tmpout;
   }
 /*************** transition probabilities ***************/  
   /***************** f1dim *************************/
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  extern int ncom; 
 {  extern double *pcom,*xicom;
   double s1, s2;  extern double (*nrfunc)(double []); 
   /*double t34;*/   
   int i,j,j1, nc, ii, jj;  double f1dim(double x) 
   { 
     for(i=1; i<= nlstate; i++){    int j; 
     for(j=1; j<i;j++){    double f;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double *xt; 
         /*s2 += param[i][j][nc]*cov[nc];*/   
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    xt=vector(1,ncom); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",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); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    return f; 
     }  } 
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*****************brent *************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  { 
       }    int iter; 
       ps[i][j]=s2;    double a,b,d,etemp;
     }    double fu,fv,fw,fx;
   }    double ftemp;
     /*ps[3][2]=1;*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
   for(i=1; i<= nlstate; i++){   
      s1=0;    a=(ax < cx ? ax : cx); 
     for(j=1; j<i; j++)    b=(ax > cx ? ax : cx); 
       s1+=exp(ps[i][j]);    x=w=v=bx; 
     for(j=i+1; j<=nlstate+ndeath; j++)    fw=fv=fx=(*f)(x); 
       s1+=exp(ps[i][j]);    for (iter=1;iter<=ITMAX;iter++) { 
     ps[i][i]=1./(s1+1.);      xm=0.5*(a+b); 
     for(j=1; j<i; j++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for(j=i+1; j<=nlstate+ndeath; j++)      printf(".");fflush(stdout);
       ps[i][j]= exp(ps[i][j])*ps[i][i];      fprintf(ficlog,".");fflush(ficlog);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #ifdef DEBUG
   } /* end i */      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=nlstate+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
       ps[ii][jj]=0;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       ps[ii][ii]=1;        *xmin=x; 
     }        return fx; 
   }      } 
       ftemp=fu;
       if (fabs(e) > tol1) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        r=(x-w)*(fx-fv); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        q=(x-v)*(fx-fw); 
      printf("%lf ",ps[ii][jj]);        p=(x-v)*q-(x-w)*r; 
    }        q=2.0*(q-r); 
     printf("\n ");        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     printf("\n ");printf("%lf ",cov[2]);*/        etemp=e; 
 /*        e=d; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   goto end;*/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     return ps;        else { 
 }          d=p/q; 
           u=x+d; 
 /**************** Product of 2 matrices ******************/          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        } 
 {      } else { 
   /* 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(...) */      } 
   /* in, b, out are matrice of pointers which should have been initialized      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
      before: only the contents of out is modified. The function returns      fu=(*f)(u); 
      a pointer to pointers identical to out */      if (fu <= fx) { 
   long i, j, k;        if (u >= x) a=x; else b=x; 
   for(i=nrl; i<= nrh; i++)        SHFT(v,w,x,u) 
     for(k=ncolol; k<=ncoloh; k++)          SHFT(fv,fw,fx,fu) 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          } else { 
         out[i][k] +=in[i][j]*b[j][k];            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
   return out;              v=w; 
 }              w=u; 
               fv=fw; 
               fw=fu; 
 /************* Higher Matrix Product ***************/            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )              fv=fu; 
 {            } 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          } 
      duration (i.e. until    } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    nrerror("Too many iterations in brent"); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    *xmin=x; 
      (typically every 2 years instead of every month which is too big).    return fx; 
      Model is determined by parameters x and covariates have to be  } 
      included manually here.  
   /****************** mnbrak ***********************/
      */  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   int i, j, d, h, k;              double (*func)(double)) 
   double **out, cov[NCOVMAX];  { 
   double **newm;    double ulim,u,r,q, dum;
     double fu; 
   /* Hstepm could be zero and should return the unit matrix */   
   for (i=1;i<=nlstate+ndeath;i++)    *fa=(*func)(*ax); 
     for (j=1;j<=nlstate+ndeath;j++){    *fb=(*func)(*bx); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    if (*fb > *fa) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        } 
   for(h=1; h <=nhstepm; h++){    *cx=(*bx)+GOLD*(*bx-*ax); 
     for(d=1; d <=hstepm; d++){    *fc=(*func)(*cx); 
       newm=savm;    while (*fb > *fc) { 
       /* Covariates have to be included here again */      r=(*bx-*ax)*(*fb-*fc); 
       cov[1]=1.;      q=(*bx-*cx)*(*fb-*fa); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       for (k=1; k<=cptcovage;k++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      if ((*bx-u)*(u-*cx) > 0.0) { 
       for (k=1; k<=cptcovprod;k++)        fu=(*func)(u); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
         if (fu < *fc) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,            } 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       savm=oldm;        u=ulim; 
       oldm=newm;        fu=(*func)(u); 
     }      } else { 
     for(i=1; i<=nlstate+ndeath; i++)        u=(*cx)+GOLD*(*cx-*bx); 
       for(j=1;j<=nlstate+ndeath;j++) {        fu=(*func)(u); 
         po[i][j][h]=newm[i][j];      } 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      SHFT(*ax,*bx,*cx,u) 
          */        SHFT(*fa,*fb,*fc,fu) 
       }        } 
   } /* end h */  } 
   return po;  
 }  /*************** linmin ************************/
   
   int ncom; 
 /*************** log-likelihood *************/  double *pcom,*xicom;
 double func( double *x)  double (*nrfunc)(double []); 
 {   
   int i, ii, j, k, mi, d, kk;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  { 
   double **out;    double brent(double ax, double bx, double cx, 
   double sw; /* Sum of weights */                 double (*f)(double), double tol, double *xmin); 
   double lli; /* Individual log likelihood */    double f1dim(double x); 
   long ipmx;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   /*extern weight */                double *fc, double (*func)(double)); 
   /* We are differentiating ll according to initial status */    int j; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double xx,xmin,bx,ax; 
   /*for(i=1;i<imx;i++)    double fx,fb,fa;
     printf(" %d\n",s[4][i]);   
   */    ncom=n; 
   cov[1]=1.;    pcom=vector(1,n); 
     xicom=vector(1,n); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    nrfunc=func; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (j=1;j<=n;j++) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      pcom[j]=p[j]; 
     for(mi=1; mi<= wav[i]-1; mi++){      xicom[j]=xi[j]; 
       for (ii=1;ii<=nlstate+ndeath;ii++)    } 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    ax=0.0; 
       for(d=0; d<dh[mi][i]; d++){    xx=1.0; 
         newm=savm;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         for (kk=1; kk<=cptcovage;kk++) {  #ifdef DEBUG
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
          #endif
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    for (j=1;j<=n;j++) { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      xi[j] *= xmin; 
         savm=oldm;      p[j] += xi[j]; 
         oldm=newm;    } 
            free_vector(xicom,1,n); 
            free_vector(pcom,1,n); 
       } /* end mult */  } 
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  char *asc_diff_time(long time_sec, char ascdiff[])
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  {
       ipmx +=1;    long sec_left, days, hours, minutes;
       sw += weight[i];    days = (time_sec) / (60*60*24);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    sec_left = (time_sec) % (60*60*24);
     } /* end of wave */    hours = (sec_left) / (60*60) ;
   } /* end of individual */    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    sec_left = (sec_left) % (60);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    return ascdiff;
   return -l;  }
 }  
   /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 /*********** Maximum Likelihood Estimation ***************/              double (*func)(double [])) 
   { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    void linmin(double p[], double xi[], int n, double *fret, 
 {                double (*func)(double [])); 
   int i,j, iter;    int i,ibig,j; 
   double **xi,*delti;    double del,t,*pt,*ptt,*xit;
   double fret;    double fp,fptt;
   xi=matrix(1,npar,1,npar);    double *xits;
   for (i=1;i<=npar;i++)    int niterf, itmp;
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);    pt=vector(1,n); 
   printf("Powell\n");    ptt=vector(1,n); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    xit=vector(1,n); 
     xits=vector(1,n); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    *fret=(*func)(p); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
 }      fp=(*fret); 
       ibig=0; 
 /**** Computes Hessian and covariance matrix ***/      del=0.0; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      last_time=curr_time;
 {      (void) gettimeofday(&curr_time,&tzp);
   double  **a,**y,*x,pd;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   double **hess;      /*    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);
   int i, j,jk;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   int *indx;      */
      for (i=1;i<=n;i++) {
   double hessii(double p[], double delta, int theta, double delti[]);        printf(" %d %.12f",i, p[i]);
   double hessij(double p[], double delti[], int i, int j);        fprintf(ficlog," %d %.12lf",i, p[i]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;        fprintf(ficrespow," %.12lf", p[i]);
   void ludcmp(double **a, int npar, int *indx, double *d) ;      }
       printf("\n");
   hess=matrix(1,npar,1,npar);      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
   printf("\nCalculation of the hessian matrix. Wait...\n");      if(*iter <=3){
   for (i=1;i<=npar;i++){        tm = *localtime(&curr_time.tv_sec);
     printf("%d",i);fflush(stdout);        strcpy(strcurr,asctime(&tm));
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*       asctime_r(&tm,strcurr); */
     /*printf(" %f ",p[i]);*/        forecast_time=curr_time; 
     /*printf(" %lf ",hess[i][i]);*/        itmp = strlen(strcurr);
   }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
            strcurr[itmp-1]='\0';
   for (i=1;i<=npar;i++) {        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (j=1;j<=npar;j++)  {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       if (j>i) {        for(niterf=10;niterf<=30;niterf+=10){
         printf(".%d%d",i,j);fflush(stdout);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         hess[i][j]=hessij(p,delti,i,j);          tmf = *localtime(&forecast_time.tv_sec);
         hess[j][i]=hess[i][j];      /*      asctime_r(&tmf,strfor); */
         /*printf(" %lf ",hess[i][j]);*/          strcpy(strfor,asctime(&tmf));
       }          itmp = strlen(strfor);
     }          if(strfor[itmp-1]=='\n')
   }          strfor[itmp-1]='\0';
   printf("\n");          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);
           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);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        }
        }
   a=matrix(1,npar,1,npar);      for (i=1;i<=n;i++) { 
   y=matrix(1,npar,1,npar);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   x=vector(1,npar);        fptt=(*fret); 
   indx=ivector(1,npar);  #ifdef DEBUG
   for (i=1;i<=npar;i++)        printf("fret=%lf \n",*fret);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fprintf(ficlog,"fret=%lf \n",*fret);
   ludcmp(a,npar,indx,&pd);  #endif
         printf("%d",i);fflush(stdout);
   for (j=1;j<=npar;j++) {        fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=1;i<=npar;i++) x[i]=0;        linmin(p,xit,n,fret,func); 
     x[j]=1;        if (fabs(fptt-(*fret)) > del) { 
     lubksb(a,npar,indx,x);          del=fabs(fptt-(*fret)); 
     for (i=1;i<=npar;i++){          ibig=i; 
       matcov[i][j]=x[i];        } 
     }  #ifdef DEBUG
   }        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   printf("\n#Hessian matrix#\n");        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++) {          printf(" x(%d)=%.12e",j,xit[j]);
       printf("%.3e ",hess[i][j]);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
     printf("\n");        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
   /* Recompute Inverse */        }
   for (i=1;i<=npar;i++)        printf("\n");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        fprintf(ficlog,"\n");
   ludcmp(a,npar,indx,&pd);  #endif
       } 
   /*  printf("\n#Hessian matrix recomputed#\n");      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
   for (j=1;j<=npar;j++) {        int k[2],l;
     for (i=1;i<=npar;i++) x[i]=0;        k[0]=1;
     x[j]=1;        k[1]=-1;
     lubksb(a,npar,indx,x);        printf("Max: %.12e",(*func)(p));
     for (i=1;i<=npar;i++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
       y[i][j]=x[i];        for (j=1;j<=n;j++) {
       printf("%.3e ",y[i][j]);          printf(" %.12e",p[j]);
     }          fprintf(ficlog," %.12e",p[j]);
     printf("\n");        }
   }        printf("\n");
   */        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
   free_matrix(a,1,npar,1,npar);          for (j=1;j<=n;j++) {
   free_matrix(y,1,npar,1,npar);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   free_vector(x,1,npar);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   free_ivector(indx,1,npar);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   free_matrix(hess,1,npar,1,npar);          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 }        }
   #endif
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  
 {        free_vector(xit,1,n); 
   int i;        free_vector(xits,1,n); 
   int l=1, lmax=20;        free_vector(ptt,1,n); 
   double k1,k2;        free_vector(pt,1,n); 
   double p2[NPARMAX+1];        return; 
   double res;      } 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double fx;      for (j=1;j<=n;j++) { 
   int k=0,kmax=10;        ptt[j]=2.0*p[j]-pt[j]; 
   double l1;        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   fx=func(x);      } 
   for (i=1;i<=npar;i++) p2[i]=x[i];      fptt=(*func)(ptt); 
   for(l=0 ; l <=lmax; l++){      if (fptt < fp) { 
     l1=pow(10,l);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     delts=delt;        if (t < 0.0) { 
     for(k=1 ; k <kmax; k=k+1){          linmin(p,xit,n,fret,func); 
       delt = delta*(l1*k);          for (j=1;j<=n;j++) { 
       p2[theta]=x[theta] +delt;            xi[j][ibig]=xi[j][n]; 
       k1=func(p2)-fx;            xi[j][n]=xit[j]; 
       p2[theta]=x[theta]-delt;          }
       k2=func(p2)-fx;  #ifdef DEBUG
       /*res= (k1-2.0*fx+k2)/delt/delt; */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                for(j=1;j<=n;j++){
 #ifdef DEBUG            printf(" %.12e",xit[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);            fprintf(ficlog," %.12e",xit[j]);
 #endif          }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          printf("\n");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          fprintf(ficlog,"\n");
         k=kmax;  #endif
       }        }
       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)){  
         delts=delt;  /**** Prevalence limit (stable prevalence)  ****************/
       }  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
   delti[theta]=delts;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   return res;       matrix by transitions matrix until convergence is reached */
    
 }    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
 double hessij( double x[], double delti[], int thetai,int thetaj)    double **matprod2();
 {    double **out, cov[NCOVMAX], **pmij();
   int i;    double **newm;
   int l=1, l1, lmax=20;    double agefin, delaymax=50 ; /* Max number of years to converge */
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    for (ii=1;ii<=nlstate+ndeath;ii++)
   int k;      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fx=func(x);      }
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];     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 */
     k1=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;
     k2=func(p2)-fx;    
          for (k=1; k<=cptcovn;k++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     k3=func(p2)-fx;        }
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for (k=1; k<=cptcovprod;k++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 #ifdef DEBUG        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     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 cov[3]=%lf \n",ij, cov[3]);*/
 #endif      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
   return res;      savm=oldm;
 }      oldm=newm;
       maxmax=0.;
 /************** Inverse of matrix **************/      for(j=1;j<=nlstate;j++){
 void ludcmp(double **a, int n, int *indx, double *d)        min=1.;
 {        max=0.;
   int i,imax,j,k;        for(i=1; i<=nlstate; i++) {
   double big,dum,sum,temp;          sumnew=0;
   double *vv;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            prlim[i][j]= newm[i][j]/(1-sumnew);
   vv=vector(1,n);          max=FMAX(max,prlim[i][j]);
   *d=1.0;          min=FMIN(min,prlim[i][j]);
   for (i=1;i<=n;i++) {        }
     big=0.0;        maxmin=max-min;
     for (j=1;j<=n;j++)        maxmax=FMAX(maxmax,maxmin);
       if ((temp=fabs(a[i][j])) > big) big=temp;      }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      if(maxmax < ftolpl){
     vv[i]=1.0/big;        return prlim;
   }      }
   for (j=1;j<=n;j++) {    }
     for (i=1;i<j;i++) {  }
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*************** transition probabilities ***************/ 
       a[i][j]=sum;  
     }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     big=0.0;  {
     for (i=j;i<=n;i++) {    double s1, s2;
       sum=a[i][j];    /*double t34;*/
       for (k=1;k<j;k++)    int i,j,j1, nc, ii, jj;
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;      for(i=1; i<= nlstate; i++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(j=1; j<i;j++){
         big=dum;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         imax=i;            /*s2 += param[i][j][nc]*cov[nc];*/
       }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     if (j != imax) {          }
       for (k=1;k<=n;k++) {          ps[i][j]=s2;
         dum=a[imax][k];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;        for(j=i+1; j<=nlstate+ndeath;j++){
       }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       *d = -(*d);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       vv[imax]=vv[j];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     }          }
     indx[j]=imax;          ps[i][j]=s2;
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {      }
       dum=1.0/(a[j][j]);      /*ps[3][2]=1;*/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      
     }      for(i=1; i<= nlstate; i++){
   }        s1=0;
   free_vector(vv,1,n);  /* Doesn't work */        for(j=1; j<i; j++)
 ;          s1+=exp(ps[i][j]);
 }        for(j=i+1; j<=nlstate+ndeath; j++)
           s1+=exp(ps[i][j]);
 void lubksb(double **a, int n, int *indx, double b[])        ps[i][i]=1./(s1+1.);
 {        for(j=1; j<i; j++)
   int i,ii=0,ip,j;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   double sum;        for(j=i+1; j<=nlstate+ndeath; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (i=1;i<=n;i++) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     ip=indx[i];      } /* end i */
     sum=b[ip];      
     b[ip]=b[i];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     if (ii)        for(jj=1; jj<= nlstate+ndeath; jj++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          ps[ii][jj]=0;
     else if (sum) ii=i;          ps[ii][ii]=1;
     b[i]=sum;        }
   }      }
   for (i=n;i>=1;i--) {      
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     b[i]=sum/a[i][i];  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   }  /*         printf("ddd %lf ",ps[ii][jj]); */
 }  /*       } */
   /*       printf("\n "); */
 /************ 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)  /*        printf("\n ");printf("%lf ",cov[2]); */
 {  /* Some frequencies */         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        goto end;*/
   double ***freq; /* Frequencies */      return ps;
   double *pp;  }
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;  /**************** Product of 2 matrices ******************/
   char fileresp[FILENAMELENGTH];  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   pp=vector(1,nlstate);  {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   strcpy(fileresp,"p");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   strcat(fileresp,fileres);    /* in, b, out are matrice of pointers which should have been initialized 
   if((ficresp=fopen(fileresp,"w"))==NULL) {       before: only the contents of out is modified. The function returns
     printf("Problem with prevalence resultfile: %s\n", fileresp);       a pointer to pointers identical to out */
     exit(0);    long i, j, k;
   }    for(i=nrl; i<= nrh; i++)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for(k=ncolol; k<=ncoloh; k++)
   j1=0;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    return out;
   }
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;  /************* Higher Matrix Product ***************/
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
          scanf("%d", i);*/  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         for (i=-1; i<=nlstate+ndeath; i++)    {
          for (jk=-1; jk<=nlstate+ndeath; jk++)      /* Computes the transition matrix starting at age 'age' over 
            for(m=agemin; m <= agemax+3; m++)       'nhstepm*hstepm*stepm' months (i.e. until
              freq[i][jk][m]=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
         dateintsum=0;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         k2cpt=0;       (typically every 2 years instead of every month which is too big 
        for (i=1; i<=imx; i++) {       for the memory).
          bool=1;       Model is determined by parameters x and covariates have to be 
          if  (cptcovn>0) {       included manually here. 
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       */
                bool=0;  
          }    int i, j, d, h, k;
          if (bool==1) {    double **out, cov[NCOVMAX];
            for(m=firstpass; m<=lastpass; m++){    double **newm;
              k2=anint[m][i]+(mint[m][i]/12.);  
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    /* Hstepm could be zero and should return the unit matrix */
                if(agev[m][i]==0) agev[m][i]=agemax+1;    for (i=1;i<=nlstate+ndeath;i++)
                if(agev[m][i]==1) agev[m][i]=agemax+2;      for (j=1;j<=nlstate+ndeath;j++){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        oldm[i][j]=(i==j ? 1.0 : 0.0);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        po[i][j][0]=(i==j ? 1.0 : 0.0);
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      }
                  dateintsum=dateintsum+k2;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                  k2cpt++;    for(h=1; h <=nhstepm; h++){
                }      for(d=1; d <=hstepm; d++){
         newm=savm;
              }        /* Covariates have to be included here again */
            }        cov[1]=1.;
          }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
        }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         if  (cptcovn>0) {        for (k=1; k<=cptcovage;k++)
          fprintf(ficresp, "\n#********** Variable ");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (k=1; k<=cptcovprod;k++)
        fprintf(ficresp, "**********\n#");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         }  
        for(i=1; i<=nlstate;i++)  
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        fprintf(ficresp, "\n");        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   for(i=(int)agemin; i <= (int)agemax+3; i++){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     if(i==(int)agemax+3)        savm=oldm;
       printf("Total");        oldm=newm;
     else      }
       printf("Age %d", i);      for(i=1; i<=nlstate+ndeath; i++)
     for(jk=1; jk <=nlstate ; jk++){        for(j=1;j<=nlstate+ndeath;j++) {
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          po[i][j][h]=newm[i][j];
         pp[jk] += freq[jk][m][i];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     }           */
     for(jk=1; jk <=nlstate ; jk++){        }
       for(m=-1, pos=0; m <=0 ; m++)    } /* end h */
         pos += freq[jk][m][i];    return po;
       if(pp[jk]>=1.e-10)  }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
       else  
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*************** log-likelihood *************/
     }  double func( double *x)
   {
      for(jk=1; jk <=nlstate ; jk++){    int i, ii, j, k, mi, d, kk;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         pp[jk] += freq[jk][m][i];    double **out;
      }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
     for(jk=1,pos=0; jk <=nlstate ; jk++)    int s1, s2;
       pos += pp[jk];    double bbh, survp;
     for(jk=1; jk <=nlstate ; jk++){    long ipmx;
       if(pos>=1.e-5)    /*extern weight */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    /* We are differentiating ll according to initial status */
       else    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /*for(i=1;i<imx;i++) 
       if( i <= (int) agemax){      printf(" %d\n",s[4][i]);
         if(pos>=1.e-5){    */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    cov[1]=1.;
           probs[i][jk][j1]= pp[jk]/pos;  
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
       else    if(mle==1){
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     for(jk=-1; jk <=nlstate+ndeath; jk++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(m=-1; m <=nlstate+ndeath; m++)            for (j=1;j<=nlstate+ndeath;j++){
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if(i <= (int) agemax)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresp,"\n");            }
     printf("\n");          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  }            for (kk=1; kk<=cptcovage;kk++) {
   dateintmean=dateintsum/k2cpt;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   fclose(ficresp);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(pp,1,nlstate);            savm=oldm;
             oldm=newm;
   /* End of Freq */          } /* end mult */
 }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 /************ Prevalence ********************/          /* But now since version 0.9 we anticipate for bias at large stepm.
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 {  /* Some frequencies */           * (in months) between two waves is not a multiple of stepm, we rounded to 
             * the nearest (and in case of equal distance, to the lowest) interval but now
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double ***freq; /* Frequencies */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double *pp;           * probability in order to take into account the bias as a fraction of the way
   double pos, k2;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   pp=vector(1,nlstate);           * For stepm=1 the results are the same as for previous versions of Imach.
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * For stepm > 1 the results are less biased than in previous versions. 
             */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          s1=s[mw[mi][i]][i];
   j1=0;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   j=cptcoveff;          /* bias bh is positive if real duration
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * is higher than the multiple of stepm and negative otherwise.
             */
  for(k1=1; k1<=j;k1++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for(i1=1; i1<=ncodemax[k1];i1++){          if( s2 > nlstate){ 
       j1++;            /* i.e. if s2 is a death state and if the date of death is known 
                 then the contribution to the likelihood is the probability to 
       for (i=-1; i<=nlstate+ndeath; i++)                 die between last step unit time and current  step unit time, 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                 which is also equal to probability to die before dh 
           for(m=agemin; m <= agemax+3; m++)               minus probability to die before dh-stepm . 
             freq[i][jk][m]=0;               In version up to 0.92 likelihood was computed
                as if date of death was unknown. Death was treated as any other
       for (i=1; i<=imx; i++) {          health state: the date of the interview describes the actual state
         bool=1;          and not the date of a change in health state. The former idea was
         if  (cptcovn>0) {          to consider that at each interview the state was recorded
           for (z1=1; z1<=cptcoveff; z1++)          (healthy, disable or death) and IMaCh was corrected; but when we
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          introduced the exact date of death then we should have modified
               bool=0;          the contribution of an exact death to the likelihood. This new
         }          contribution is smaller and very dependent of the step unit
         if (bool==1) {          stepm. It is no more the probability to die between last interview
           for(m=firstpass; m<=lastpass; m++){          and month of death but the probability to survive from last
             k2=anint[m][i]+(mint[m][i]/12.);          interview up to one month before death multiplied by the
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          probability to die within a month. Thanks to Chris
               if(agev[m][i]==0) agev[m][i]=agemax+1;          Jackson for correcting this bug.  Former versions increased
               if(agev[m][i]==1) agev[m][i]=agemax+2;          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%
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            lower mortality.
             }            */
           }            lli=log(out[s1][s2] - savm[s1][s2]);
         }  
       }  
                } else if  (s2==-2) {
         for(i=(int)agemin; i <= (int)agemax+3; i++){            for (j=1,survp=0. ; j<=nlstate; j++) 
           for(jk=1; jk <=nlstate ; jk++){              survp += out[s1][j];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            lli= survp;
               pp[jk] += freq[jk][m][i];          }
           }          
           for(jk=1; jk <=nlstate ; jk++){          else if  (s2==-4) {
             for(m=-1, pos=0; m <=0 ; m++)            for (j=3,survp=0. ; j<=nlstate; j++) 
             pos += freq[jk][m][i];              survp += out[s1][j];
         }            lli= survp;
                  }
          for(jk=1; jk <=nlstate ; jk++){          
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          else if  (s2==-5) {
              pp[jk] += freq[jk][m][i];            for (j=1,survp=0. ; j<=2; j++) 
          }              survp += out[s1][j];
                      lli= survp;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          }
   
          for(jk=1; jk <=nlstate ; jk++){            
            if( i <= (int) agemax){          else{
              if(pos>=1.e-5){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                probs[i][jk][j1]= pp[jk]/pos;            /*  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 */
              }          } 
            }          /*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 */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    }  else if(mle==2){
   free_vector(pp,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }  /* End of Freq */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************* Waves Concatenation ***************/            for (j=1;j<=nlstate+ndeath;j++){
               oldm[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)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for(d=0; d<=dh[mi][i]; d++){
      Death is a valid wave (if date is known).            newm=savm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            for (kk=1; kk<=cptcovage;kk++) {
      and mw[mi+1][i]. dh depends on stepm.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, mi, m;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            savm=oldm;
      double sum=0., jmean=0.;*/            oldm=newm;
           } /* end mult */
   int j, k=0,jk, ju, jl;        
   double sum=0.;          s1=s[mw[mi][i]][i];
   jmin=1e+5;          s2=s[mw[mi+1][i]][i];
   jmax=-1;          bbh=(double)bh[mi][i]/(double)stepm; 
   jmean=0.;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   for(i=1; i<=imx; i++){          ipmx +=1;
     mi=0;          sw += weight[i];
     m=firstpass;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     while(s[m][i] <= nlstate){        } /* end of wave */
       if(s[m][i]>=1)      } /* end of individual */
         mw[++mi][i]=m;    }  else if(mle==3){  /* exponential inter-extrapolation */
       if(m >=lastpass)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         break;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else        for(mi=1; mi<= wav[i]-1; mi++){
         m++;          for (ii=1;ii<=nlstate+ndeath;ii++)
     }/* end while */            for (j=1;j<=nlstate+ndeath;j++){
     if (s[m][i] > nlstate){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       mi++;     /* Death is another wave */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */            }
          /* Only death is a correct wave */          for(d=0; d<dh[mi][i]; d++){
       mw[mi][i]=m;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     wav[i]=mi;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if(mi==0)            }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for(i=1; i<=imx; i++){            oldm=newm;
     for(mi=1; mi<wav[i];mi++){          } /* end mult */
       if (stepm <=0)        
         dh[mi][i]=1;          s1=s[mw[mi][i]][i];
       else{          s2=s[mw[mi+1][i]][i];
         if (s[mw[mi+1][i]][i] > nlstate) {          bbh=(double)bh[mi][i]/(double)stepm; 
           if (agedc[i] < 2*AGESUP) {          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 */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          ipmx +=1;
           if(j==0) j=1;  /* Survives at least one month after exam */          sw += weight[i];
           k=k+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if (j >= jmax) jmax=j;        } /* end of wave */
           if (j <= jmin) jmin=j;      } /* end of individual */
           sum=sum+j;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           /* if (j<10) printf("j=%d num=%d ",j,i); */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
         else{          for (ii=1;ii<=nlstate+ndeath;ii++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            for (j=1;j<=nlstate+ndeath;j++){
           k=k+1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (j >= jmax) jmax=j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           else if (j <= jmin)jmin=j;            }
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          for(d=0; d<dh[mi][i]; d++){
           sum=sum+j;            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         jk= j/stepm;            for (kk=1; kk<=cptcovage;kk++) {
         jl= j -jk*stepm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         ju= j -(jk+1)*stepm;            }
         if(jl <= -ju)          
           dh[mi][i]=jk;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           dh[mi][i]=jk+1;            savm=oldm;
         if(dh[mi][i]==0)            oldm=newm;
           dh[mi][i]=1; /* At least one step */          } /* end mult */
       }        
     }          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   jmean=sum/k;          if( s2 > nlstate){ 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            lli=log(out[s1][s2] - savm[s1][s2]);
  }          }else{
 /*********** Tricode ****************************/            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 void tricode(int *Tvar, int **nbcode, int imx)          }
 {          ipmx +=1;
   int Ndum[20],ij=1, k, j, i;          sw += weight[i];
   int cptcode=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   cptcoveff=0;  /*      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 */
   for (k=1; k<=7; k++) ncodemax[k]=0;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (i=1; i<=imx; i++) {        for(mi=1; mi<= wav[i]-1; mi++){
       ij=(int)(covar[Tvar[j]][i]);          for (ii=1;ii<=nlstate+ndeath;ii++)
       Ndum[ij]++;            for (j=1;j<=nlstate+ndeath;j++){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (ij > cptcode) cptcode=ij;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
           for(d=0; d<dh[mi][i]; d++){
     for (i=0; i<=cptcode; i++) {            newm=savm;
       if(Ndum[i]!=0) ncodemax[j]++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     ij=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
           
     for (i=1; i<=ncodemax[j]; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=0; k<=19; k++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (Ndum[k] != 0) {            savm=oldm;
           nbcode[Tvar[j]][ij]=k;            oldm=newm;
           ij++;          } /* end mult */
         }        
         if (ij > ncodemax[j]) break;          s1=s[mw[mi][i]][i];
       }            s2=s[mw[mi+1][i]][i];
     }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   }            ipmx +=1;
           sw += weight[i];
  for (k=0; k<19; k++) Ndum[k]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
  for (i=1; i<=ncovmodel-2; i++) {        } /* end of wave */
       ij=Tvar[i];      } /* end of individual */
       Ndum[ij]++;    } /* End of if */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  ij=1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  for (i=1; i<=10; i++) {    return -l;
    if((Ndum[i]!=0) && (i<=ncov)){  }
      Tvaraff[ij]=i;  
      ij++;  /*************** log-likelihood *************/
    }  double funcone( double *x)
  }  {
      /* Same as likeli but slower because of a lot of printf and if */
     cptcoveff=ij-1;    int i, ii, j, k, mi, d, kk;
 }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 /*********** Health Expectancies ****************/    double lli; /* Individual log likelihood */
     double llt;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    int s1, s2;
 {    double bbh, survp;
   /* Health expectancies */    /*extern weight */
   int i, j, nhstepm, hstepm, h;    /* We are differentiating ll according to initial status */
   double age, agelim,hf;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double ***p3mat;    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   fprintf(ficreseij,"# Health expectancies\n");    */
   fprintf(ficreseij,"# Age");    cov[1]=1.;
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   hstepm=1*YEARM; /*  Every j years of age (in month) */      for(mi=1; mi<= wav[i]-1; mi++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   agelim=AGESUP;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* nhstepm age range expressed in number of stepm */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for(d=0; d<dh[mi][i]; d++){
     /* Typically if 20 years = 20*12/6=40 stepm */          newm=savm;
     if (stepm >= YEARM) hstepm=1;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          for (kk=1; kk<=cptcovage;kk++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
           oldm=newm;
     for(i=1; i<=nlstate;i++)        } /* end mult */
       for(j=1; j<=nlstate;j++)        
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        s1=s[mw[mi][i]][i];
           eij[i][j][(int)age] +=p3mat[i][j][h];        s2=s[mw[mi+1][i]][i];
         }        bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
     hf=1;         * is higher than the multiple of stepm and negative otherwise.
     if (stepm >= YEARM) hf=stepm/YEARM;         */
     fprintf(ficreseij,"%.0f",age );        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     for(i=1; i<=nlstate;i++)          lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<=nlstate;j++){        } else if (mle==1){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }        } else if(mle==2){
     fprintf(ficreseij,"\n");          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 */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } else if(mle==3){  /* exponential inter-extrapolation */
   }          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 */
 }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
 /************ Variance ******************/        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
 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)          lli=log(out[s1][s2]); /* Original formula */
 {        } /* End of if */
   /* Variance of health expectancies */        ipmx +=1;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        sw += weight[i];
   double **newm;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **dnewm,**doldm;  /*       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 i, j, nhstepm, hstepm, h;        if(globpr){
   int k, cptcode;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   double *xp;   %10.6f %10.6f %10.6f ", \
   double **gp, **gm;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double ***gradg, ***trgradg;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double ***p3mat;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double age,agelim;            llt +=ll[k]*gipmx/gsw;
   int theta;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
    fprintf(ficresvij,"# Covariances of life expectancies\n");          fprintf(ficresilk," %10.6f\n", -llt);
   fprintf(ficresvij,"# Age");        }
   for(i=1; i<=nlstate;i++)      } /* end of wave */
     for(j=1; j<=nlstate;j++)    } /* end of individual */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   fprintf(ficresvij,"\n");    /* 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 */
   xp=vector(1,npar);    if(globpr==0){ /* First time we count the contributions and weights */
   dnewm=matrix(1,nlstate,1,npar);      gipmx=ipmx;
   doldm=matrix(1,nlstate,1,nlstate);      gsw=sw;
      }
   hstepm=1*YEARM; /* Every year of age */    return -l;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  }
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /*************** function likelione ***********/
     if (stepm >= YEARM) hstepm=1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* This routine should help understanding what is done with 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);       the selection of individuals/waves and
     gp=matrix(0,nhstepm,1,nlstate);       to check the exact contribution to the likelihood.
     gm=matrix(0,nhstepm,1,nlstate);       Plotting could be done.
      */
     for(theta=1; theta <=npar; theta++){    int k;
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    if(*globpri !=0){ /* Just counts and sums, no printings */
       }      strcpy(fileresilk,"ilk"); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        strcat(fileresilk,fileres);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
       if (popbased==1) {        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
            /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(j=1; j<= nlstate; j++){      for(k=1; k<=nlstate; k++) 
         for(h=0; h<=nhstepm; h++){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }  
       }    *fretone=(*funcone)(p);
        if(*globpri !=0){
       for(i=1; i<=npar; i++) /* Computes gradient */      fclose(ficresilk);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fflush(fichtm); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } 
     return;
       if (popbased==1) {  }
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  
       }  /*********** Maximum Likelihood Estimation ***************/
   
       for(j=1; j<= nlstate; j++){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         for(h=0; h<=nhstepm; h++){  {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    int i,j, iter;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double **xi;
         }    double fret;
       }    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
       for(j=1; j<= nlstate; j++)    xi=matrix(1,npar,1,npar);
         for(h=0; h<=nhstepm; h++){    for (i=1;i<=npar;i++)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      for (j=1;j<=npar;j++)
         }        xi[i][j]=(i==j ? 1.0 : 0.0);
     } /* End theta */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(h=0; h<=nhstepm; h++)      printf("Problem with resultfile: %s\n", filerespow);
       for(j=1; j<=nlstate;j++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         for(theta=1; theta <=npar; theta++)    }
           trgradg[h][j][theta]=gradg[h][theta][j];    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
     for(i=1;i<=nlstate;i++)      for(j=1;j<=nlstate+ndeath;j++)
       for(j=1;j<=nlstate;j++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         vareij[i][j][(int)age] =0.;    fprintf(ficrespow,"\n");
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    powell(p,xi,npar,ftol,&iter,&fret,func);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    fclose(ficrespow);
         for(i=1;i<=nlstate;i++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           for(j=1;j<=nlstate;j++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
             vareij[i][j][(int)age] += doldm[i][j];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
     }  }
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;  /**** Computes Hessian and covariance matrix ***/
     fprintf(ficresvij,"%.0f ",age );  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(i=1; i<=nlstate;i++)  {
       for(j=1; j<=nlstate;j++){    double  **a,**y,*x,pd;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double **hess;
       }    int i, j,jk;
     fprintf(ficresvij,"\n");    int *indx;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   } /* End age */    double gompertz(double p[]);
      hess=matrix(1,npar,1,npar);
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    printf("\nCalculation of the hessian matrix. Wait...\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
 }      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
 /************ Variance of prevlim ******************/     
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
 {      
   /* Variance of prevalence limit */      /*  printf(" %f ",p[i]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   double **newm;    }
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm;    for (i=1;i<=npar;i++) {
   int k, cptcode;      for (j=1;j<=npar;j++)  {
   double *xp;        if (j>i) { 
   double *gp, *gm;          printf(".%d%d",i,j);fflush(stdout);
   double **gradg, **trgradg;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double age,agelim;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   int theta;          
              hess[j][i]=hess[i][j];    
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          /*printf(" %lf ",hess[i][j]);*/
   fprintf(ficresvpl,"# Age");        }
   for(i=1; i<=nlstate;i++)      }
       fprintf(ficresvpl," %1d-%1d",i,i);    }
   fprintf(ficresvpl,"\n");    printf("\n");
     fprintf(ficlog,"\n");
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   doldm=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
      
   hstepm=1*YEARM; /* Every year of age */    a=matrix(1,npar,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    y=matrix(1,npar,1,npar);
   agelim = AGESUP;    x=vector(1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    indx=ivector(1,npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for (i=1;i<=npar;i++)
     if (stepm >= YEARM) hstepm=1;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    ludcmp(a,npar,indx,&pd);
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);    for (j=1;j<=npar;j++) {
     gm=vector(1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for(theta=1; theta <=npar; theta++){      lubksb(a,npar,indx,x);
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (i=1;i<=npar;i++){ 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        matcov[i][j]=x[i];
       }      }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];    printf("\n#Hessian matrix#\n");
        fprintf(ficlog,"\n#Hessian matrix#\n");
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=1;i<=npar;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        printf("%.3e ",hess[i][j]);
       for(i=1;i<=nlstate;i++)        fprintf(ficlog,"%.3e ",hess[i][j]);
         gm[i] = prlim[i][i];      }
       printf("\n");
       for(i=1;i<=nlstate;i++)      fprintf(ficlog,"\n");
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    }
     } /* End theta */  
     /* Recompute Inverse */
     trgradg =matrix(1,nlstate,1,npar);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(j=1; j<=nlstate;j++)    ludcmp(a,npar,indx,&pd);
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];    /*  printf("\n#Hessian matrix recomputed#\n");
   
     for(i=1;i<=nlstate;i++)    for (j=1;j<=npar;j++) {
       varpl[i][(int)age] =0.;      for (i=1;i<=npar;i++) x[i]=0;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      x[j]=1;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      lubksb(a,npar,indx,x);
     for(i=1;i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
     fprintf(ficresvpl,"%.0f ",age );        fprintf(ficlog,"%.3e ",y[i][j]);
     for(i=1; i<=nlstate;i++)      }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      printf("\n");
     fprintf(ficresvpl,"\n");      fprintf(ficlog,"\n");
     free_vector(gp,1,nlstate);    }
     free_vector(gm,1,nlstate);    */
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);    free_matrix(a,1,npar,1,npar);
   } /* End age */    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   free_vector(xp,1,npar);    free_ivector(indx,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(hess,1,npar,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   
 }  }
   
 /************ Variance of one-step probabilities  ******************/  /*************** hessian matrix ****************/
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  {
   int i, j;    int i;
   int k=0, cptcode;    int l=1, lmax=20;
   double **dnewm,**doldm;    double k1,k2;
   double *xp;    double p2[NPARMAX+1];
   double *gp, *gm;    double res;
   double **gradg, **trgradg;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double age,agelim, cov[NCOVMAX];    double fx;
   int theta;    int k=0,kmax=10;
   char fileresprob[FILENAMELENGTH];    double l1;
   
   strcpy(fileresprob,"prob");    fx=func(x);
   strcat(fileresprob,fileres);    for (i=1;i<=npar;i++) p2[i]=x[i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    for(l=0 ; l <=lmax; l++){
     printf("Problem with resultfile: %s\n", fileresprob);      l1=pow(10,l);
   }      delts=delt;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for(k=1 ; k <kmax; k=k+1){
          delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   xp=vector(1,npar);        k1=func(p2)-fx;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        p2[theta]=x[theta]-delt;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        k2=func(p2)-fx;
          /*res= (k1-2.0*fx+k2)/delt/delt; */
   cov[1]=1;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   for (age=bage; age<=fage; age ++){        
     cov[2]=age;  #ifdef DEBUG
     gradg=matrix(1,npar,1,9);        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);
     trgradg=matrix(1,9,1,npar);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  #endif
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for(theta=1; theta <=npar; theta++){          k=kmax;
       for(i=1; i<=npar; i++)        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                k=kmax; l=lmax*10.;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        }
            else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       k=0;          delts=delt;
       for(i=1; i<= (nlstate+ndeath); i++){        }
         for(j=1; j<=(nlstate+ndeath);j++){      }
            k=k+1;    }
           gp[k]=pmmij[i][j];    delti[theta]=delts;
         }    return res; 
       }    
   }
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
      {
     int i;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    int l=1, l1, lmax=20;
       k=0;    double k1,k2,k3,k4,res,fx;
       for(i=1; i<=(nlstate+ndeath); i++){    double p2[NPARMAX+1];
         for(j=1; j<=(nlstate+ndeath);j++){    int k;
           k=k+1;  
           gm[k]=pmmij[i][j];    fx=func(x);
         }    for (k=1; k<=2; k++) {
       }      for (i=1;i<=npar;i++) p2[i]=x[i];
            p2[thetai]=x[thetai]+delti[thetai]/k;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        k1=func(p2)-fx;
     }    
       p2[thetai]=x[thetai]+delti[thetai]/k;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(theta=1; theta <=npar; theta++)      k2=func(p2)-fx;
       trgradg[j][theta]=gradg[theta][j];    
        p2[thetai]=x[thetai]-delti[thetai]/k;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      k3=func(p2)-fx;
     
      pmij(pmmij,cov,ncovmodel,x,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      k=0;      k4=func(p2)-fx;
      for(i=1; i<=(nlstate+ndeath); i++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
        for(j=1; j<=(nlstate+ndeath);j++){  #ifdef DEBUG
          k=k+1;      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);
          gm[k]=pmmij[i][j];      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
      }    }
          return res;
      /*printf("\n%d ",(int)age);  }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
          /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  { 
      }*/    int i,imax,j,k; 
     double big,dum,sum,temp; 
   fprintf(ficresprob,"\n%d ",(int)age);    double *vv; 
    
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    vv=vector(1,n); 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    *d=1.0; 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    for (i=1;i<=n;i++) { 
   }      big=0.0; 
       for (j=1;j<=n;j++) 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        if ((temp=fabs(a[i][j])) > big) big=temp; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      vv[i]=1.0/big; 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    } 
 }    for (j=1;j<=n;j++) { 
  free_vector(xp,1,npar);      for (i=1;i<j;i++) { 
 fclose(ficresprob);        sum=a[i][j]; 
  exit(0);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 }        a[i][j]=sum; 
       } 
 /***********************************************/      big=0.0; 
 /**************** Main Program *****************/      for (i=j;i<=n;i++) { 
 /***********************************************/        sum=a[i][j]; 
         for (k=1;k<j;k++) 
 int main(int argc, char *argv[])          sum -= a[i][k]*a[k][j]; 
 {        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          big=dum; 
   double agedeb, agefin,hf;          imax=i; 
   double agemin=1.e20, agemax=-1.e20;        } 
       } 
   double fret;      if (j != imax) { 
   double **xi,tmp,delta;        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
   double dum; /* Dummy variable */          a[imax][k]=a[j][k]; 
   double ***p3mat;          a[j][k]=dum; 
   int *indx;        } 
   char line[MAXLINE], linepar[MAXLINE];        *d = -(*d); 
   char title[MAXLINE];        vv[imax]=vv[j]; 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      } 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      indx[j]=imax; 
        if (a[j][j] == 0.0) a[j][j]=TINY; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      if (j != n) { 
         dum=1.0/(a[j][j]); 
   char filerest[FILENAMELENGTH];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   char fileregp[FILENAMELENGTH];      } 
   char popfile[FILENAMELENGTH];    } 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    free_vector(vv,1,n);  /* Doesn't work */
   int firstobs=1, lastobs=10;  ;
   int sdeb, sfin; /* Status at beginning and end */  } 
   int c,  h , cpt,l;  
   int ju,jl, mi;  void lubksb(double **a, int n, int *indx, double b[]) 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  { 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int i,ii=0,ip,j; 
   int mobilav=0,popforecast=0;    double sum; 
   int hstepm, nhstepm;   
   int *popage;/*boolprev=0 if date and zero if wave*/    for (i=1;i<=n;i++) { 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;      ip=indx[i]; 
       sum=b[ip]; 
   double bage, fage, age, agelim, agebase;      b[ip]=b[i]; 
   double ftolpl=FTOL;      if (ii) 
   double **prlim;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double *severity;      else if (sum) ii=i; 
   double ***param; /* Matrix of parameters */      b[i]=sum; 
   double  *p;    } 
   double **matcov; /* Matrix of covariance */    for (i=n;i>=1;i--) { 
   double ***delti3; /* Scale */      sum=b[i]; 
   double *delti; /* Scale */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double ***eij, ***vareij;      b[i]=sum/a[i][i]; 
   double **varpl; /* Variances of prevalence limits by age */    } 
   double *epj, vepp;  } 
   double kk1, kk2;  
   double *popeffectif,*popcount;  /************ Frequencies ********************/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;  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[])
   double yp,yp1,yp2;  {  /* Some frequencies */
     
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    int first;
     double ***freq; /* Frequencies */
     double *pp, **prop;
   char z[1]="c", occ;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 #include <sys/time.h>    FILE *ficresp;
 #include <time.h>    char fileresp[FILENAMELENGTH];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    
      pp=vector(1,nlstate);
   /* long total_usecs;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   struct timeval start_time, end_time;    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   printf("\n%s",version);      exit(0);
   if(argc <=1){    }
     printf("\nEnter the parameter file name: ");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     scanf("%s",pathtot);    j1=0;
   }    
   else{    j=cptcoveff;
     strcpy(pathtot,argv[1]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    first=1;
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for(k1=1; k1<=j;k1++){
   /* cutv(path,optionfile,pathtot,'\\');*/      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          scanf("%d", i);*/
   chdir(path);        for (i=-5; i<=nlstate+ndeath; i++)  
   replace(pathc,path);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
 /*-------- arguments in the command line --------*/              freq[i][jk][m]=0;
   
   strcpy(fileres,"r");      for (i=1; i<=nlstate; i++)  
   strcat(fileres, optionfilefiname);        for(m=iagemin; m <= iagemax+3; m++)
   strcat(fileres,".txt");    /* Other files have txt extension */          prop[i][m]=0;
         
   /*---------arguments file --------*/        dateintsum=0;
         k2cpt=0;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for (i=1; i<=imx; i++) {
     printf("Problem with optionfile %s\n",optionfile);          bool=1;
     goto end;          if  (cptcovn>0) {
   }            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   strcpy(filereso,"o");                bool=0;
   strcat(filereso,fileres);          }
   if((ficparo=fopen(filereso,"w"))==NULL) {          if (bool==1){
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            for(m=firstpass; m<=lastpass; m++){
   }              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   /* Reads comments: lines beginning with '#' */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   while((c=getc(ficpar))=='#' && c!= EOF){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     ungetc(c,ficpar);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fgets(line, MAXLINE, ficpar);                if (m<lastpass) {
     puts(line);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     fputs(line,ficparo);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   }                }
   ungetc(c,ficpar);                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                  dateintsum=dateintsum+k2;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);                  k2cpt++;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);                }
 while((c=getc(ficpar))=='#' && c!= EOF){                /*}*/
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          }
     puts(line);        }
     fputs(line,ficparo);         
   }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   ungetc(c,ficpar);  fprintf(ficresp, "#Local time at start: %s", strstart);
          if  (cptcovn>0) {
              fprintf(ficresp, "\n#********** Variable "); 
   covar=matrix(0,NCOVMAX,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   cptcovn=0;          fprintf(ficresp, "**********\n#");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        }
         for(i=1; i<=nlstate;i++) 
   ncovmodel=2+cptcovn;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        fprintf(ficresp, "\n");
          
   /* Read guess parameters */        for(i=iagemin; i <= iagemax+3; i++){
   /* Reads comments: lines beginning with '#' */          if(i==iagemax+3){
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficlog,"Total");
     ungetc(c,ficpar);          }else{
     fgets(line, MAXLINE, ficpar);            if(first==1){
     puts(line);              first=0;
     fputs(line,ficparo);              printf("See log file for details...\n");
   }            }
   ungetc(c,ficpar);            fprintf(ficlog,"Age %d", i);
            }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for(jk=1; jk <=nlstate ; jk++){
     for(i=1; i <=nlstate; i++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for(j=1; j <=nlstate+ndeath-1; j++){              pp[jk] += freq[jk][m][i]; 
       fscanf(ficpar,"%1d%1d",&i1,&j1);          }
       fprintf(ficparo,"%1d%1d",i1,j1);          for(jk=1; jk <=nlstate ; jk++){
       printf("%1d%1d",i,j);            for(m=-1, pos=0; m <=0 ; m++)
       for(k=1; k<=ncovmodel;k++){              pos += freq[jk][m][i];
         fscanf(ficpar," %lf",&param[i][j][k]);            if(pp[jk]>=1.e-10){
         printf(" %lf",param[i][j][k]);              if(first==1){
         fprintf(ficparo," %lf",param[i][j][k]);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       }              }
       fscanf(ficpar,"\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       printf("\n");            }else{
       fprintf(ficparo,"\n");              if(first==1)
     }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            }
           }
   p=param[1][1];  
            for(jk=1; jk <=nlstate ; jk++){
   /* Reads comments: lines beginning with '#' */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   while((c=getc(ficpar))=='#' && c!= EOF){              pp[jk] += freq[jk][m][i];
     ungetc(c,ficpar);          }       
     fgets(line, MAXLINE, ficpar);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     puts(line);            pos += pp[jk];
     fputs(line,ficparo);            posprop += prop[jk][i];
   }          }
   ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              if(first==1)
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   for(i=1; i <=nlstate; i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(j=1; j <=nlstate+ndeath-1; j++){            }else{
       fscanf(ficpar,"%1d%1d",&i1,&j1);              if(first==1)
       printf("%1d%1d",i,j);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficparo,"%1d%1d",i1,j1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(k=1; k<=ncovmodel;k++){            }
         fscanf(ficpar,"%le",&delti3[i][j][k]);            if( i <= iagemax){
         printf(" %le",delti3[i][j][k]);              if(pos>=1.e-5){
         fprintf(ficparo," %le",delti3[i][j][k]);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       }                /*probs[i][jk][j1]= pp[jk]/pos;*/
       fscanf(ficpar,"\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]);*/
       printf("\n");              }
       fprintf(ficparo,"\n");              else
     }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   }            }
   delti=delti3[1][1];          }
            
   /* Reads comments: lines beginning with '#' */          for(jk=-1; jk <=nlstate+ndeath; jk++)
   while((c=getc(ficpar))=='#' && c!= EOF){            for(m=-1; m <=nlstate+ndeath; m++)
     ungetc(c,ficpar);              if(freq[jk][m][i] !=0 ) {
     fgets(line, MAXLINE, ficpar);              if(first==1)
     puts(line);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     fputs(line,ficparo);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   }              }
   ungetc(c,ficpar);          if(i <= iagemax)
              fprintf(ficresp,"\n");
   matcov=matrix(1,npar,1,npar);          if(first==1)
   for(i=1; i <=npar; i++){            printf("Others in log...\n");
     fscanf(ficpar,"%s",&str);          fprintf(ficlog,"\n");
     printf("%s",str);        }
     fprintf(ficparo,"%s",str);      }
     for(j=1; j <=i; j++){    }
       fscanf(ficpar," %le",&matcov[i][j]);    dateintmean=dateintsum/k2cpt; 
       printf(" %.5le",matcov[i][j]);   
       fprintf(ficparo," %.5le",matcov[i][j]);    fclose(ficresp);
     }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     fscanf(ficpar,"\n");    free_vector(pp,1,nlstate);
     printf("\n");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     fprintf(ficparo,"\n");    /* End of Freq */
   }  }
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  /************ Prevalence ********************/
       matcov[i][j]=matcov[j][i];  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
      {  
   printf("\n");    /* 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).
        We still use firstpass and lastpass as another selection.
     /*-------- data file ----------*/    */
     if((ficres =fopen(fileres,"w"))==NULL) {   
       printf("Problem with resultfile: %s\n", fileres);goto end;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     }    double ***freq; /* Frequencies */
     fprintf(ficres,"#%s\n",version);    double *pp, **prop;
        double pos,posprop; 
     if((fic=fopen(datafile,"r"))==NULL)    {    double  y2; /* in fractional years */
       printf("Problem with datafile: %s\n", datafile);goto end;    int iagemin, iagemax;
     }  
     iagemin= (int) agemin;
     n= lastobs;    iagemax= (int) agemax;
     severity = vector(1,maxwav);    /*pp=vector(1,nlstate);*/
     outcome=imatrix(1,maxwav+1,1,n);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     num=ivector(1,n);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     moisnais=vector(1,n);    j1=0;
     annais=vector(1,n);    
     moisdc=vector(1,n);    j=cptcoveff;
     andc=vector(1,n);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     agedc=vector(1,n);    
     cod=ivector(1,n);    for(k1=1; k1<=j;k1++){
     weight=vector(1,n);      for(i1=1; i1<=ncodemax[k1];i1++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        j1++;
     mint=matrix(1,maxwav,1,n);        
     anint=matrix(1,maxwav,1,n);        for (i=1; i<=nlstate; i++)  
     s=imatrix(1,maxwav+1,1,n);          for(m=iagemin; m <= iagemax+3; m++)
     adl=imatrix(1,maxwav+1,1,n);                prop[i][m]=0.0;
     tab=ivector(1,NCOVMAX);       
     ncodemax=ivector(1,8);        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
     i=1;          if  (cptcovn>0) {
     while (fgets(line, MAXLINE, fic) != NULL)    {            for (z1=1; z1<=cptcoveff; z1++) 
       if ((i >= firstobs) && (i <=lastobs)) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                        bool=0;
         for (j=maxwav;j>=1;j--){          } 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          if (bool==1) { 
           strcpy(line,stra);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                        if(agev[m][i]==1) agev[m][i]=iagemax+2;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              }
         for (j=ncov;j>=1;j--){            } /* end selection of waves */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }        }
         num[i]=atol(stra);        for(i=iagemin; i <= iagemax+3; i++){  
                  
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           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;}*/            posprop += prop[jk][i]; 
           } 
         i=i+1;  
       }          for(jk=1; jk <=nlstate ; jk++){     
     }            if( i <=  iagemax){ 
     /* printf("ii=%d", ij);              if(posprop>=1.e-5){ 
        scanf("%d",i);*/                probs[i][jk][j1]= prop[jk][i]/posprop;
   imx=i-1; /* Number of individuals */              } 
             } 
   /* for (i=1; i<=imx; i++){          }/* end jk */ 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        }/* end i */ 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      } /* end i1 */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    } /* end k1 */
     }    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     for (i=1; i<=imx; i++)    /*free_vector(pp,1,nlstate);*/
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);  /************* Waves Concatenation ***************/
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);  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)
   Tvard=imatrix(1,15,1,2);  {
   Tage=ivector(1,15);          /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           Death is a valid wave (if date is known).
   if (strlen(model) >1){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     j=0, j1=0, k1=1, k2=1;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     j=nbocc(model,'+');       and mw[mi+1][i]. dh depends on stepm.
     j1=nbocc(model,'*');       */
     cptcovn=j+1;  
     cptcovprod=j1;    int i, mi, m;
        /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           double sum=0., jmean=0.;*/
     strcpy(modelsav,model);    int first;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    int j, k=0,jk, ju, jl;
       printf("Error. Non available option model=%s ",model);    double sum=0.;
       goto end;    first=0;
     }    jmin=1e+5;
        jmax=-1;
     for(i=(j+1); i>=1;i--){    jmean=0.;
       cutv(stra,strb,modelsav,'+');    for(i=1; i<=imx; i++){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      mi=0;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      m=firstpass;
       /*scanf("%d",i);*/      while(s[m][i] <= nlstate){
       if (strchr(strb,'*')) {        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         cutv(strd,strc,strb,'*');          mw[++mi][i]=m;
         if (strcmp(strc,"age")==0) {        if(m >=lastpass)
           cptcovprod--;          break;
           cutv(strb,stre,strd,'V');        else
           Tvar[i]=atoi(stre);          m++;
           cptcovage++;      }/* end while */
             Tage[cptcovage]=i;      if (s[m][i] > nlstate){
             /*printf("stre=%s ", stre);*/        mi++;     /* Death is another wave */
         }        /* if(mi==0)  never been interviewed correctly before death */
         else if (strcmp(strd,"age")==0) {           /* Only death is a correct wave */
           cptcovprod--;        mw[mi][i]=m;
           cutv(strb,stre,strc,'V');      }
           Tvar[i]=atoi(stre);  
           cptcovage++;      wav[i]=mi;
           Tage[cptcovage]=i;      if(mi==0){
         }        nbwarn++;
         else {        if(first==0){
           cutv(strb,stre,strc,'V');          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           Tvar[i]=ncov+k1;          first=1;
           cutv(strb,strc,strd,'V');        }
           Tprod[k1]=i;        if(first==1){
           Tvard[k1][1]=atoi(strc);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           Tvard[k1][2]=atoi(stre);        }
           Tvar[cptcovn+k2]=Tvard[k1][1];      } /* end mi==0 */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    } /* End individuals */
           for (k=1; k<=lastobs;k++)  
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    for(i=1; i<=imx; i++){
           k1++;      for(mi=1; mi<wav[i];mi++){
           k2=k2+2;        if (stepm <=0)
         }          dh[mi][i]=1;
       }        else{
       else {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            if (agedc[i] < 2*AGESUP) {
        /*  scanf("%d",i);*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       cutv(strd,strc,strb,'V');              if(j==0) j=1;  /* Survives at least one month after exam */
       Tvar[i]=atoi(strc);              else if(j<0){
       }                nberr++;
       strcpy(modelsav,stra);                  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]);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                j=1; /* Temporary Dangerous patch */
         scanf("%d",i);*/                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);
                }
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);              k=k+1;
   printf("cptcovprod=%d ", cptcovprod);              if (j >= jmax){
   scanf("%d ",i);*/                jmax=j;
     fclose(fic);                ijmax=i;
               }
     /*  if(mle==1){*/              if (j <= jmin){
     if (weightopt != 1) { /* Maximisation without weights*/                jmin=j;
       for(i=1;i<=n;i++) weight[i]=1.0;                ijmin=i;
     }              }
     /*-calculation of age at interview from date of interview and age at death -*/              sum=sum+j;
     agev=matrix(1,maxwav,1,imx);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
    for (i=1; i<=imx; i++)            }
      for(m=2; (m<= maxwav); m++)          }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          else{
          anint[m][i]=9999;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
          s[m][i]=-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;
     for (i=1; i<=imx; i++)  {            if (j >= jmax) {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              jmax=j;
       for(m=1; (m<= maxwav); m++){              ijmax=i;
         if(s[m][i] >0){            }
           if (s[m][i] == nlstate+1) {            else if (j <= jmin){
             if(agedc[i]>0)              jmin=j;
               if(moisdc[i]!=99 && andc[i]!=9999)              ijmin=i;
               agev[m][i]=agedc[i];            }
             else {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
               if (andc[i]!=9999){            /*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]);*/
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            if(j<0){
               agev[m][i]=-1;              nberr++;
               }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }              fprintf(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]);
           }            }
           else if(s[m][i] !=9){ /* Should no more exist */            sum=sum+j;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          }
             if(mint[m][i]==99 || anint[m][i]==9999)          jk= j/stepm;
               agev[m][i]=1;          jl= j -jk*stepm;
             else if(agev[m][i] <agemin){          ju= j -(jk+1)*stepm;
               agemin=agev[m][i];          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/            if(jl==0){
             }              dh[mi][i]=jk;
             else if(agev[m][i] >agemax){              bh[mi][i]=0;
               agemax=agev[m][i];            }else{ /* We want a negative bias in order to only have interpolation ie
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                    * at the price of an extra matrix product in likelihood */
             }              dh[mi][i]=jk+1;
             /*agev[m][i]=anint[m][i]-annais[i];*/              bh[mi][i]=ju;
             /*   agev[m][i] = age[i]+2*m;*/            }
           }          }else{
           else { /* =9 */            if(jl <= -ju){
             agev[m][i]=1;              dh[mi][i]=jk;
             s[m][i]=-1;              bh[mi][i]=jl;       /* bias is positive if real duration
           }                                   * is higher than the multiple of stepm and negative otherwise.
         }                                   */
         else /*= 0 Unknown */            }
           agev[m][i]=1;            else{
       }              dh[mi][i]=jk+1;
                  bh[mi][i]=ju;
     }            }
     for (i=1; i<=imx; i++)  {            if(dh[mi][i]==0){
       for(m=1; (m<= maxwav); m++){              dh[mi][i]=1; /* At least one step */
         if (s[m][i] > (nlstate+ndeath)) {              bh[mi][i]=ju; /* At least one step */
           printf("Error: Wrong value in nlstate or ndeath\n");                /*  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);*/
           goto end;            }
         }          } /* end if mle */
       }        }
     }      } /* end wave */
     }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    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);
     free_vector(severity,1,maxwav);    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);
     free_imatrix(outcome,1,maxwav+1,1,n);   }
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);  /*********** Tricode ****************************/
     /* free_matrix(mint,1,maxwav,1,n);  void tricode(int *Tvar, int **nbcode, int imx)
        free_matrix(anint,1,maxwav,1,n);*/  {
     free_vector(moisdc,1,n);    
     free_vector(andc,1,n);    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
        cptcoveff=0; 
     wav=ivector(1,imx);   
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    for (k=1; k<=7; k++) ncodemax[k]=0;
      
     /* Concatenates waves */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       Tcode=ivector(1,100);        Ndum[ij]++; /*store the modality */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       ncodemax[1]=1;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                                         Tvar[j]. If V=sex and male is 0 and 
                                               female is 1, then  cptcode=1.*/
    codtab=imatrix(1,100,1,10);      }
    h=0;  
    m=pow(2,cptcoveff);      for (i=0; i<=cptcode; i++) {
          if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
    for(k=1;k<=cptcoveff; k++){      }
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){      ij=1; 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      for (i=1; i<=ncodemax[j]; i++) {
            h++;        for (k=0; k<= maxncov; k++) {
            if (h>m) h=1;codtab[h][k]=j;          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; 
    /*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");   for (k=0; k< maxncov; k++) Ndum[k]=0;
    }  
    scanf("%d",i);*/   for (i=1; i<=ncovmodel-2; i++) { 
         /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    /* Calculates basic frequencies. Computes observed prevalence at single age     ij=Tvar[i];
        and prints on file fileres'p'. */     Ndum[ij]++;
    }
      
       ij=1;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   for (i=1; i<= maxncov; i++) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     if((Ndum[i]!=0) && (i<=ncovcol)){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       Tvaraff[ij]=i; /*For printing */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       ij++;
     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] */   cptcoveff=ij-1; /*Number of simple covariates*/
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  }
   
     if(mle==1){  /*********** Health Expectancies ****************/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  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[] )
      
     /*--------- results files --------------*/  {
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    /* Health expectancies */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
    jk=1;    double ***p3mat,***varhe;
    fprintf(ficres,"# Parameters\n");    double **dnewm,**doldm;
    printf("# Parameters\n");    double *xp;
    for(i=1,jk=1; i <=nlstate; i++){    double **gp, **gm;
      for(k=1; k <=(nlstate+ndeath); k++){    double ***gradg, ***trgradg;
        if (k != i)    int theta;
          {  
            printf("%d%d ",i,k);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            fprintf(ficres,"%1d%1d ",i,k);    xp=vector(1,npar);
            for(j=1; j <=ncovmodel; j++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
              printf("%f ",p[jk]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
              fprintf(ficres,"%f ",p[jk]);    
              jk++;    fprintf(ficreseij,"# Local time at start: %s", strstart);
            }    fprintf(ficreseij,"# Health expectancies\n");
            printf("\n");    fprintf(ficreseij,"# Age");
            fprintf(ficres,"\n");    for(i=1; i<=nlstate;i++)
          }      for(j=1; j<=nlstate;j++)
      }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
    }    fprintf(ficreseij,"\n");
  if(mle==1){  
     /* Computing hessian and covariance matrix */    if(estepm < stepm){
     ftolhess=ftol; /* Usually correct */      printf ("Problem %d lower than %d\n",estepm, stepm);
     hesscov(matcov, p, npar, delti, ftolhess, func);    }
  }    else  hstepm=estepm;   
     fprintf(ficres,"# Scales\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
     printf("# Scales\n");     * This is mainly to measure the difference between two models: for example
      for(i=1,jk=1; i <=nlstate; i++){     * if stepm=24 months pijx are given only every 2 years and by summing them
       for(j=1; j <=nlstate+ndeath; j++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
         if (j!=i) {     * progression in between and thus overestimating or underestimating according
           fprintf(ficres,"%1d%1d",i,j);     * to the curvature of the survival function. If, for the same date, we 
           printf("%1d%1d",i,j);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           for(k=1; k<=ncovmodel;k++){     * to compare the new estimate of Life expectancy with the same linear 
             printf(" %.5e",delti[jk]);     * hypothesis. A more precise result, taking into account a more precise
             fprintf(ficres," %.5e",delti[jk]);     * curvature will be obtained if estepm is as small as stepm. */
             jk++;  
           }    /* For example we decided to compute the life expectancy with the smallest unit */
           printf("\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficres,"\n");       nhstepm is the number of hstepm from age to agelim 
         }       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
      }       and note for a fixed period like estepm months */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     k=1;       survival function given by stepm (the optimization length). Unfortunately it
     fprintf(ficres,"# Covariance\n");       means that if the survival funtion is printed only each two years of age and if
     printf("# Covariance\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     for(i=1;i<=npar;i++){       results. So we changed our mind and took the option of the best precision.
       /*  if (k>nlstate) k=1;    */
       i1=(i-1)/(ncovmodel*nlstate)+1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    agelim=AGESUP;
       fprintf(ficres,"%3d",i);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       printf("%3d",i);      /* nhstepm age range expressed in number of stepm */
       for(j=1; j<=i;j++){      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         fprintf(ficres," %.5e",matcov[i][j]);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         printf(" %.5e",matcov[i][j]);      /* if (stepm >= YEARM) hstepm=1;*/
       }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficres,"\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       k++;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
      
     while((c=getc(ficpar))=='#' && c!= EOF){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       ungetc(c,ficpar);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       fgets(line, MAXLINE, ficpar);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       puts(line);   
       fputs(line,ficparo);  
     }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     ungetc(c,ficpar);  
        /* Computing  Variances of health expectancies */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
           for(theta=1; theta <=npar; theta++){
     if (fage <= 2) {        for(i=1; i<=npar; i++){ 
       bage = agemin;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fage = agemax;        }
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        cptj=0;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        for(j=1; j<= nlstate; j++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
     while((c=getc(ficpar))=='#' && c!= EOF){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     ungetc(c,ficpar);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }
     fputs(line,ficparo);        }
   }       
   ungetc(c,ficpar);       
          for(i=1; i<=npar; i++) 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);        
              cptj=0;
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<= nlstate; j++){
     ungetc(c,ficpar);          for(i=1;i<=nlstate;i++){
     fgets(line, MAXLINE, ficpar);            cptj=cptj+1;
     puts(line);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     fputs(line,ficparo);  
   }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   ungetc(c,ficpar);            }
            }
         }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        for(j=1; j<= nlstate*nlstate; j++)
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   fscanf(ficpar,"pop_based=%d\n",&popbased);          }
    fprintf(ficparo,"pop_based=%d\n",popbased);         } 
    fprintf(ficres,"pop_based=%d\n",popbased);       
   /* End theta */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);       for(h=0; h<=nhstepm-1; h++)
     fputs(line,ficparo);        for(j=1; j<=nlstate*nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
   ungetc(c,ficpar);            trgradg[h][j][theta]=gradg[h][theta][j];
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);       
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);       for(i=1;i<=nlstate*nlstate;i++)
         for(j=1;j<=nlstate*nlstate;j++)
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);          varhe[i][j][(int)age] =0.;
   
           printf("%d|",(int)age);fflush(stdout);
     /*------------ gnuplot -------------*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     /*chdir(pathcd);*/       for(h=0;h<=nhstepm-1;h++){
     strcpy(optionfilegnuplot,optionfilefiname);        for(k=0;k<=nhstepm-1;k++){
     strcat(optionfilegnuplot,".plt");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       printf("Problem with file %s",optionfilegnuplot);goto end;          for(i=1;i<=nlstate*nlstate;i++)
     }            for(j=1;j<=nlstate*nlstate;j++)
 #ifdef windows              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     fprintf(ficgp,"cd \"%s\" \n",pathc);        }
 #endif      }
 m=pow(2,cptcoveff);      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
  /* 1eme*/        for(j=1; j<=nlstate;j++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
    for (k1=1; k1<= m ; k1 ++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
 #ifdef windows  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);  
 #endif          }
 #ifdef unix  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      fprintf(ficreseij,"%3.0f",age );
 #endif      cptj=0;
       for(i=1; i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate;j++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          cptj++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 }        }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficreseij,"\n");
     for (i=1; i<= nlstate ; i ++) {     
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      for (i=1; i<= nlstate ; i ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    printf("\n");
 }      fprintf(ficlog,"\n");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    free_vector(xp,1,npar);
 fprintf(ficgp,"\nset ter gif small size 400,300");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 #endif    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }  }
   }  
   /*2 eme*/  /************ 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 (k1=1; k1<= m ; k1 ++) {  {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    /* Variance of health expectancies */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     for (i=1; i<= nlstate+1 ; i ++) {    /* double **newm;*/
       k=2*i;    double **dnewm,**doldm;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double **dnewmp,**doldmp;
       for (j=1; j<= nlstate+1 ; j ++) {    int i, j, nhstepm, hstepm, h, nstepm ;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int k, cptcode;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *xp;
 }      double **gp, **gm;  /* for var eij */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double ***gradg, ***trgradg; /*for var eij */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double **gradgp, **trgradgp; /* for var p point j */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double *gpp, *gmp; /* for var p point j */
       for (j=1; j<= nlstate+1 ; j ++) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***p3mat;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double age,agelim, hf;
 }      double ***mobaverage;
       fprintf(ficgp,"\" t\"\" w l 0,");    int theta;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    char digit[4];
       for (j=1; j<= nlstate+1 ; j ++) {    char digitp[25];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    char fileresprobmorprev[FILENAMELENGTH];
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    if(popbased==1){
       else fprintf(ficgp,"\" t\"\" w l 0,");      if(mobilav!=0)
     }        strcpy(digitp,"-populbased-mobilav-");
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      else strcpy(digitp,"-populbased-nomobil-");
   }    }
      else 
   /*3eme*/      strcpy(digitp,"-stablbased-");
   
   for (k1=1; k1<= m ; k1 ++) {    if (mobilav!=0) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       k=2+nlstate*(cpt-1);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       for (i=1; i< nlstate ; i ++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      }
       }    }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }    strcpy(fileresprobmorprev,"prmorprev"); 
   }    sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   /* CV preval stat */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   for (k1=1; k1<= m ; k1 ++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for (cpt=1; cpt<nlstate ; cpt ++) {    strcat(fileresprobmorprev,fileres);
       k=3;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       for (i=1; i< nlstate ; i ++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         fprintf(ficgp,"+$%d",k+i+1);    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         
       l=3+(nlstate+ndeath)*cpt;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
       for (i=1; i< nlstate ; i ++) {    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
         l=3+(nlstate+ndeath)*cpt;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         fprintf(ficgp,"+$%d",l+i+1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       }      fprintf(ficresprobmorprev," p.%-d SE",j);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }    }  
   }      fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   /* proba elementaires */    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    for(i=1,jk=1; i <=nlstate; i++){    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");
     for(k=1; k <=(nlstate+ndeath); k++){    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       if (k != i) {  /*   } */
         for(j=1; j <=ncovmodel; j++){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/   fprintf(ficresvij, "#Local time at start: %s", strstart);
           /*fprintf(ficgp,"%s",alph[1]);*/    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(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficresvij,"# Age");
           jk++;    for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"\n");      for(j=1; j<=nlstate;j++)
         }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
       }    fprintf(ficresvij,"\n");
     }  
     }    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   for(jk=1; jk <=m; jk++) {    doldm=matrix(1,nlstate,1,nlstate);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
    i=1;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      for(k=1; k<=(nlstate+ndeath); k++) {    gpp=vector(nlstate+1,nlstate+ndeath);
        if (k != k2){    gmp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 ij=1;    
         for(j=3; j <=ncovmodel; j++) {    if(estepm < stepm){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      printf ("Problem %d lower than %d\n",estepm, stepm);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }
             ij++;    else  hstepm=estepm;   
           }    /* For example we decided to compute the life expectancy with the smallest unit */
           else    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       nhstepm is the number of hstepm from age to agelim 
         }       nstepm is the number of stepm from age to agelin. 
           fprintf(ficgp,")/(1");       Look at hpijx to understand the reason of that which relies in memory size
               and note for a fixed period like k years */
         for(k1=1; k1 <=nlstate; k1++){      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);       survival function given by stepm (the optimization length). Unfortunately it
 ij=1;       means that if the survival funtion is printed every two years of age and if
           for(j=3; j <=ncovmodel; j++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       results. So we changed our mind and took the option of the best precision.
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    */
             ij++;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           }    agelim = AGESUP;
           else    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      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 */
           fprintf(ficgp,")");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      gp=matrix(0,nhstepm,1,nlstate);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      gm=matrix(0,nhstepm,1,nlstate);
         i=i+ncovmodel;  
        }  
      }      for(theta=1; theta <=npar; theta++){
    }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fclose(ficgp);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* end gnuplot */  
            if (popbased==1) {
 chdir(path);          if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
     free_ivector(wav,1,imx);              prlim[i][i]=probs[(int)age][i][ij];
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          }else{ /* mobilav */ 
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              for(i=1; i<=nlstate;i++)
     free_ivector(num,1,n);              prlim[i][i]=mobaverage[(int)age][i][ij];
     free_vector(agedc,1,n);          }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        }
     fclose(ficparo);    
     fclose(ficres);        for(j=1; j<= nlstate; j++){
     /*  }*/          for(h=0; h<=nhstepm; h++){
                for(i=1, gp[h][j]=0.;i<=nlstate;i++)
    /*________fin mle=1_________*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
         }
          /* This for computing probability of death (h=1 means
     /* No more information from the sample is required now */           computed over hstepm matrices product = hstepm*stepm months) 
   /* Reads comments: lines beginning with '#' */           as a weighted average of prlim.
   while((c=getc(ficpar))=='#' && c!= EOF){        */
     ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     puts(line);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fputs(line,ficparo);        }    
   }        /* end probability of death */
   ungetc(c,ficpar);  
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 /*--------- index.htm --------*/   
         if (popbased==1) {
   strcpy(optionfilehtm,optionfile);          if(mobilav ==0){
   strcat(optionfilehtm,".htm");            for(i=1; i<=nlstate;i++)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {              prlim[i][i]=probs[(int)age][i][ij];
     printf("Problem with %s \n",optionfilehtm);goto end;          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          }
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        }
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        for(j=1; j<= nlstate; j++){
 <hr  size=\"2\" color=\"#EC5E5E\">          for(h=0; h<=nhstepm; h++){
 <li>Outputs files<br><br>\n            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          }
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        /* This for computing probability of death (h=1 means
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>           computed over hstepm matrices product = hstepm*stepm months) 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>           as a weighted average of prlim.
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>          for(i=1,gmp[j]=0.; i<= nlstate; i++)
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        }    
         /* end probability of death */
  fprintf(fichtm," <li>Graphs</li><p>");  
         for(j=1; j<= nlstate; j++) /* vareij */
  m=cptcoveff;          for(h=0; h<=nhstepm; h++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
  j1=0;  
  for(k1=1; k1<=m;k1++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    for(i1=1; i1<=ncodemax[k1];i1++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        j1++;        }
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      } /* End theta */
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }      for(h=0; h<=nhstepm; h++) /* veij */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        for(j=1; j<=nlstate;j++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              for(theta=1; theta <=npar; theta++)
        for(cpt=1; cpt<nlstate;cpt++){            trgradg[h][j][theta]=gradg[h][theta][j];
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
        }        for(theta=1; theta <=npar; theta++)
     for(cpt=1; cpt<=nlstate;cpt++) {          trgradgp[j][theta]=gradgp[theta][j];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      }      for(i=1;i<=nlstate;i++)
      for(cpt=1; cpt<=nlstate;cpt++) {        for(j=1;j<=nlstate;j++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          vareij[i][j][(int)age] =0.;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }      for(h=0;h<=nhstepm;h++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(k=0;k<=nhstepm;k++){
 health expectancies in states (1) and (2): e%s%d.gif<br>          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 fprintf(fichtm,"\n</body>");          for(i=1;i<=nlstate;i++)
    }            for(j=1;j<=nlstate;j++)
  }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 fclose(fichtm);        }
       }
   /*--------------- Prevalence limit --------------*/    
        /* pptj */
   strcpy(filerespl,"pl");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   strcat(filerespl,fileres);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   }          varppt[j][i]=doldmp[j][i];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      /* end ppptj */
   fprintf(ficrespl,"#Prevalence limit\n");      /*  x centered again */
   fprintf(ficrespl,"#Age ");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   fprintf(ficrespl,"\n");   
        if (popbased==1) {
   prlim=matrix(1,nlstate,1,nlstate);        if(mobilav ==0){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1; i<=nlstate;i++)
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            prlim[i][i]=probs[(int)age][i][ij];
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }else{ /* mobilav */ 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1; i<=nlstate;i++)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            prlim[i][i]=mobaverage[(int)age][i][ij];
   k=0;        }
   agebase=agemin;      }
   agelim=agemax;               
   ftolpl=1.e-10;      /* This for computing probability of death (h=1 means
   i1=cptcoveff;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   if (cptcovn < 1){i1=1;}         as a weighted average of prlim.
       */
   for(cptcov=1;cptcov<=i1;cptcov++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         k=k+1;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      }    
         fprintf(ficrespl,"\n#******");      /* end probability of death */
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         fprintf(ficrespl,"******\n");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for (age=agebase; age<=agelim; age++){        for(i=1; i<=nlstate;i++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           fprintf(ficrespl,"%.0f",age );        }
           for(i=1; i<=nlstate;i++)      } 
           fprintf(ficrespl," %.5f", prlim[i][i]);      fprintf(ficresprobmorprev,"\n");
           fprintf(ficrespl,"\n");  
         }      fprintf(ficresvij,"%.0f ",age );
       }      for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++){
   fclose(ficrespl);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
   /*------------- h Pij x at various ages ------------*/      fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      free_matrix(gm,0,nhstepm,1,nlstate);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing pij: result on file '%s' \n", filerespij);    } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_vector(gmp,nlstate+1,nlstate+ndeath);
   /*if (stepm<=24) stepsize=2;*/    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   agelim=AGESUP;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   hstepm=stepsize*YEARM; /* Every year of age */    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   k=0;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   for(cptcov=1;cptcov<=i1;cptcov++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       k=k+1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         fprintf(ficrespij,"\n#****** ");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         for(j=1;j<=cptcoveff;j++)    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         fprintf(ficrespij,"******\n");    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
          */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(xp,1,npar);
           oldm=oldms;savm=savms;    free_matrix(doldm,1,nlstate,1,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      free_matrix(dnewm,1,nlstate,1,npar);
           fprintf(ficrespij,"# Age");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(i=1; i<=nlstate;i++)    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             for(j=1; j<=nlstate+ndeath;j++)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               fprintf(ficrespij," %1d-%1d",i,j);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrespij,"\n");    fclose(ficresprobmorprev);
           for (h=0; h<=nhstepm; h++){    fflush(ficgp);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fflush(fichtm); 
             for(i=1; i<=nlstate;i++)  }  /* end varevsij */
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  /************ Variance of prevlim ******************/
             fprintf(ficrespij,"\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[])
           }  {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* Variance of prevalence limit */
           fprintf(ficrespij,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         }    double **newm;
     }    double **dnewm,**doldm;
   }    int i, j, nhstepm, hstepm;
     int k, cptcode;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    double *xp;
     double *gp, *gm;
   fclose(ficrespij);    double **gradg, **trgradg;
     double age,agelim;
   if(stepm == 1) {    int theta;
   /*---------- Forecasting ------------------*/    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
   /*printf("calage= %f", calagedate);*/    for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
   strcpy(fileresf,"f");    dnewm=matrix(1,nlstate,1,npar);
   strcat(fileresf,fileres);    doldm=matrix(1,nlstate,1,nlstate);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    hstepm=1*YEARM; /* Every year of age */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   printf("Computing forecasting: result on file '%s' \n", fileresf);    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   free_matrix(mint,1,maxwav,1,n);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   free_matrix(anint,1,maxwav,1,n);      if (stepm >= YEARM) hstepm=1;
   free_matrix(agev,1,maxwav,1,imx);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   /* Mobile average */      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      gm=vector(1,nlstate);
   
   if (mobilav==1) {      for(theta=1; theta <=npar; theta++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1; i<=npar; i++){ /* Computes gradient */
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (i=1; i<=nlstate;i++)        }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           mobaverage[(int)agedeb][i][cptcod]=0.;        for(i=1;i<=nlstate;i++)
              gp[i] = prlim[i][i];
     for (agedeb=bage+4; agedeb<=fage; agedeb++){      
       for (i=1; i<=nlstate;i++){        for(i=1; i<=npar; i++) /* Computes gradient */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for (cpt=0;cpt<=4;cpt++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for(i=1;i<=nlstate;i++)
           }          gm[i] = prlim[i][i];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }        for(i=1;i<=nlstate;i++)
       }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     }        } /* End theta */
   }  
       trgradg =matrix(1,nlstate,1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
   agelim=AGESUP;          trgradg[j][theta]=gradg[theta][j];
   /*hstepm=stepsize*YEARM; *//* Every year of age */  
   hstepm=1;      for(i=1;i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        varpl[i][(int)age] =0.;
   yp1=modf(dateintmean,&yp);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   anprojmean=yp;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   yp2=modf((yp1*12),&yp);      for(i=1;i<=nlstate;i++)
   mprojmean=yp;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;      fprintf(ficresvpl,"%.0f ",age );
   if(jprojmean==0) jprojmean=1;      for(i=1; i<=nlstate;i++)
   if(mprojmean==0) jprojmean=1;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
   if (popforecast==1) {      free_matrix(gradg,1,npar,1,nlstate);
     if((ficpop=fopen(popfile,"r"))==NULL)    {      free_matrix(trgradg,1,nlstate,1,npar);
       printf("Problem with population file : %s\n",popfile);goto end;    } /* End age */
     }  
     popage=ivector(0,AGESUP);    free_vector(xp,1,npar);
     popeffectif=vector(0,AGESUP);    free_matrix(doldm,1,nlstate,1,npar);
     popcount=vector(0,AGESUP);    free_matrix(dnewm,1,nlstate,1,nlstate);
   
     i=1;    }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)  
       {  /************ Variance of one-step probabilities  ******************/
         i=i+1;  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[])
       }  {
     imx=i;    int i, j=0,  i1, k1, l1, t, tj;
        int k2, l2, j1,  z1;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    int k=0,l, cptcode;
   }    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   for(cptcov=1;cptcov<=i1;cptcov++){    double **dnewm,**doldm;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double *xp;
       k=k+1;    double *gp, *gm;
       fprintf(ficresf,"\n#******");    double **gradg, **trgradg;
       for(j=1;j<=cptcoveff;j++) {    double **mu;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double age,agelim, cov[NCOVMAX];
       }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       fprintf(ficresf,"******\n");    int theta;
       fprintf(ficresf,"# StartingAge FinalAge");    char fileresprob[FILENAMELENGTH];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    char fileresprobcov[FILENAMELENGTH];
       if (popforecast==1)  fprintf(ficresf," [Population]");    char fileresprobcor[FILENAMELENGTH];
      
       for (cpt=0; cpt<4;cpt++) {    double ***varpij;
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      printf("Problem with resultfile: %s\n", fileresprob);
         nhstepm = nhstepm/hstepm;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    }
     strcpy(fileresprobcov,"probcov"); 
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresprobcov,fileres);
         oldm=oldms;savm=savms;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf("Problem with resultfile: %s\n", fileresprobcov);
              fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         for (h=0; h<=nhstepm; h++){    }
           if (h==(int) (calagedate+YEARM*cpt)) {    strcpy(fileresprobcor,"probcor"); 
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    strcat(fileresprobcor,fileres);
           }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           for(j=1; j<=nlstate+ndeath;j++) {      printf("Problem with resultfile: %s\n", fileresprobcor);
             kk1=0.;kk2=0;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
             for(i=1; i<=nlstate;i++) {            }
               if (mobilav==1)    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
               else {    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
               }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficresprob, "#Local time at start: %s", strstart);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
             }    fprintf(ficresprob,"# Age");
              fprintf(ficresprobcov, "#Local time at start: %s", strstart);
             if (h==(int)(calagedate+12*cpt)){    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
               fprintf(ficresf," %.3f", kk1);    fprintf(ficresprobcov,"# Age");
                  fprintf(ficresprobcor, "#Local time at start: %s", strstart);
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
             }    fprintf(ficresprobcov,"# Age");
           }  
         }  
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=(nlstate+ndeath);j++){
       }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }  
   if (popforecast==1) {   /* fprintf(ficresprob,"\n");
     free_ivector(popage,0,AGESUP);    fprintf(ficresprobcov,"\n");
     free_vector(popeffectif,0,AGESUP);    fprintf(ficresprobcor,"\n");
     free_vector(popcount,0,AGESUP);   */
   }   xp=vector(1,npar);
   free_imatrix(s,1,maxwav+1,1,n);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   free_vector(weight,1,n);*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   fclose(ficresf);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   }/* End forecasting */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   else{    first=1;
     erreur=108;    fprintf(ficgp,"\n# Routine varprob");
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   }    fprintf(fichtm,"\n");
   
   /*---------- Health expectancies and variances ------------*/    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\
   strcpy(filerest,"t");    file %s<br>\n",optionfilehtmcov);
   strcat(filerest,fileres);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   if((ficrest=fopen(filerest,"w"))==NULL) {  and drawn. It helps understanding how is the covariance between two incidences.\
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
   strcpy(filerese,"e");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   strcat(filerese,fileres);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   if((ficreseij=fopen(filerese,"w"))==NULL) {  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    cov[1]=1;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
  strcpy(fileresv,"v");    j1=0;
   strcat(fileresv,fileres);    for(t=1; t<=tj;t++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      for(i1=1; i1<=ncodemax[t];i1++){ 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        j1++;
   }        if  (cptcovn>0) {
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   k=0;          fprintf(ficresprob, "**********\n#\n");
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresprobcov, "\n#********** Variable "); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=k+1;          fprintf(ficresprobcov, "**********\n#\n");
       fprintf(ficrest,"\n#****** ");          
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp, "\n#********** Variable "); 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficrest,"******\n");          fprintf(ficgp, "**********\n#\n");
           
       fprintf(ficreseij,"\n#****** ");          
       for(j=1;j<=cptcoveff;j++)          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficreseij,"******\n");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
       fprintf(ficresvij,"\n#****** ");          fprintf(ficresprobcor, "\n#********** Variable ");    
       for(j=1;j<=cptcoveff;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficresprobcor, "**********\n#");    
       fprintf(ficresvij,"******\n");        }
         
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for (age=bage; age<=fage; age ++){ 
       oldm=oldms;savm=savms;          cov[2]=age;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            for (k=1; k<=cptcovn;k++) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       oldm=oldms;savm=savms;          }
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                for (k=1; k<=cptcovprod;k++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          
       fprintf(ficrest,"\n");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                  trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       hf=1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
       if (stepm >= YEARM) hf=stepm/YEARM;          gm=vector(1,(nlstate)*(nlstate+ndeath));
       epj=vector(1,nlstate+1);      
       for(age=bage; age <=fage ;age++){          for(theta=1; theta <=npar; theta++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            for(i=1; i<=npar; i++)
         if (popbased==1) {              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
           for(i=1; i<=nlstate;i++)            
             prlim[i][i]=probs[(int)age][i][k];            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         }            
                    k=0;
         fprintf(ficrest," %.0f",age);            for(i=1; i<= (nlstate); i++){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              for(j=1; j<=(nlstate+ndeath);j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                k=k+1;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                gp[k]=pmmij[i][j];
           }              }
           epj[nlstate+1] +=epj[j];            }
         }            
         for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1; i<=npar; i++)
           for(j=1;j <=nlstate;j++)              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
             vepp += vareij[i][j][(int)age];      
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         for(j=1;j <=nlstate;j++){            k=0;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));            for(i=1; i<=(nlstate); i++){
         }              for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrest,"\n");                k=k+1;
       }                gm[k]=pmmij[i][j];
     }              }
   }            }
               
                    for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
  fclose(ficreseij);  
  fclose(ficresvij);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   fclose(ficrest);            for(theta=1; theta <=npar; theta++)
   fclose(ficpar);              trgradg[j][theta]=gradg[theta][j];
   free_vector(epj,1,nlstate+1);          
   /*  scanf("%d ",i); */          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);
   /*------- Variance limit prevalence------*/            free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
 strcpy(fileresvpl,"vpl");          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   strcat(fileresvpl,fileres);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     exit(0);          
   }          k=0;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
  k=0;              k=k+1;
  for(cptcov=1;cptcov<=i1;cptcov++){              mu[k][(int) age]=pmmij[i][j];
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            }
      k=k+1;          }
      fprintf(ficresvpl,"\n#****** ");          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
      for(j=1;j<=cptcoveff;j++)            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              varpij[i][j][(int)age] = doldm[i][j];
      fprintf(ficresvpl,"******\n");  
                /*printf("\n%d ",(int)age);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      oldm=oldms;savm=savms;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    }            }*/
  }  
           fprintf(ficresprob,"\n%d ",(int)age);
   fclose(ficresvpl);          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
              fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          i=0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          for (k=1; k<=(nlstate);k++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            for (l=1; l<=(nlstate+ndeath);l++){ 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);              i=i++;
                fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   free_matrix(matcov,1,npar,1,npar);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   free_vector(delti,1,npar);              for (j=1; j<=i;j++){
                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
   if(erreur >0)            }
     printf("End of Imach with error %d\n",erreur);          }/* end of loop for state */
   else   printf("End of Imach\n");        } /* end of loop for age */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
          /* Confidence intervalle of pij  */
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        /*
   /*printf("Total time was %d uSec.\n", total_usecs);*/          fprintf(ficgp,"\nset noparametric;unset label");
   /*------ End -----------*/          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
  end:          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
 #ifdef windows          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   /* chdir(pathcd);*/          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
 #endif        */
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
  /*system("cd ../gp37mgw");*/        first1=1;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        for (k2=1; k2<=(nlstate);k2++){
  strcpy(plotcmd,GNUPLOTPROGRAM);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
  strcat(plotcmd," ");            if(l2==k2) continue;
  strcat(plotcmd,optionfilegnuplot);            j=(k2-1)*(nlstate+ndeath)+l2;
  system(plotcmd);            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
 #ifdef windows                if(l1==k1) continue;
   while (z[0] != 'q') {                i=(k1-1)*(nlstate+ndeath)+l1;
     chdir(path);                if(i<=j) continue;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                for (age=bage; age<=fage; age ++){ 
     scanf("%s",z);                  if ((int)age %5==0){
     if (z[0] == 'c') system("./imach");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     else if (z[0] == 'e') {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       chdir(path);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       system(optionfilehtm);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     }                    mu2=mu[j][(int) age]/stepm*YEARM;
     else if (z[0] == 'q') exit(0);                    c12=cv12/sqrt(v1*v2);
   }                    /* Computing eigen value of matrix of covariance */
 #endif                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     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: ");
       scanf("%s",pathtot);
     }
     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.1.24  
changed lines
  Added in v.1.113


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