Diff for /imach/src/imach.c between versions 1.29 and 1.112

version 1.29, 2002/03/06 19:02:50 version 1.112, 2006/01/30 09:55:26
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.112  2006/01/30 09:55:26  brouard
      (Module): Back to gnuplot.exe instead of wgnuplot.exe
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.111  2006/01/25 20:38:18  brouard
   first survey ("cross") where individuals from different ages are    (Module): Lots of cleaning and bugs added (Gompertz)
   interviewed on their health status or degree of disability (in the    (Module): Comments can be added in data file. Missing date values
   case of a health survey which is our main interest) -2- at least a    can be a simple dot '.'.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.110  2006/01/25 00:51:50  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  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.109  2006/01/24 19:37:15  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): Comments (lines starting with a #) are allowed in data.
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.108  2006/01/19 18:05:42  lievre
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Gnuplot problem appeared...
   'age' is age and 'sex' is a covariate. If you want to have a more    To be fixed
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.107  2006/01/19 16:20:37  brouard
   you to do it.  More covariates you add, slower the    Test existence of gnuplot in imach path
   convergence.  
     Revision 1.106  2006/01/19 13:24:36  brouard
   The advantage of this computer programme, compared to a simple    Some cleaning and links added in html output
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.105  2006/01/05 20:23:19  lievre
   intermediate interview, the information is lost, but taken into    *** empty log message ***
   account using an interpolation or extrapolation.    
     Revision 1.104  2005/09/30 16:11:43  lievre
   hPijx is the probability to be observed in state i at age x+h    (Module): sump fixed, loop imx fixed, and simplifications.
   conditional to the observed state i at age x. The delay 'h' can be    (Module): If the status is missing at the last wave but we know
   split into an exact number (nh*stepm) of unobserved intermediate    that the person is alive, then we can code his/her status as -2
   states. This elementary transition (by month or quarter trimester,    (instead of missing=-1 in earlier versions) and his/her
   semester or year) is model as a multinomial logistic.  The hPx    contributions to the likelihood is 1 - Prob of dying from last
   matrix is simply the matrix product of nh*stepm elementary matrices    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   and the contribution of each individual to the likelihood is simply    the healthy state at last known wave). Version is 0.98
   hPijx.  
     Revision 1.103  2005/09/30 15:54:49  lievre
   Also this programme outputs the covariance matrix of the parameters but also    (Module): sump fixed, loop imx fixed, and simplifications.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.102  2004/09/15 17:31:30  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Add the possibility to read data file including tab characters.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.101  2004/09/15 10:38:38  brouard
   from the European Union.    Fix on curr_time
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.100  2004/07/12 18:29:06  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Add version for Mac OS X. Just define UNIX in Makefile
   **********************************************************************/  
      Revision 1.99  2004/06/05 08:57:40  brouard
 #include <math.h>    *** empty log message ***
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.98  2004/05/16 15:05:56  brouard
 #include <unistd.h>    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 #define MAXLINE 256    state at each age, but using a Gompertz model: log u =a + b*age .
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    This is the basic analysis of mortality and should be done before any
 #define FILENAMELENGTH 80    other analysis, in order to test if the mortality estimated from the
 /*#define DEBUG*/    cross-longitudinal survey is different from the mortality estimated
 #define windows    from other sources like vital statistic data.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    The same imach parameter file can be used but the option for mle should be -3.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Agnès, who wrote this part of the code, tried to keep most of the
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    former routines in order to include the new code within the former code.
   
 #define NINTERVMAX 8    The output is very simple: only an estimate of the intercept and of
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    the slope with 95% confident intervals.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Current limitations:
 #define MAXN 20000    A) Even if you enter covariates, i.e. with the
 #define YEARM 12. /* Number of months per year */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define AGESUP 130    B) There is no computation of Life Expectancy nor Life Table.
 #define AGEBASE 40  
     Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 int erreur; /* Error number */    suppressed.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.96  2003/07/15 15:38:55  brouard
 int npar=NPARMAX;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 int nlstate=2; /* Number of live states */    rewritten within the same printf. Workaround: many printfs.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.95  2003/07/08 07:54:34  brouard
 int popbased=0;    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 int *wav; /* Number of waves for this individuual 0 is possible */    matrix (cov(a12,c31) instead of numbers.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.94  2003/06/27 13:00:02  brouard
 int mle, weightopt;    Just cleaning
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.93  2003/06/25 16:33:55  brouard
 double jmean; /* Mean space between 2 waves */    (Module): On windows (cygwin) function asctime_r doesn't
 double **oldm, **newm, **savm; /* Working pointers to matrices */    exist so I changed back to asctime which exists.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Version 0.96b
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.92  2003/06/25 16:30:45  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;  
   char fileresv[FILENAMELENGTH];    Revision 1.91  2003/06/25 15:30:29  brouard
  FILE  *ficresvpl;    * imach.c (Repository): Duplicated warning errors corrected.
   char fileresvpl[FILENAMELENGTH];    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 #define NR_END 1    is stamped in powell.  We created a new html file for the graphs
 #define FREE_ARG char*    concerning matrix of covariance. It has extension -cov.htm.
 #define FTOL 1.0e-10  
     Revision 1.90  2003/06/24 12:34:15  brouard
 #define NRANSI    (Module): Some bugs corrected for windows. Also, when
 #define ITMAX 200    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 #define TOL 2.0e-4  
     Revision 1.89  2003/06/24 12:30:52  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 1.88  2003/06/23 17:54:56  brouard
 #define GLIMIT 100.0    * 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 TINY 1.0e-20  
     Revision 1.87  2003/06/18 12:26:01  brouard
 static double maxarg1,maxarg2;    Version 0.96
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.86  2003/06/17 20:04:08  brouard
      (Module): Change position of html and gnuplot routines and added
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    routine fileappend.
 #define rint(a) floor(a+0.5)  
     Revision 1.85  2003/06/17 13:12:43  brouard
 static double sqrarg;    * imach.c (Repository): Check when date of death was earlier that
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    current date of interview. It may happen when the death was just
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 int imx;    assuming that the date of death was just one stepm after the
 int stepm;    interview.
 /* Stepm, step in month: minimum step interpolation*/    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 int m,nb;    memory allocation. But we also truncated to 8 characters (left
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    truncation)
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Repository): No more line truncation errors.
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 double *weight;    place. It differs from routine "prevalence" which may be called
 int **s; /* Status */    many times. Probs is memory consuming and must be used with
 double *agedc, **covar, idx;    parcimony.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.83  2003/06/10 13:39:11  lievre
 double ftolhess; /* Tolerance for computing hessian */    *** empty log message ***
   
 /**************** split *************************/    Revision 1.82  2003/06/05 15:57:20  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Add log in  imach.c and  fullversion number is now printed.
 {  
    char *s;                             /* pointer */  */
    int  l1, l2;                         /* length counters */  /*
      Interpolated Markov Chain
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Short summary of the programme:
 #ifdef windows    
    s = strrchr( path, '\\' );           /* find last / */    This program computes Healthy Life Expectancies from
 #else    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    s = strrchr( path, '/' );            /* find last / */    first survey ("cross") where individuals from different ages are
 #endif    interviewed on their health status or degree of disability (in the
    if ( s == NULL ) {                   /* no directory, so use current */    case of a health survey which is our main interest) -2- at least a
 #if     defined(__bsd__)                /* get current working directory */    second wave of interviews ("longitudinal") which measure each change
       extern char       *getwd( );    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
       if ( getwd( dirc ) == NULL ) {    model. More health states you consider, more time is necessary to reach the
 #else    Maximum Likelihood of the parameters involved in the model.  The
       extern char       *getcwd( );    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    conditional to be observed in state i at the first wave. Therefore
 #endif    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
          return( GLOCK_ERROR_GETCWD );    'age' is age and 'sex' is a covariate. If you want to have a more
       }    complex model than "constant and age", you should modify the program
       strcpy( name, path );             /* we've got it */    where the markup *Covariates have to be included here again* invites
    } else {                             /* strip direcotry from path */    you to do it.  More covariates you add, slower the
       s++;                              /* after this, the filename */    convergence.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    The advantage of this computer programme, compared to a simple
       strcpy( name, s );                /* save file name */    multinomial logistic model, is clear when the delay between waves is not
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    identical for each individual. Also, if a individual missed an
       dirc[l1-l2] = 0;                  /* add zero */    intermediate interview, the information is lost, but taken into
    }    account using an interpolation or extrapolation.  
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    hPijx is the probability to be observed in state i at age x+h
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    conditional to the observed state i at age x. The delay 'h' can be
 #else    split into an exact number (nh*stepm) of unobserved intermediate
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    states. This elementary transition (by month, quarter,
 #endif    semester or year) is modelled as a multinomial logistic.  The hPx
    s = strrchr( name, '.' );            /* find last / */    matrix is simply the matrix product of nh*stepm elementary matrices
    s++;    and the contribution of each individual to the likelihood is simply
    strcpy(ext,s);                       /* save extension */    hPijx.
    l1= strlen( name);  
    l2= strlen( s)+1;    Also this programme outputs the covariance matrix of the parameters but also
    strncpy( finame, name, l1-l2);    of the life expectancies. It also computes the stable prevalence. 
    finame[l1-l2]= 0;    
    return( 0 );                         /* we're done */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 }             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 /******************************************/    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 void replace(char *s, char*t)    can be accessed at http://euroreves.ined.fr/imach .
 {  
   int i;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int lg=20;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   i=0;    
   lg=strlen(t);    **********************************************************************/
   for(i=0; i<= lg; i++) {  /*
     (s[i] = t[i]);    main
     if (t[i]== '\\') s[i]='/';    read parameterfile
   }    read datafile
 }    concatwav
     freqsummary
 int nbocc(char *s, char occ)    if (mle >= 1)
 {      mlikeli
   int i,j=0;    print results files
   int lg=20;    if mle==1 
   i=0;       computes hessian
   lg=strlen(s);    read end of parameter file: agemin, agemax, bage, fage, estepm
   for(i=0; i<= lg; i++) {        begin-prev-date,...
   if  (s[i] == occ ) j++;    open gnuplot file
   }    open html file
   return j;    stable prevalence
 }     for age prevalim()
     h Pij x
 void cutv(char *u,char *v, char*t, char occ)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   int i,lg,j,p=0;    health expectancies
   i=0;    Variance-covariance of DFLE
   for(j=0; j<=strlen(t)-1; j++) {    prevalence()
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;     movingaverage()
   }    varevsij() 
     if popbased==1 varevsij(,popbased)
   lg=strlen(t);    total life expectancies
   for(j=0; j<p; j++) {    Variance of stable prevalence
     (u[j] = t[j]);   end
   }  */
      u[p]='\0';  
   
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);   
   }  #include <math.h>
 }  #include <stdio.h>
   #include <stdlib.h>
 /********************** nrerror ********************/  #include <string.h>
   #include <unistd.h>
 void nrerror(char error_text[])  
 {  #include <limits.h>
   fprintf(stderr,"ERREUR ...\n");  #include <sys/types.h>
   fprintf(stderr,"%s\n",error_text);  #include <sys/stat.h>
   exit(1);  #include <errno.h>
 }  extern int errno;
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  /* #include <sys/time.h> */
 {  #include <time.h>
   double *v;  #include "timeval.h"
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  /* #include <libintl.h> */
   return v-nl+NR_END;  /* #define _(String) gettext (String) */
 }  
   #define MAXLINE 256
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  #define GNUPLOTPROGRAM "gnuplot"
 {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free((FREE_ARG)(v+nl-NR_END));  #define FILENAMELENGTH 132
 }  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /************************ivector *******************************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 int *ivector(long nl,long nh)  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   int *v;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  #define NINTERVMAX 8
   return v-nl+NR_END;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 /******************free ivector **************************/  #define MAXN 20000
 void free_ivector(int *v, long nl, long nh)  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   free((FREE_ARG)(v+nl-NR_END));  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /******************* imatrix *******************************/  #define DIRSEPARATOR '/'
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define CHARSEPARATOR "/"
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define ODIRSEPARATOR '\\'
 {  #else
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define DIRSEPARATOR '\\'
   int **m;  #define CHARSEPARATOR "\\"
    #define ODIRSEPARATOR '/'
   /* allocate pointers to rows */  #endif
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /* $Id$ */
   m += NR_END;  /* $State$ */
   m -= nrl;  
    char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
    char fullversion[]="$Revision$ $Date$"; 
   /* allocate rows and set pointers to them */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int nvar;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m[nrl] += NR_END;  int npar=NPARMAX;
   m[nrl] -= ncl;  int nlstate=2; /* Number of live states */
    int ndeath=1; /* Number of dead states */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
   /* return pointer to array of pointers to rows */  
   return m;  int *wav; /* Number of waves for this individuual 0 is possible */
 }  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 /****************** free_imatrix *************************/  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 void free_imatrix(m,nrl,nrh,ncl,nch)  int gipmx, gsw; /* Global variables on the number of contributions 
       int **m;                     to the likelihood and the sum of weights (done by funcone)*/
       long nch,ncl,nrh,nrl;  int mle, weightopt;
      /* free an int matrix allocated by imatrix() */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   free((FREE_ARG) (m+nrl-NR_END));             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 }  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 /******************* matrix *******************************/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 {  FILE *ficlog, *ficrespow;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int globpr; /* Global variable for printing or not */
   double **m;  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double sw; /* Sum of weights */
   if (!m) nrerror("allocation failure 1 in matrix()");  char filerespow[FILENAMELENGTH];
   m += NR_END;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   m -= nrl;  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  FILE *ficresprobmorprev;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *fichtm, *fichtmcov; /* Html File */
   m[nrl] += NR_END;  FILE *ficreseij;
   m[nrl] -= ncl;  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char fileresv[FILENAMELENGTH];
   return m;  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /*************************free matrix ************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char command[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char fileregp[FILENAMELENGTH];
   double ***m;  char popfile[FILENAMELENGTH];
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m -= nrl;  struct timezone tzp;
   extern int gettimeofday();
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  long time_value;
   m[nrl] += NR_END;  extern long time();
   m[nrl] -= ncl;  char strcurr[80], strfor[80];
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char *endptr;
   long lval;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define NR_END 1
   m[nrl][ncl] += NR_END;  #define FREE_ARG char*
   m[nrl][ncl] -= nll;  #define FTOL 1.0e-10
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  #define NRANSI 
    #define ITMAX 200 
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define TOL 2.0e-4 
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define CGOLD 0.3819660 
   }  #define ZEPS 1.0e-10 
   return m;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /*************************free ma3x ************************/  #define GLIMIT 100.0 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define TINY 1.0e-20 
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  static double maxarg1,maxarg2;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   free((FREE_ARG)(m+nrl-NR_END));  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /***************** f1dim *************************/  #define rint(a) floor(a+0.5)
 extern int ncom;  
 extern double *pcom,*xicom;  static double sqrarg;
 extern double (*nrfunc)(double []);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 double f1dim(double x)  int agegomp= AGEGOMP;
 {  
   int j;  int imx; 
   double f;  int stepm=1;
   double *xt;  /* Stepm, step in month: minimum step interpolation*/
    
   xt=vector(1,ncom);  int estepm;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  int m,nb;
   return f;  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /*****************brent *************************/  double **pmmij, ***probs;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double *ageexmed,*agecens;
 {  double dateintmean=0;
   int iter;  
   double a,b,d,etemp;  double *weight;
   double fu,fv,fw,fx;  int **s; /* Status */
   double ftemp;  double *agedc, **covar, idx;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double e=0.0;  double *lsurv, *lpop, *tpop;
    
   a=(ax < cx ? ax : cx);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   b=(ax > cx ? ax : cx);  double ftolhess; /* Tolerance for computing hessian */
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  /**************** split *************************/
   for (iter=1;iter<=ITMAX;iter++) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     xm=0.5*(a+b);  {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     printf(".");fflush(stdout);    */ 
 #ifdef DEBUG    char  *ss;                            /* pointer */
     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);    int   l1, l2;                         /* length counters */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    l1 = strlen(path );                   /* length of path */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       *xmin=x;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       return fx;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     }      strcpy( name, path );               /* we got the fullname name because no directory */
     ftemp=fu;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     if (fabs(e) > tol1) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       r=(x-w)*(fx-fv);      /* get current working directory */
       q=(x-v)*(fx-fw);      /*    extern  char* getcwd ( char *buf , int len);*/
       p=(x-v)*q-(x-w)*r;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       q=2.0*(q-r);        return( GLOCK_ERROR_GETCWD );
       if (q > 0.0) p = -p;      }
       q=fabs(q);      /* got dirc from getcwd*/
       etemp=e;      printf(" DIRC = %s \n",dirc);
       e=d;    } else {                              /* strip direcotry from path */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      ss++;                               /* after this, the filename */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      l2 = strlen( ss );                  /* length of filename */
       else {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         d=p/q;      strcpy( name, ss );         /* save file name */
         u=x+d;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         if (u-a < tol2 || b-u < tol2)      dirc[l1-l2] = 0;                    /* add zero */
           d=SIGN(tol1,xm-x);      printf(" DIRC2 = %s \n",dirc);
       }    }
     } else {    /* We add a separator at the end of dirc if not exists */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    l1 = strlen( dirc );                  /* length of directory */
     }    if( dirc[l1-1] != DIRSEPARATOR ){
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      dirc[l1] =  DIRSEPARATOR;
     fu=(*f)(u);      dirc[l1+1] = 0; 
     if (fu <= fx) {      printf(" DIRC3 = %s \n",dirc);
       if (u >= x) a=x; else b=x;    }
       SHFT(v,w,x,u)    ss = strrchr( name, '.' );            /* find last / */
         SHFT(fv,fw,fx,fu)    if (ss >0){
         } else {      ss++;
           if (u < x) a=u; else b=u;      strcpy(ext,ss);                     /* save extension */
           if (fu <= fw || w == x) {      l1= strlen( name);
             v=w;      l2= strlen(ss)+1;
             w=u;      strncpy( finame, name, l1-l2);
             fv=fw;      finame[l1-l2]= 0;
             fw=fu;    }
           } else if (fu <= fv || v == x || v == w) {  
             v=u;    return( 0 );                          /* we're done */
             fv=fu;  }
           }  
         }  
   }  /******************************************/
   nrerror("Too many iterations in brent");  
   *xmin=x;  void replace_back_to_slash(char *s, char*t)
   return fx;  {
 }    int i;
     int lg=0;
 /****************** mnbrak ***********************/    i=0;
     lg=strlen(t);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    for(i=0; i<= lg; i++) {
             double (*func)(double))      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   double ulim,u,r,q, dum;    }
   double fu;  }
    
   *fa=(*func)(*ax);  int nbocc(char *s, char occ)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    int i,j=0;
     SHFT(dum,*ax,*bx,dum)    int lg=20;
       SHFT(dum,*fb,*fa,dum)    i=0;
       }    lg=strlen(s);
   *cx=(*bx)+GOLD*(*bx-*ax);    for(i=0; i<= lg; i++) {
   *fc=(*func)(*cx);    if  (s[i] == occ ) j++;
   while (*fb > *fc) {    }
     r=(*bx-*ax)*(*fb-*fc);    return j;
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  void cutv(char *u,char *v, char*t, char occ)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       fu=(*func)(u);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     } else if ((*cx-u)*(u-ulim) > 0.0) {       gives u="abcedf" and v="ghi2j" */
       fu=(*func)(u);    int i,lg,j,p=0;
       if (fu < *fc) {    i=0;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    for(j=0; j<=strlen(t)-1; j++) {
           SHFT(*fb,*fc,fu,(*func)(u))      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           }    }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    lg=strlen(t);
       fu=(*func)(u);    for(j=0; j<p; j++) {
     } else {      (u[j] = t[j]);
       u=(*cx)+GOLD*(*cx-*bx);    }
       fu=(*func)(u);       u[p]='\0';
     }  
     SHFT(*ax,*bx,*cx,u)     for(j=0; j<= lg; j++) {
       SHFT(*fa,*fb,*fc,fu)      if (j>=(p+1))(v[j-p-1] = t[j]);
       }    }
 }  }
   
 /*************** linmin ************************/  /********************** nrerror ********************/
   
 int ncom;  void nrerror(char error_text[])
 double *pcom,*xicom;  {
 double (*nrfunc)(double []);    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    exit(EXIT_FAILURE);
 {  }
   double brent(double ax, double bx, double cx,  /*********************** vector *******************/
                double (*f)(double), double tol, double *xmin);  double *vector(int nl, int nh)
   double f1dim(double x);  {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    double *v;
               double *fc, double (*func)(double));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   int j;    if (!v) nrerror("allocation failure in vector");
   double xx,xmin,bx,ax;    return v-nl+NR_END;
   double fx,fb,fa;  }
    
   ncom=n;  /************************ free vector ******************/
   pcom=vector(1,n);  void free_vector(double*v, int nl, int nh)
   xicom=vector(1,n);  {
   nrfunc=func;    free((FREE_ARG)(v+nl-NR_END));
   for (j=1;j<=n;j++) {  }
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /************************ivector *******************************/
   }  int *ivector(long nl,long nh)
   ax=0.0;  {
   xx=1.0;    int *v;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  /******************free ivector **************************/
     xi[j] *= xmin;  void free_ivector(int *v, long nl, long nh)
     p[j] += xi[j];  {
   }    free((FREE_ARG)(v+nl-NR_END));
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 /*************** powell ************************/  {
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    long *v;
             double (*func)(double []))    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 {    if (!v) nrerror("allocation failure in ivector");
   void linmin(double p[], double xi[], int n, double *fret,    return v-nl+NR_END;
               double (*func)(double []));  }
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  /******************free lvector **************************/
   double fp,fptt;  void free_lvector(long *v, long nl, long nh)
   double *xits;  {
   pt=vector(1,n);    free((FREE_ARG)(v+nl-NR_END));
   ptt=vector(1,n);  }
   xit=vector(1,n);  
   xits=vector(1,n);  /******************* imatrix *******************************/
   *fret=(*func)(p);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for (j=1;j<=n;j++) pt[j]=p[j];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (*iter=1;;++(*iter)) {  { 
     fp=(*fret);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     ibig=0;    int **m; 
     del=0.0;    
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    /* allocate pointers to rows */ 
     for (i=1;i<=n;i++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       printf(" %d %.12f",i, p[i]);    if (!m) nrerror("allocation failure 1 in matrix()"); 
     printf("\n");    m += NR_END; 
     for (i=1;i<=n;i++) {    m -= nrl; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    
       fptt=(*fret);    
 #ifdef DEBUG    /* allocate rows and set pointers to them */ 
       printf("fret=%lf \n",*fret);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       printf("%d",i);fflush(stdout);    m[nrl] += NR_END; 
       linmin(p,xit,n,fret,func);    m[nrl] -= ncl; 
       if (fabs(fptt-(*fret)) > del) {    
         del=fabs(fptt-(*fret));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         ibig=i;    
       }    /* return pointer to array of pointers to rows */ 
 #ifdef DEBUG    return m; 
       printf("%d %.12e",i,(*fret));  } 
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /****************** free_imatrix *************************/
         printf(" x(%d)=%.12e",j,xit[j]);  void free_imatrix(m,nrl,nrh,ncl,nch)
       }        int **m;
       for(j=1;j<=n;j++)        long nch,ncl,nrh,nrl; 
         printf(" p=%.12e",p[j]);       /* free an int matrix allocated by imatrix() */ 
       printf("\n");  { 
 #endif    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     }    free((FREE_ARG) (m+nrl-NR_END)); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  } 
 #ifdef DEBUG  
       int k[2],l;  /******************* matrix *******************************/
       k[0]=1;  double **matrix(long nrl, long nrh, long ncl, long nch)
       k[1]=-1;  {
       printf("Max: %.12e",(*func)(p));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       for (j=1;j<=n;j++)    double **m;
         printf(" %.12e",p[j]);  
       printf("\n");    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for(l=0;l<=1;l++) {    if (!m) nrerror("allocation failure 1 in matrix()");
         for (j=1;j<=n;j++) {    m += NR_END;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    m -= nrl;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
 #endif    m[nrl] -= ncl;
   
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       free_vector(xit,1,n);    return m;
       free_vector(xits,1,n);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       free_vector(ptt,1,n);     */
       free_vector(pt,1,n);  }
       return;  
     }  /*************************free matrix ************************/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     for (j=1;j<=n;j++) {  {
       ptt[j]=2.0*p[j]-pt[j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       xit[j]=p[j]-pt[j];    free((FREE_ARG)(m+nrl-NR_END));
       pt[j]=p[j];  }
     }  
     fptt=(*func)(ptt);  /******************* ma3x *******************************/
     if (fptt < fp) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  {
       if (t < 0.0) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         linmin(p,xit,n,fret,func);    double ***m;
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           xi[j][n]=xit[j];    if (!m) nrerror("allocation failure 1 in matrix()");
         }    m += NR_END;
 #ifdef DEBUG    m -= nrl;
         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[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           printf(" %.12e",xit[j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         printf("\n");    m[nrl] += NR_END;
 #endif    m[nrl] -= ncl;
       }  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   }  
 }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 /**** Prevalence limit ****************/    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    for (j=ncl+1; j<=nch; j++) 
 {      m[nrl][j]=m[nrl][j-1]+nlay;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    
      matrix by transitions matrix until convergence is reached */    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   int i, ii,j,k;      for (j=ncl+1; j<=nch; j++) 
   double min, max, maxmin, maxmax,sumnew=0.;        m[i][j]=m[i][j-1]+nlay;
   double **matprod2();    }
   double **out, cov[NCOVMAX], **pmij();    return m; 
   double **newm;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   double agefin, delaymax=50 ; /* Max number of years to converge */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
   for (ii=1;ii<=nlstate+ndeath;ii++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
    cov[1]=1.;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    free((FREE_ARG)(m+nrl-NR_END));
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  }
     newm=savm;  
     /* Covariates have to be included here again */  /*************** function subdirf ***********/
      cov[2]=agefin;  char *subdirf(char fileres[])
    {
       for (k=1; k<=cptcovn;k++) {    /* Caution optionfilefiname is hidden */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    strcpy(tmpout,optionfilefiname);
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    strcat(tmpout,"/"); /* Add to the right */
       }    strcat(tmpout,fileres);
       for (k=1; k<=cptcovage;k++)    return tmpout;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  }
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    
     /* Caution optionfilefiname is hidden */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     savm=oldm;    strcat(tmpout,preop);
     oldm=newm;    strcat(tmpout,fileres);
     maxmax=0.;    return tmpout;
     for(j=1;j<=nlstate;j++){  }
       min=1.;  
       max=0.;  /*************** function subdirf3 ***********/
       for(i=1; i<=nlstate; i++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
         sumnew=0;  {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    
         prlim[i][j]= newm[i][j]/(1-sumnew);    /* Caution optionfilefiname is hidden */
         max=FMAX(max,prlim[i][j]);    strcpy(tmpout,optionfilefiname);
         min=FMIN(min,prlim[i][j]);    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
       maxmin=max-min;    strcat(tmpout,preop2);
       maxmax=FMAX(maxmax,maxmin);    strcat(tmpout,fileres);
     }    return tmpout;
     if(maxmax < ftolpl){  }
       return prlim;  
     }  /***************** f1dim *************************/
   }  extern int ncom; 
 }  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
 /*************** transition probabilities ***************/   
   double f1dim(double x) 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  { 
 {    int j; 
   double s1, s2;    double f;
   /*double t34;*/    double *xt; 
   int i,j,j1, nc, ii, jj;   
     xt=vector(1,ncom); 
     for(i=1; i<= nlstate; i++){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for(j=1; j<i;j++){    f=(*nrfunc)(xt); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free_vector(xt,1,ncom); 
         /*s2 += param[i][j][nc]*cov[nc];*/    return f; 
         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);*/  
       }  /*****************brent *************************/
       ps[i][j]=s2;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  { 
     }    int iter; 
     for(j=i+1; j<=nlstate+ndeath;j++){    double a,b,d,etemp;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double fu,fv,fw,fx;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double ftemp;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       }    double e=0.0; 
       ps[i][j]=s2;   
     }    a=(ax < cx ? ax : cx); 
   }    b=(ax > cx ? ax : cx); 
     /*ps[3][2]=1;*/    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
   for(i=1; i<= nlstate; i++){    for (iter=1;iter<=ITMAX;iter++) { 
      s1=0;      xm=0.5*(a+b); 
     for(j=1; j<i; j++)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       s1+=exp(ps[i][j]);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for(j=i+1; j<=nlstate+ndeath; j++)      printf(".");fflush(stdout);
       s1+=exp(ps[i][j]);      fprintf(ficlog,".");fflush(ficlog);
     ps[i][i]=1./(s1+1.);  #ifdef DEBUG
     for(j=1; j<i; j++)      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       ps[i][j]= exp(ps[i][j])*ps[i][i];      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(j=i+1; j<=nlstate+ndeath; j++)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #endif
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   } /* end i */        *xmin=x; 
         return fx; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      } 
     for(jj=1; jj<= nlstate+ndeath; jj++){      ftemp=fu;
       ps[ii][jj]=0;      if (fabs(e) > tol1) { 
       ps[ii][ii]=1;        r=(x-w)*(fx-fv); 
     }        q=(x-v)*(fx-fw); 
   }        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        q=fabs(q); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        etemp=e; 
      printf("%lf ",ps[ii][jj]);        e=d; 
    }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     printf("\n ");          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }        else { 
     printf("\n ");printf("%lf ",cov[2]);*/          d=p/q; 
 /*          u=x+d; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          if (u-a < tol2 || b-u < tol2) 
   goto end;*/            d=SIGN(tol1,xm-x); 
     return ps;        } 
 }      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 /**************** Product of 2 matrices ******************/      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      fu=(*f)(u); 
 {      if (fu <= fx) { 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        if (u >= x) a=x; else b=x; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        SHFT(v,w,x,u) 
   /* in, b, out are matrice of pointers which should have been initialized          SHFT(fv,fw,fx,fu) 
      before: only the contents of out is modified. The function returns          } else { 
      a pointer to pointers identical to out */            if (u < x) a=u; else b=u; 
   long i, j, k;            if (fu <= fw || w == x) { 
   for(i=nrl; i<= nrh; i++)              v=w; 
     for(k=ncolol; k<=ncoloh; k++)              w=u; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)              fv=fw; 
         out[i][k] +=in[i][j]*b[j][k];              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
   return out;              v=u; 
 }              fv=fu; 
             } 
           } 
 /************* Higher Matrix Product ***************/    } 
     nrerror("Too many iterations in brent"); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    *xmin=x; 
 {    return fx; 
   /* 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.  /****************** mnbrak ***********************/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
      Model is determined by parameters x and covariates have to be              double (*func)(double)) 
      included manually here.  { 
     double ulim,u,r,q, dum;
      */    double fu; 
    
   int i, j, d, h, k;    *fa=(*func)(*ax); 
   double **out, cov[NCOVMAX];    *fb=(*func)(*bx); 
   double **newm;    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
   /* Hstepm could be zero and should return the unit matrix */        SHFT(dum,*fb,*fa,dum) 
   for (i=1;i<=nlstate+ndeath;i++)        } 
     for (j=1;j<=nlstate+ndeath;j++){    *cx=(*bx)+GOLD*(*bx-*ax); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    *fc=(*func)(*cx); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    while (*fb > *fc) { 
     }      r=(*bx-*ax)*(*fb-*fc); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      q=(*bx-*cx)*(*fb-*fa); 
   for(h=1; h <=nhstepm; h++){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(d=1; d <=hstepm; d++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       newm=savm;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       /* Covariates have to be included here again */      if ((*bx-u)*(u-*cx) > 0.0) { 
       cov[1]=1.;        fu=(*func)(u); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fu=(*func)(u); 
       for (k=1; k<=cptcovage;k++)        if (fu < *fc) { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for (k=1; k<=cptcovprod;k++)            SHFT(*fb,*fc,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 ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        fu=(*func)(u); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      } else { 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        u=(*cx)+GOLD*(*cx-*bx); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        fu=(*func)(u); 
       savm=oldm;      } 
       oldm=newm;      SHFT(*ax,*bx,*cx,u) 
     }        SHFT(*fa,*fb,*fc,fu) 
     for(i=1; i<=nlstate+ndeath; i++)        } 
       for(j=1;j<=nlstate+ndeath;j++) {  } 
         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]);  /*************** linmin ************************/
          */  
       }  int ncom; 
   } /* end h */  double *pcom,*xicom;
   return po;  double (*nrfunc)(double []); 
 }   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
 /*************** log-likelihood *************/    double brent(double ax, double bx, double cx, 
 double func( double *x)                 double (*f)(double), double tol, double *xmin); 
 {    double f1dim(double x); 
   int i, ii, j, k, mi, d, kk;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];                double *fc, double (*func)(double)); 
   double **out;    int j; 
   double sw; /* Sum of weights */    double xx,xmin,bx,ax; 
   double lli; /* Individual log likelihood */    double fx,fb,fa;
   long ipmx;   
   /*extern weight */    ncom=n; 
   /* We are differentiating ll according to initial status */    pcom=vector(1,n); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    xicom=vector(1,n); 
   /*for(i=1;i<imx;i++)    nrfunc=func; 
     printf(" %d\n",s[4][i]);    for (j=1;j<=n;j++) { 
   */      pcom[j]=p[j]; 
   cov[1]=1.;      xicom[j]=xi[j]; 
     } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    ax=0.0; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    xx=1.0; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for(mi=1; mi<= wav[i]-1; mi++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       for (ii=1;ii<=nlstate+ndeath;ii++)  #ifdef DEBUG
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for(d=0; d<dh[mi][i]; d++){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         newm=savm;  #endif
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    for (j=1;j<=n;j++) { 
         for (kk=1; kk<=cptcovage;kk++) {      xi[j] *= xmin; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      p[j] += xi[j]; 
         }    } 
            free_vector(xicom,1,n); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    free_vector(pcom,1,n); 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  } 
         savm=oldm;  
         oldm=newm;  char *asc_diff_time(long time_sec, char ascdiff[])
          {
            long sec_left, days, hours, minutes;
       } /* end mult */    days = (time_sec) / (60*60*24);
          sec_left = (time_sec) % (60*60*24);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    hours = (sec_left) / (60*60) ;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    sec_left = (sec_left) %(60*60);
       ipmx +=1;    minutes = (sec_left) /60;
       sw += weight[i];    sec_left = (sec_left) % (60);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     } /* end of wave */    return ascdiff;
   } /* end of individual */  }
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  /*************** powell ************************/
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */              double (*func)(double [])) 
   return -l;  { 
 }    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
     int i,ibig,j; 
 /*********** Maximum Likelihood Estimation ***************/    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    double *xits;
 {    int niterf, itmp;
   int i,j, iter;  
   double **xi,*delti;    pt=vector(1,n); 
   double fret;    ptt=vector(1,n); 
   xi=matrix(1,npar,1,npar);    xit=vector(1,n); 
   for (i=1;i<=npar;i++)    xits=vector(1,n); 
     for (j=1;j<=npar;j++)    *fret=(*func)(p); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    for (j=1;j<=n;j++) pt[j]=p[j]; 
   printf("Powell\n");    for (*iter=1;;++(*iter)) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);      fp=(*fret); 
       ibig=0; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      del=0.0; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
 }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
 /**** Computes Hessian and covariance matrix ***/      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      */
 {     for (i=1;i<=n;i++) {
   double  **a,**y,*x,pd;        printf(" %d %.12f",i, p[i]);
   double **hess;        fprintf(ficlog," %d %.12lf",i, p[i]);
   int i, j,jk;        fprintf(ficrespow," %.12lf", p[i]);
   int *indx;      }
       printf("\n");
   double hessii(double p[], double delta, int theta, double delti[]);      fprintf(ficlog,"\n");
   double hessij(double p[], double delti[], int i, int j);      fprintf(ficrespow,"\n");fflush(ficrespow);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      if(*iter <=3){
   void ludcmp(double **a, int npar, int *indx, double *d) ;        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
   hess=matrix(1,npar,1,npar);  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
   printf("\nCalculation of the hessian matrix. Wait...\n");        itmp = strlen(strcurr);
   for (i=1;i<=npar;i++){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     printf("%d",i);fflush(stdout);          strcurr[itmp-1]='\0';
     hess[i][i]=hessii(p,ftolhess,i,delti);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     /*printf(" %f ",p[i]);*/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     /*printf(" %lf ",hess[i][i]);*/        for(niterf=10;niterf<=30;niterf+=10){
   }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
            tmf = *localtime(&forecast_time.tv_sec);
   for (i=1;i<=npar;i++) {  /*      asctime_r(&tmf,strfor); */
     for (j=1;j<=npar;j++)  {          strcpy(strfor,asctime(&tmf));
       if (j>i) {          itmp = strlen(strfor);
         printf(".%d%d",i,j);fflush(stdout);          if(strfor[itmp-1]=='\n')
         hess[i][j]=hessij(p,delti,i,j);          strfor[itmp-1]='\0';
         hess[j][i]=hess[i][j];              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);
         /*printf(" %lf ",hess[i][j]);*/          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }        }
     }      }
   }      for (i=1;i<=n;i++) { 
   printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  #ifdef DEBUG
          printf("fret=%lf \n",*fret);
   a=matrix(1,npar,1,npar);        fprintf(ficlog,"fret=%lf \n",*fret);
   y=matrix(1,npar,1,npar);  #endif
   x=vector(1,npar);        printf("%d",i);fflush(stdout);
   indx=ivector(1,npar);        fprintf(ficlog,"%d",i);fflush(ficlog);
   for (i=1;i<=npar;i++)        linmin(p,xit,n,fret,func); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        if (fabs(fptt-(*fret)) > del) { 
   ludcmp(a,npar,indx,&pd);          del=fabs(fptt-(*fret)); 
           ibig=i; 
   for (j=1;j<=npar;j++) {        } 
     for (i=1;i<=npar;i++) x[i]=0;  #ifdef DEBUG
     x[j]=1;        printf("%d %.12e",i,(*fret));
     lubksb(a,npar,indx,x);        fprintf(ficlog,"%d %.12e",i,(*fret));
     for (i=1;i<=npar;i++){        for (j=1;j<=n;j++) {
       matcov[i][j]=x[i];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     }          printf(" x(%d)=%.12e",j,xit[j]);
   }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   printf("\n#Hessian matrix#\n");        for(j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) {          printf(" p=%.12e",p[j]);
     for (j=1;j<=npar;j++) {          fprintf(ficlog," p=%.12e",p[j]);
       printf("%.3e ",hess[i][j]);        }
     }        printf("\n");
     printf("\n");        fprintf(ficlog,"\n");
   }  #endif
       } 
   /* Recompute Inverse */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        int k[2],l;
   ludcmp(a,npar,indx,&pd);        k[0]=1;
         k[1]=-1;
   /*  printf("\n#Hessian matrix recomputed#\n");        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (j=1;j<=npar;j++) {        for (j=1;j<=n;j++) {
     for (i=1;i<=npar;i++) x[i]=0;          printf(" %.12e",p[j]);
     x[j]=1;          fprintf(ficlog," %.12e",p[j]);
     lubksb(a,npar,indx,x);        }
     for (i=1;i<=npar;i++){        printf("\n");
       y[i][j]=x[i];        fprintf(ficlog,"\n");
       printf("%.3e ",y[i][j]);        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
     printf("\n");            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
   free_matrix(a,1,npar,1,npar);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   free_matrix(y,1,npar,1,npar);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   free_vector(x,1,npar);        }
   free_ivector(indx,1,npar);  #endif
   free_matrix(hess,1,npar,1,npar);  
   
         free_vector(xit,1,n); 
 }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 /*************** hessian matrix ****************/        free_vector(pt,1,n); 
 double hessii( double x[], double delta, int theta, double delti[])        return; 
 {      } 
   int i;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   int l=1, lmax=20;      for (j=1;j<=n;j++) { 
   double k1,k2;        ptt[j]=2.0*p[j]-pt[j]; 
   double p2[NPARMAX+1];        xit[j]=p[j]-pt[j]; 
   double res;        pt[j]=p[j]; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      } 
   double fx;      fptt=(*func)(ptt); 
   int k=0,kmax=10;      if (fptt < fp) { 
   double l1;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   fx=func(x);          linmin(p,xit,n,fret,func); 
   for (i=1;i<=npar;i++) p2[i]=x[i];          for (j=1;j<=n;j++) { 
   for(l=0 ; l <=lmax; l++){            xi[j][ibig]=xi[j][n]; 
     l1=pow(10,l);            xi[j][n]=xit[j]; 
     delts=delt;          }
     for(k=1 ; k <kmax; k=k+1){  #ifdef DEBUG
       delt = delta*(l1*k);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       p2[theta]=x[theta] +delt;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       k1=func(p2)-fx;          for(j=1;j<=n;j++){
       p2[theta]=x[theta]-delt;            printf(" %.12e",xit[j]);
       k2=func(p2)-fx;            fprintf(ficlog," %.12e",xit[j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */          }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          printf("\n");
                fprintf(ficlog,"\n");
 #ifdef DEBUG  #endif
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        }
 #endif      } 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    } 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  } 
         k=kmax;  
       }  /**** Prevalence limit (stable prevalence)  ****************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         delts=delt;       matrix by transitions matrix until convergence is reached */
       }  
     }    int i, ii,j,k;
   }    double min, max, maxmin, maxmax,sumnew=0.;
   delti[theta]=delts;    double **matprod2();
   return res;    double **out, cov[NCOVMAX], **pmij();
      double **newm;
 }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
 double hessij( double x[], double delti[], int thetai,int thetaj)    for (ii=1;ii<=nlstate+ndeath;ii++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   int i;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int l=1, l1, lmax=20;      }
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];     cov[1]=1.;
   int k;   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fx=func(x);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for (k=1; k<=2; k++) {      newm=savm;
     for (i=1;i<=npar;i++) p2[i]=x[i];      /* Covariates have to be included here again */
     p2[thetai]=x[thetai]+delti[thetai]/k;       cov[2]=agefin;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    
     k1=func(p2)-fx;        for (k=1; k<=cptcovn;k++) {
            cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetai]=x[thetai]+delti[thetai]/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]]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k2=func(p2)-fx;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
          /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetai]=x[thetai]-delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      savm=oldm;
 #ifdef DEBUG      oldm=newm;
     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);      maxmax=0.;
 #endif      for(j=1;j<=nlstate;j++){
   }        min=1.;
   return res;        max=0.;
 }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
 /************** Inverse of matrix **************/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 void ludcmp(double **a, int n, int *indx, double *d)          prlim[i][j]= newm[i][j]/(1-sumnew);
 {          max=FMAX(max,prlim[i][j]);
   int i,imax,j,k;          min=FMIN(min,prlim[i][j]);
   double big,dum,sum,temp;        }
   double *vv;        maxmin=max-min;
          maxmax=FMAX(maxmax,maxmin);
   vv=vector(1,n);      }
   *d=1.0;      if(maxmax < ftolpl){
   for (i=1;i<=n;i++) {        return prlim;
     big=0.0;      }
     for (j=1;j<=n;j++)    }
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /*************** transition probabilities ***************/ 
   }  
   for (j=1;j<=n;j++) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    double s1, s2;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    /*double t34;*/
       a[i][j]=sum;    int i,j,j1, nc, ii, jj;
     }  
     big=0.0;      for(i=1; i<= nlstate; i++){
     for (i=j;i<=n;i++) {        for(j=1; j<i;j++){
       sum=a[i][j];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<j;k++)            /*s2 += param[i][j][nc]*cov[nc];*/
         sum -= a[i][k]*a[k][j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       a[i][j]=sum;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       if ( (dum=vv[i]*fabs(sum)) >= big) {          }
         big=dum;          ps[i][j]=s2;
         imax=i;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       }        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
     if (j != imax) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<=n;k++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         dum=a[imax][k];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         a[imax][k]=a[j][k];          }
         a[j][k]=dum;          ps[i][j]=s2;
       }        }
       *d = -(*d);      }
       vv[imax]=vv[j];      /*ps[3][2]=1;*/
     }      
     indx[j]=imax;      for(i=1; i<= nlstate; i++){
     if (a[j][j] == 0.0) a[j][j]=TINY;        s1=0;
     if (j != n) {        for(j=1; j<i; j++)
       dum=1.0/(a[j][j]);          s1+=exp(ps[i][j]);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(j=i+1; j<=nlstate+ndeath; j++)
     }          s1+=exp(ps[i][j]);
   }        ps[i][i]=1./(s1+1.);
   free_vector(vv,1,n);  /* Doesn't work */        for(j=1; j<i; j++)
 ;          ps[i][j]= exp(ps[i][j])*ps[i][i];
 }        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
 void lubksb(double **a, int n, int *indx, double b[])        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {      } /* end i */
   int i,ii=0,ip,j;      
   double sum;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
          for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=n;i++) {          ps[ii][jj]=0;
     ip=indx[i];          ps[ii][ii]=1;
     sum=b[ip];        }
     b[ip]=b[i];      }
     if (ii)      
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     b[i]=sum;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   }  /*         printf("ddd %lf ",ps[ii][jj]); */
   for (i=n;i>=1;i--) {  /*       } */
     sum=b[i];  /*       printf("\n "); */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*        } */
     b[i]=sum/a[i][i];  /*        printf("\n ");printf("%lf ",cov[2]); */
   }         /*
 }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
 /************ Frequencies ********************/      return ps;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  }
 {  /* Some frequencies */  
    /**************** Product of 2 matrices ******************/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double *pp;  {
   double pos, k2, dateintsum=0,k2cpt=0;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   FILE *ficresp;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   char fileresp[FILENAMELENGTH];    /* in, b, out are matrice of pointers which should have been initialized 
         before: only the contents of out is modified. The function returns
   pp=vector(1,nlstate);       a pointer to pointers identical to out */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    long i, j, k;
   strcpy(fileresp,"p");    for(i=nrl; i<= nrh; i++)
   strcat(fileresp,fileres);      for(k=ncolol; k<=ncoloh; k++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     printf("Problem with prevalence resultfile: %s\n", fileresp);          out[i][k] +=in[i][j]*b[j][k];
     exit(0);  
   }    return out;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  
   
   j=cptcoveff;  /************* Higher Matrix Product ***************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   for(k1=1; k1<=j;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    /* Computes the transition matrix starting at age 'age' over 
        j1++;       'nhstepm*hstepm*stepm' months (i.e. until
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
          scanf("%d", i);*/       nhstepm*hstepm matrices. 
         for (i=-1; i<=nlstate+ndeath; i++)         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
          for (jk=-1; jk<=nlstate+ndeath; jk++)         (typically every 2 years instead of every month which is too big 
            for(m=agemin; m <= agemax+3; m++)       for the memory).
              freq[i][jk][m]=0;       Model is determined by parameters x and covariates have to be 
        included manually here. 
         dateintsum=0;  
         k2cpt=0;       */
        for (i=1; i<=imx; i++) {  
          bool=1;    int i, j, d, h, k;
          if  (cptcovn>0) {    double **out, cov[NCOVMAX];
            for (z1=1; z1<=cptcoveff; z1++)    double **newm;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;    /* Hstepm could be zero and should return the unit matrix */
          }    for (i=1;i<=nlstate+ndeath;i++)
          if (bool==1) {      for (j=1;j<=nlstate+ndeath;j++){
            for(m=firstpass; m<=lastpass; m++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
              k2=anint[m][i]+(mint[m][i]/12.);        po[i][j][0]=(i==j ? 1.0 : 0.0);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      }
                if(agev[m][i]==0) agev[m][i]=agemax+1;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                if(agev[m][i]==1) agev[m][i]=agemax+2;    for(h=1; h <=nhstepm; h++){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for(d=1; d <=hstepm; d++){
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        newm=savm;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        /* Covariates have to be included here again */
                  dateintsum=dateintsum+k2;        cov[1]=1.;
                  k2cpt++;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
              }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
            }        for (k=1; k<=cptcovprod;k++)
          }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        }  
          
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         if  (cptcovn>0) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
          fprintf(ficresp, "\n#********** Variable ");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        savm=oldm;
        fprintf(ficresp, "**********\n#");        oldm=newm;
         }      }
        for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate+ndeath; i++)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for(j=1;j<=nlstate+ndeath;j++) {
        fprintf(ficresp, "\n");          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]);
   for(i=(int)agemin; i <= (int)agemax+3; i++){           */
     if(i==(int)agemax+3)        }
       printf("Total");    } /* end h */
     else    return po;
       printf("Age %d", i);  }
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
         pp[jk] += freq[jk][m][i];  /*************** log-likelihood *************/
     }  double func( double *x)
     for(jk=1; jk <=nlstate ; jk++){  {
       for(m=-1, pos=0; m <=0 ; m++)    int i, ii, j, k, mi, d, kk;
         pos += freq[jk][m][i];    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       if(pp[jk]>=1.e-10)    double **out;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    double sw; /* Sum of weights */
       else    double lli; /* Individual log likelihood */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    int s1, s2;
     }    double bbh, survp;
     long ipmx;
      for(jk=1; jk <=nlstate ; jk++){    /*extern weight */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    /* We are differentiating ll according to initial status */
         pp[jk] += freq[jk][m][i];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     for(jk=1,pos=0; jk <=nlstate ; jk++)    */
       pos += pp[jk];    cov[1]=1.;
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
       else    if(mle==1){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if( i <= (int) agemax){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if(pos>=1.e-5){        for(mi=1; mi<= wav[i]-1; mi++){
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          for (ii=1;ii<=nlstate+ndeath;ii++)
           probs[i][jk][j1]= pp[jk]/pos;            for (j=1;j<=nlstate+ndeath;j++){
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else            }
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(jk=-1; jk <=nlstate+ndeath; jk++)            for (kk=1; kk<=cptcovage;kk++) {
       for(m=-1; m <=nlstate+ndeath; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            }
     if(i <= (int) agemax)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficresp,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("\n");            savm=oldm;
     }            oldm=newm;
     }          } /* end mult */
  }        
   dateintmean=dateintsum/k2cpt;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            /* But now since version 0.9 we anticipate for bias at large stepm.
   fclose(ficresp);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   free_vector(pp,1,nlstate);           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   /* End of Freq */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 }           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 /************ Prevalence ********************/           * -stepm/2 to stepm/2 .
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)           * For stepm=1 the results are the same as for previous versions of Imach.
 {  /* Some frequencies */           * For stepm > 1 the results are less biased than in previous versions. 
             */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          s1=s[mw[mi][i]][i];
   double ***freq; /* Frequencies */          s2=s[mw[mi+1][i]][i];
   double *pp;          bbh=(double)bh[mi][i]/(double)stepm; 
   double pos, k2;          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   pp=vector(1,nlstate);           */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            if( s2 > nlstate){ 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            /* i.e. if s2 is a death state and if the date of death is known 
   j1=0;               then the contribution to the likelihood is the probability to 
                 die between last step unit time and current  step unit time, 
   j=cptcoveff;               which is also equal to probability to die before dh 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}               minus probability to die before dh-stepm . 
                 In version up to 0.92 likelihood was computed
  for(k1=1; k1<=j;k1++){          as if date of death was unknown. Death was treated as any other
     for(i1=1; i1<=ncodemax[k1];i1++){          health state: the date of the interview describes the actual state
       j1++;          and not the date of a change in health state. The former idea was
            to consider that at each interview the state was recorded
       for (i=-1; i<=nlstate+ndeath; i++)            (healthy, disable or death) and IMaCh was corrected; but when we
         for (jk=-1; jk<=nlstate+ndeath; jk++)            introduced the exact date of death then we should have modified
           for(m=agemin; m <= agemax+3; m++)          the contribution of an exact death to the likelihood. This new
             freq[i][jk][m]=0;          contribution is smaller and very dependent of the step unit
                stepm. It is no more the probability to die between last interview
       for (i=1; i<=imx; i++) {          and month of death but the probability to survive from last
         bool=1;          interview up to one month before death multiplied by the
         if  (cptcovn>0) {          probability to die within a month. Thanks to Chris
           for (z1=1; z1<=cptcoveff; z1++)          Jackson for correcting this bug.  Former versions increased
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          mortality artificially. The bad side is that we add another loop
               bool=0;          which slows down the processing. The difference can be up to 10%
         }          lower mortality.
         if (bool==1) {            */
           for(m=firstpass; m<=lastpass; m++){            lli=log(out[s1][s2] - savm[s1][s2]);
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;          } else if  (s2==-2) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=1,survp=0. ; j<=nlstate; j++) 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              survp += out[s1][j];
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            lli= survp;
             }          }
           }          
         }          else if  (s2==-4) {
       }            for (j=3,survp=0. ; j<=nlstate; j++) 
         for(i=(int)agemin; i <= (int)agemax+3; i++){              survp += out[s1][j];
           for(jk=1; jk <=nlstate ; jk++){            lli= survp;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          }
               pp[jk] += freq[jk][m][i];          
           }          else if  (s2==-5) {
           for(jk=1; jk <=nlstate ; jk++){            for (j=1,survp=0. ; j<=2; j++) 
             for(m=-1, pos=0; m <=0 ; m++)              survp += out[s1][j];
             pos += freq[jk][m][i];            lli= survp;
         }          }
          
          for(jk=1; jk <=nlstate ; jk++){  
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          else{
              pp[jk] += freq[jk][m][i];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                    } 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
          for(jk=1; jk <=nlstate ; jk++){                    /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            if( i <= (int) agemax){          ipmx +=1;
              if(pos>=1.e-5){          sw += weight[i];
                probs[i][jk][j1]= pp[jk]/pos;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              }        } /* end of wave */
            }      } /* end of individual */
          }    }  else if(mle==2){
                for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(pp,1,nlstate);            }
            for(d=0; d<=dh[mi][i]; d++){
 }  /* End of Freq */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /************* Waves Concatenation ***************/            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      Death is a valid wave (if date is known).            savm=oldm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            oldm=newm;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          } /* end mult */
      and mw[mi+1][i]. dh depends on stepm.        
      */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   int i, mi, m;          bbh=(double)bh[mi][i]/(double)stepm; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
      double sum=0., jmean=0.;*/          ipmx +=1;
           sw += weight[i];
   int j, k=0,jk, ju, jl;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double sum=0.;        } /* end of wave */
   jmin=1e+5;      } /* end of individual */
   jmax=-1;    }  else if(mle==3){  /* exponential inter-extrapolation */
   jmean=0.;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=imx; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     mi=0;        for(mi=1; mi<= wav[i]-1; mi++){
     m=firstpass;          for (ii=1;ii<=nlstate+ndeath;ii++)
     while(s[m][i] <= nlstate){            for (j=1;j<=nlstate+ndeath;j++){
       if(s[m][i]>=1)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         mw[++mi][i]=m;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(m >=lastpass)            }
         break;          for(d=0; d<dh[mi][i]; d++){
       else            newm=savm;
         m++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }/* end while */            for (kk=1; kk<=cptcovage;kk++) {
     if (s[m][i] > nlstate){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       mi++;     /* Death is another wave */            }
       /* if(mi==0)  never been interviewed correctly before death */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          /* Only death is a correct wave */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       mw[mi][i]=m;            savm=oldm;
     }            oldm=newm;
           } /* end mult */
     wav[i]=mi;        
     if(mi==0)          s1=s[mw[mi][i]][i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   for(i=1; i<=imx; i++){          ipmx +=1;
     for(mi=1; mi<wav[i];mi++){          sw += weight[i];
       if (stepm <=0)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         dh[mi][i]=1;        } /* end of wave */
       else{      } /* end of individual */
         if (s[mw[mi+1][i]][i] > nlstate) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           if (agedc[i] < 2*AGESUP) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if(j==0) j=1;  /* Survives at least one month after exam */        for(mi=1; mi<= wav[i]-1; mi++){
           k=k+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
           if (j >= jmax) jmax=j;            for (j=1;j<=nlstate+ndeath;j++){
           if (j <= jmin) jmin=j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           sum=sum+j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           /* if (j<10) printf("j=%d num=%d ",j,i); */            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
         else{            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            for (kk=1; kk<=cptcovage;kk++) {
           k=k+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if (j >= jmax) jmax=j;            }
           else if (j <= jmin)jmin=j;          
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           sum=sum+j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
         jk= j/stepm;            oldm=newm;
         jl= j -jk*stepm;          } /* end mult */
         ju= j -(jk+1)*stepm;        
         if(jl <= -ju)          s1=s[mw[mi][i]][i];
           dh[mi][i]=jk;          s2=s[mw[mi+1][i]][i];
         else          if( s2 > nlstate){ 
           dh[mi][i]=jk+1;            lli=log(out[s1][s2] - savm[s1][s2]);
         if(dh[mi][i]==0)          }else{
           dh[mi][i]=1; /* At least one step */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
     }          ipmx +=1;
   }          sw += weight[i];
   jmean=sum/k;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  /*      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 */
 /*********** Tricode ****************************/      } /* end of individual */
 void tricode(int *Tvar, int **nbcode, int imx)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int Ndum[20],ij=1, k, j, i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int cptcode=0;        for(mi=1; mi<= wav[i]-1; mi++){
   cptcoveff=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   for (k=0; k<19; k++) Ndum[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (k=1; k<=7; k++) ncodemax[k]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1; i<=imx; i++) {            newm=savm;
       ij=(int)(covar[Tvar[j]][i]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       Ndum[ij]++;            for (kk=1; kk<=cptcovage;kk++) {
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (ij > cptcode) cptcode=ij;            }
     }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=0; i<=cptcode; i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(Ndum[i]!=0) ncodemax[j]++;            savm=oldm;
     }            oldm=newm;
     ij=1;          } /* end mult */
         
           s1=s[mw[mi][i]][i];
     for (i=1; i<=ncodemax[j]; i++) {          s2=s[mw[mi+1][i]][i];
       for (k=0; k<=19; k++) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         if (Ndum[k] != 0) {          ipmx +=1;
           nbcode[Tvar[j]][ij]=k;          sw += weight[i];
           ij++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         if (ij > ncodemax[j]) break;        } /* end of wave */
       }        } /* end of individual */
     }    } /* End of if */
   }      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  for (k=0; k<19; k++) Ndum[k]=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
  for (i=1; i<=ncovmodel-2; i++) {  }
       ij=Tvar[i];  
       Ndum[ij]++;  /*************** log-likelihood *************/
     }  double funcone( double *x)
   {
  ij=1;    /* Same as likeli but slower because of a lot of printf and if */
  for (i=1; i<=10; i++) {    int i, ii, j, k, mi, d, kk;
    if((Ndum[i]!=0) && (i<=ncov)){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      Tvaraff[ij]=i;    double **out;
      ij++;    double lli; /* Individual log likelihood */
    }    double llt;
  }    int s1, s2;
      double bbh, survp;
     cptcoveff=ij-1;    /*extern weight */
 }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 /*********** Health Expectancies ****************/    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    */
 {    cov[1]=1.;
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double age, agelim,hf;  
   double ***p3mat;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficreseij,"# Health expectancies\n");      for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficreseij,"# Age");        for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
     for(j=1; j<=nlstate;j++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficreseij," %1d-%1d",i,j);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"\n");          }
         for(d=0; d<dh[mi][i]; d++){
   hstepm=1*YEARM; /*  Every j years of age (in month) */          newm=savm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
   agelim=AGESUP;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     /* nhstepm age range expressed in number of stepm */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     /* Typically if 20 years = 20*12/6=40 stepm */          savm=oldm;
     if (stepm >= YEARM) hstepm=1;          oldm=newm;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        } /* end mult */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        s1=s[mw[mi][i]][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        s2=s[mw[mi+1][i]][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
     for(i=1; i<=nlstate;i++)         */
       for(j=1; j<=nlstate;j++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          lli=log(out[s1][s2] - savm[s1][s2]);
           eij[i][j][(int)age] +=(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;        } else if (mle==1){
         }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
            } else if(mle==2){
     hf=1;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     if (stepm >= YEARM) hf=stepm/YEARM;        } 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 */
     for(i=1; i<=nlstate;i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       for(j=1; j<=nlstate;j++){          lli=log(out[s1][s2]); /* Original formula */
         if (j==i) eij[i][j][(int)age]= (eij[i][j][(int)age]-0.5*stepm/12./hf);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         }          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
     fprintf(ficreseij,"%3.0f",age );        ipmx +=1;
     for(i=1; i<=nlstate;i++)        sw += weight[i];
       for(j=1; j<=nlstate;j++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficreseij," %9.4f", hf*eij[i][j][(int)age]);  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        if(globpr){
     fprintf(ficreseij,"\n");          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   %10.6f %10.6f %10.6f ", \
   }                  num[i],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(k=1,llt=0.,l=0.; k<=nlstate; k++){
 /************ Variance ******************/            llt +=ll[k]*gipmx/gsw;
 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)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
 {          }
   /* Variance of health expectancies */          fprintf(ficresilk," %10.6f\n", -llt);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }
   double **newm;      } /* end of wave */
   double **dnewm,**doldm;    } /* end of individual */
   int i, j, nhstepm, hstepm, h;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   int k, cptcode;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double *xp;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double **gp, **gm;    if(globpr==0){ /* First time we count the contributions and weights */
   double ***gradg, ***trgradg;      gipmx=ipmx;
   double ***p3mat;      gsw=sw;
   double age,agelim;    }
   int theta;    return -l;
   }
    fprintf(ficresvij,"# Covariances of life expectancies\n");  
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  /*************** function likelione ***********/
     for(j=1; j<=nlstate;j++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  {
   fprintf(ficresvij,"\n");    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
   xp=vector(1,npar);       to check the exact contribution to the likelihood.
   dnewm=matrix(1,nlstate,1,npar);       Plotting could be done.
   doldm=matrix(1,nlstate,1,nlstate);     */
      int k;
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    if(*globpri !=0){ /* Just counts and sums, no printings */
   agelim = AGESUP;      strcpy(fileresilk,"ilk"); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      strcat(fileresilk,fileres);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     if (stepm >= YEARM) hstepm=1;        printf("Problem with resultfile: %s\n", fileresilk);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      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");
     gp=matrix(0,nhstepm,1,nlstate);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     gm=matrix(0,nhstepm,1,nlstate);      /*  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(k=1; k<=nlstate; k++) 
     for(theta=1; theta <=npar; theta++){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       for(i=1; i<=npar; i++){ /* Computes gradient */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      *fretone=(*funcone)(p);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if(*globpri !=0){
       fclose(ficresilk);
       if (popbased==1) {      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         for(i=1; i<=nlstate;i++)      fflush(fichtm); 
           prlim[i][i]=probs[(int)age][i][ij];    } 
       }    return;
    }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  /*********** Maximum Likelihood Estimation ***************/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       }  {
        int i,j, iter;
       for(i=1; i<=npar; i++) /* Computes gradient */    double **xi;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double fret;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double fretone; /* Only one call to likelihood */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*  char filerespow[FILENAMELENGTH];*/
      xi=matrix(1,npar,1,npar);
       if (popbased==1) {    for (i=1;i<=npar;i++)
         for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++)
           prlim[i][i]=probs[(int)age][i][ij];        xi[i][j]=(i==j ? 1.0 : 0.0);
       }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
       for(j=1; j<= nlstate; j++){    strcat(filerespow,fileres);
         for(h=0; h<=nhstepm; h++){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      printf("Problem with resultfile: %s\n", filerespow);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      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; j++)      for(j=1;j<=nlstate+ndeath;j++)
         for(h=0; h<=nhstepm; h++){        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fprintf(ficrespow,"\n");
         }  
     } /* End theta */    powell(p,xi,npar,ftol,&iter,&fret,func);
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(h=0; h<=nhstepm; h++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(j=1; j<=nlstate;j++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  }
   
     for(i=1;i<=nlstate;i++)  /**** Computes Hessian and covariance matrix ***/
       for(j=1;j<=nlstate;j++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         vareij[i][j][(int)age] =0.;  {
     for(h=0;h<=nhstepm;h++){    double  **a,**y,*x,pd;
       for(k=0;k<=nhstepm;k++){    double **hess;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    int i, j,jk;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    int *indx;
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
             vareij[i][j][(int)age] += doldm[i][j];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     }    void ludcmp(double **a, int npar, int *indx, double *d) ;
     h=1;    double gompertz(double p[]);
     if (stepm >= YEARM) h=stepm/YEARM;    hess=matrix(1,npar,1,npar);
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    printf("\nCalculation of the hessian matrix. Wait...\n");
       for(j=1; j<=nlstate;j++){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    for (i=1;i<=npar;i++){
       }      printf("%d",i);fflush(stdout);
     fprintf(ficresvij,"\n");      fprintf(ficlog,"%d",i);fflush(ficlog);
     free_matrix(gp,0,nhstepm,1,nlstate);     
     free_matrix(gm,0,nhstepm,1,nlstate);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      /*  printf(" %f ",p[i]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   } /* End age */    }
      
   free_vector(xp,1,npar);    for (i=1;i<=npar;i++) {
   free_matrix(doldm,1,nlstate,1,npar);      for (j=1;j<=npar;j++)  {
   free_matrix(dnewm,1,nlstate,1,nlstate);        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
 }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
 /************ 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[j][i]=hess[i][j];    
 {          /*printf(" %lf ",hess[i][j]);*/
   /* Variance of prevalence limit */        }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      }
   double **newm;    }
   double **dnewm,**doldm;    printf("\n");
   int i, j, nhstepm, hstepm;    fprintf(ficlog,"\n");
   int k, cptcode;  
   double *xp;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double *gp, *gm;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **gradg, **trgradg;    
   double age,agelim;    a=matrix(1,npar,1,npar);
   int theta;    y=matrix(1,npar,1,npar);
        x=vector(1,npar);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    indx=ivector(1,npar);
   fprintf(ficresvpl,"# Age");    for (i=1;i<=npar;i++)
   for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       fprintf(ficresvpl," %1d-%1d",i,i);    ludcmp(a,npar,indx,&pd);
   fprintf(ficresvpl,"\n");  
     for (j=1;j<=npar;j++) {
   xp=vector(1,npar);      for (i=1;i<=npar;i++) x[i]=0;
   dnewm=matrix(1,nlstate,1,npar);      x[j]=1;
   doldm=matrix(1,nlstate,1,nlstate);      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   hstepm=1*YEARM; /* Every year of age */        matcov[i][j]=x[i];
   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 */    printf("\n#Hessian matrix#\n");
     if (stepm >= YEARM) hstepm=1;    fprintf(ficlog,"\n#Hessian matrix#\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for (i=1;i<=npar;i++) { 
     gradg=matrix(1,npar,1,nlstate);      for (j=1;j<=npar;j++) { 
     gp=vector(1,nlstate);        printf("%.3e ",hess[i][j]);
     gm=vector(1,nlstate);        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
     for(theta=1; theta <=npar; theta++){      printf("\n");
       for(i=1; i<=npar; i++){ /* Computes gradient */      fprintf(ficlog,"\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /* Recompute Inverse */
       for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++)
         gp[i] = prlim[i][i];      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
        ludcmp(a,npar,indx,&pd);
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /*  printf("\n#Hessian matrix recomputed#\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    for (j=1;j<=npar;j++) {
         gm[i] = prlim[i][i];      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       for(i=1;i<=nlstate;i++)      lubksb(a,npar,indx,x);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      for (i=1;i<=npar;i++){ 
     } /* End theta */        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
     trgradg =matrix(1,nlstate,1,npar);        fprintf(ficlog,"%.3e ",y[i][j]);
       }
     for(j=1; j<=nlstate;j++)      printf("\n");
       for(theta=1; theta <=npar; theta++)      fprintf(ficlog,"\n");
         trgradg[j][theta]=gradg[theta][j];    }
     */
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;    free_matrix(a,1,npar,1,npar);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    free_matrix(y,1,npar,1,npar);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    free_vector(x,1,npar);
     for(i=1;i<=nlstate;i++)    free_ivector(indx,1,npar);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    free_matrix(hess,1,npar,1,npar);
   
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");  /*************** hessian matrix ****************/
     free_vector(gp,1,nlstate);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     free_vector(gm,1,nlstate);  {
     free_matrix(gradg,1,npar,1,nlstate);    int i;
     free_matrix(trgradg,1,nlstate,1,npar);    int l=1, lmax=20;
   } /* End age */    double k1,k2;
     double p2[NPARMAX+1];
   free_vector(xp,1,npar);    double res;
   free_matrix(doldm,1,nlstate,1,npar);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double fx;
     int k=0,kmax=10;
 }    double l1;
   
 /************ Variance of one-step probabilities  ******************/    fx=func(x);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    for (i=1;i<=npar;i++) p2[i]=x[i];
 {    for(l=0 ; l <=lmax; l++){
   int i, j;      l1=pow(10,l);
   int k=0, cptcode;      delts=delt;
   double **dnewm,**doldm;      for(k=1 ; k <kmax; k=k+1){
   double *xp;        delt = delta*(l1*k);
   double *gp, *gm;        p2[theta]=x[theta] +delt;
   double **gradg, **trgradg;        k1=func(p2)-fx;
   double age,agelim, cov[NCOVMAX];        p2[theta]=x[theta]-delt;
   int theta;        k2=func(p2)-fx;
   char fileresprob[FILENAMELENGTH];        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   strcpy(fileresprob,"prob");        
   strcat(fileresprob,fileres);  #ifdef DEBUG
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     printf("Problem with resultfile: %s\n", fileresprob);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   }  #endif
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   xp=vector(1,npar);        }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          k=kmax; l=lmax*10.;
          }
   cov[1]=1;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   for (age=bage; age<=fage; age ++){          delts=delt;
     cov[2]=age;        }
     gradg=matrix(1,npar,1,9);      }
     trgradg=matrix(1,9,1,npar);    }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    delti[theta]=delts;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    return res; 
        
     for(theta=1; theta <=npar; theta++){  }
       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)
        {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    int i;
        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;  
           gp[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<=npar; i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      k1=func(p2)-fx;
        
       p2[thetai]=x[thetai]+delti[thetai]/k;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k=0;      k2=func(p2)-fx;
       for(i=1; i<=(nlstate+ndeath); i++){    
         for(j=1; j<=(nlstate+ndeath);j++){      p2[thetai]=x[thetai]-delti[thetai]/k;
           k=k+1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           gm[k]=pmmij[i][j];      k3=func(p2)-fx;
         }    
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
            p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      k4=func(p2)-fx;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     }  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);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);
       for(theta=1; theta <=npar; theta++)  #endif
       trgradg[j][theta]=gradg[theta][j];    }
      return res;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
   /************** Inverse of matrix **************/
      pmij(pmmij,cov,ncovmodel,x,nlstate);  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
      k=0;    int i,imax,j,k; 
      for(i=1; i<=(nlstate+ndeath); i++){    double big,dum,sum,temp; 
        for(j=1; j<=(nlstate+ndeath);j++){    double *vv; 
          k=k+1;   
          gm[k]=pmmij[i][j];    vv=vector(1,n); 
         }    *d=1.0; 
      }    for (i=1;i<=n;i++) { 
            big=0.0; 
      /*printf("\n%d ",(int)age);      for (j=1;j<=n;j++) 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
              if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    } 
      }*/    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
   fprintf(ficresprob,"\n%d ",(int)age);        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        a[i][j]=sum; 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      } 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      big=0.0; 
   }      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        for (k=1;k<j;k++) 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          sum -= a[i][k]*a[k][j]; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        a[i][j]=sum; 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 }          big=dum; 
  free_vector(xp,1,npar);          imax=i; 
 fclose(ficresprob);        } 
       } 
 }      if (j != imax) { 
         for (k=1;k<=n;k++) { 
 /******************* Printing html file ***********/          dum=a[imax][k]; 
 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 optionfile[],char optionfilehtm[],char rfileres[] ){          a[imax][k]=a[j][k]; 
   int jj1, k1, i1, cpt;          a[j][k]=dum; 
   FILE *fichtm;        } 
   /*char optionfilehtm[FILENAMELENGTH];*/        *d = -(*d); 
         vv[imax]=vv[j]; 
   strcpy(optionfilehtm,optionfile);      } 
   strcat(optionfilehtm,".htm");      indx[j]=imax; 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      if (a[j][j] == 0.0) a[j][j]=TINY; 
     printf("Problem with %s \n",optionfilehtm), exit(0);      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">      } 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    } 
     free_vector(vv,1,n);  /* Doesn't work */
 Total number of observations=%d <br>  ;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  } 
 <hr  size=\"2\" color=\"#EC5E5E\">  
 <li>Outputs files<br><br>\n  void lubksb(double **a, int n, int *indx, double b[]) 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  { 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    int i,ii=0,ip,j; 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    double sum; 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>   
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for (i=1;i<=n;i++) { 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      ip=indx[i]; 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      sum=b[ip]; 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      b[ip]=b[i]; 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      if (ii) 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>      else if (sum) ii=i; 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      b[i]=sum; 
      } 
 fprintf(fichtm," <li>Graphs</li><p>");    for (i=n;i>=1;i--) { 
       sum=b[i]; 
  m=cptcoveff;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      b[i]=sum/a[i][i]; 
     } 
  jj1=0;  } 
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  /************ Frequencies ********************/
        jj1++;  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[])
        if (cptcovn > 0) {  {  /* Some frequencies */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    
          for (cpt=1; cpt<=cptcoveff;cpt++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    int first;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double ***freq; /* Frequencies */
        }    double *pp, **prop;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        FILE *ficresp;
        for(cpt=1; cpt<nlstate;cpt++){    char fileresp[FILENAMELENGTH];
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    pp=vector(1,nlstate);
        }    prop=matrix(1,nlstate,iagemin,iagemax+3);
     for(cpt=1; cpt<=nlstate;cpt++) {    strcpy(fileresp,"p");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    strcat(fileresp,fileres);
 interval) in state (%d): v%s%d%d.gif <br>    if((ficresp=fopen(fileresp,"w"))==NULL) {
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        printf("Problem with prevalence resultfile: %s\n", fileresp);
      }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      for(cpt=1; cpt<=nlstate;cpt++) {      exit(0);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      }    j1=0;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.gif<br>    j=cptcoveff;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 fprintf(fichtm,"\n</body>");  
    }    first=1;
    }  
 fclose(fichtm);    for(k1=1; k1<=j;k1++){
 }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
 /******************* Gnuplot file **************/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
   strcpy(optionfilegnuplot,optionfilefiname);              freq[i][jk][m]=0;
   strcat(optionfilegnuplot,".plt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      for (i=1; i<=nlstate; i++)  
     printf("Problem with file %s",optionfilegnuplot);        for(m=iagemin; m <= iagemax+3; m++)
   }          prop[i][m]=0;
         
 #ifdef windows        dateintsum=0;
     fprintf(ficgp,"cd \"%s\" \n",pathc);        k2cpt=0;
 #endif        for (i=1; i<=imx; i++) {
 m=pow(2,cptcoveff);          bool=1;
            if  (cptcovn>0) {
  /* 1eme*/            for (z1=1; z1<=cptcoveff; z1++) 
   for (cpt=1; cpt<= nlstate ; cpt ++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    for (k1=1; k1<= m ; k1 ++) {                bool=0;
           }
 #ifdef windows          if (bool==1){
     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);            for(m=firstpass; m<=lastpass; m++){
 #endif              k2=anint[m][i]+(mint[m][i]/12.);
 #ifdef unix              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 #endif                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 for (i=1; i<= nlstate ; i ++) {                if (m<lastpass) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 }                }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                
     for (i=1; i<= nlstate ; i ++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  dateintsum=dateintsum+k2;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  k2cpt++;
 }                }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                /*}*/
      for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }           
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 #ifdef unix  fprintf(ficresp, "#Local time at start: %s", strstart);
 fprintf(ficgp,"\nset ter gif small size 400,300");        if  (cptcovn>0) {
 #endif          fprintf(ficresp, "\n#********** Variable "); 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    }          fprintf(ficresp, "**********\n#");
   }        }
   /*2 eme*/        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   for (k1=1; k1<= m ; k1 ++) {        fprintf(ficresp, "\n");
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        
            for(i=iagemin; i <= iagemax+3; i++){
     for (i=1; i<= nlstate+1 ; i ++) {          if(i==iagemax+3){
       k=2*i;            fprintf(ficlog,"Total");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          }else{
       for (j=1; j<= nlstate+1 ; j ++) {            if(first==1){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              first=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              printf("See log file for details...\n");
 }              }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            fprintf(ficlog,"Age %d", i);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(jk=1; jk <=nlstate ; jk++){
       for (j=1; j<= nlstate+1 ; j ++) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              pp[jk] += freq[jk][m][i]; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }            for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,"\" t\"\" w l 0,");            for(m=-1, pos=0; m <=0 ; m++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              pos += freq[jk][m][i];
       for (j=1; j<= nlstate+1 ; j ++) {            if(pp[jk]>=1.e-10){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if(first==1){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 }                }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       else fprintf(ficgp,"\" t\"\" w l 0,");            }else{
     }              if(first==1)
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   /*3eme*/          }
   
   for (k1=1; k1<= m ; k1 ++) {          for(jk=1; jk <=nlstate ; jk++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       k=2+nlstate*(cpt-1);              pp[jk] += freq[jk][m][i];
       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);          }       
       for (i=1; i< nlstate ; i ++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         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);            pos += pp[jk];
       }            posprop += prop[jk][i];
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
     }          for(jk=1; jk <=nlstate ; jk++){
     }            if(pos>=1.e-5){
                if(first==1)
   /* CV preval stat */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (k1=1; k1<= m ; k1 ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (cpt=1; cpt<nlstate ; cpt ++) {            }else{
       k=3;              if(first==1)
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for (i=1; i< nlstate ; i ++)            }
         fprintf(ficgp,"+$%d",k+i+1);            if( i <= iagemax){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              if(pos>=1.e-5){
                      fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       l=3+(nlstate+ndeath)*cpt;                /*probs[i][jk][j1]= pp[jk]/pos;*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for (i=1; i< nlstate ; i ++) {              }
         l=3+(nlstate+ndeath)*cpt;              else
         fprintf(ficgp,"+$%d",l+i+1);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       }            }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          
     }          for(jk=-1; jk <=nlstate+ndeath; jk++)
   }              for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
   /* proba elementaires */              if(first==1)
    for(i=1,jk=1; i <=nlstate; i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(k=1; k <=(nlstate+ndeath); k++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       if (k != i) {              }
         for(j=1; j <=ncovmodel; j++){          if(i <= iagemax)
                    fprintf(ficresp,"\n");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          if(first==1)
           jk++;            printf("Others in log...\n");
           fprintf(ficgp,"\n");          fprintf(ficlog,"\n");
         }        }
       }      }
     }    }
     }    dateintmean=dateintsum/k2cpt; 
    
     for(jk=1; jk <=m; jk++) {    fclose(ficresp);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
    i=1;    free_vector(pp,1,nlstate);
    for(k2=1; k2<=nlstate; k2++) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      k3=i;    /* End of Freq */
      for(k=1; k<=(nlstate+ndeath); k++) {  }
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  /************ Prevalence ********************/
 ij=1;  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)
         for(j=3; j <=ncovmodel; j++) {  {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       in each health status at the date of interview (if between dateprev1 and dateprev2).
             ij++;       We still use firstpass and lastpass as another selection.
           }    */
           else   
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         }    double ***freq; /* Frequencies */
           fprintf(ficgp,")/(1");    double *pp, **prop;
            double pos,posprop; 
         for(k1=1; k1 <=nlstate; k1++){      double  y2; /* in fractional years */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    int iagemin, iagemax;
 ij=1;  
           for(j=3; j <=ncovmodel; j++){    iagemin= (int) agemin;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    iagemax= (int) agemax;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /*pp=vector(1,nlstate);*/
             ij++;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           else    j1=0;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    
           }    j=cptcoveff;
           fprintf(ficgp,")");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }    
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    for(k1=1; k1<=j;k1++){
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      for(i1=1; i1<=ncodemax[k1];i1++){
         i=i+ncovmodel;        j1++;
        }        
      }        for (i=1; i<=nlstate; i++)  
    }          for(m=iagemin; m <= iagemax+3; m++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            prop[i][m]=0.0;
    }       
            for (i=1; i<=imx; i++) { /* Each individual */
   fclose(ficgp);          bool=1;
 }  /* end gnuplot */          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 /*************** Moving average **************/                bool=0;
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          } 
           if (bool==1) { 
   int i, cpt, cptcod;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for (agedeb=agemin; agedeb<=fage; agedeb++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for (i=1; i<=nlstate;i++)              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           mobaverage[(int)agedeb][i][cptcod]=0.;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for (i=1; i<=nlstate;i++){                  /*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]]);*/
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           for (cpt=0;cpt<=4;cpt++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                } 
           }              }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            } /* end selection of waves */
         }          }
       }        }
     }        for(i=iagemin; i <= iagemax+3; i++){  
              
 }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
           } 
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              if(posprop>=1.e-5){ 
   int *popage;                probs[i][jk][j1]= prop[jk][i]/posprop;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              } 
   double *popeffectif,*popcount;            } 
   double ***p3mat;          }/* end jk */ 
   char fileresf[FILENAMELENGTH];        }/* end i */ 
       } /* end i1 */
  agelim=AGESUP;    } /* end k1 */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
    }  /* End of prevalence */
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);  /************* Waves Concatenation ***************/
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);  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)
   }  {
   printf("Computing forecasting: result on file '%s' \n", fileresf);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   if (mobilav==1) {       and mw[mi+1][i]. dh depends on stepm.
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       */
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;       double sum=0., jmean=0.;*/
   if (stepm<=12) stepsize=1;    int first;
      int j, k=0,jk, ju, jl;
   agelim=AGESUP;    double sum=0.;
      first=0;
   hstepm=1;    jmin=1e+5;
   hstepm=hstepm/stepm;    jmax=-1;
   yp1=modf(dateintmean,&yp);    jmean=0.;
   anprojmean=yp;    for(i=1; i<=imx; i++){
   yp2=modf((yp1*12),&yp);      mi=0;
   mprojmean=yp;      m=firstpass;
   yp1=modf((yp2*30.5),&yp);      while(s[m][i] <= nlstate){
   jprojmean=yp;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   if(jprojmean==0) jprojmean=1;          mw[++mi][i]=m;
   if(mprojmean==0) jprojmean=1;        if(m >=lastpass)
            break;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        else
            m++;
   for(cptcov=1;cptcov<=i2;cptcov++){      }/* end while */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if (s[m][i] > nlstate){
       k=k+1;        mi++;     /* Death is another wave */
       fprintf(ficresf,"\n#******");        /* if(mi==0)  never been interviewed correctly before death */
       for(j=1;j<=cptcoveff;j++) {           /* Only death is a correct wave */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        mw[mi][i]=m;
       }      }
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");      wav[i]=mi;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      if(mi==0){
              nbwarn++;
              if(first==0){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         fprintf(ficresf,"\n");          first=1;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          }
         if(first==1){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }
           nhstepm = nhstepm/hstepm;      } /* end mi==0 */
              } /* End individuals */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    for(i=1; i<=imx; i++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(mi=1; mi<wav[i];mi++){
                if (stepm <=0)
           for (h=0; h<=nhstepm; h++){          dh[mi][i]=1;
             if (h==(int) (calagedate+YEARM*cpt)) {        else{
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             }            if (agedc[i] < 2*AGESUP) {
             for(j=1; j<=nlstate+ndeath;j++) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               kk1=0.;kk2=0;              if(j==0) j=1;  /* Survives at least one month after exam */
               for(i=1; i<=nlstate;i++) {                            else if(j<0){
                 if (mobilav==1)                nberr++;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                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]);
                 else {                j=1; /* Temporary Dangerous patch */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                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);
               }              }
               if (h==(int)(calagedate+12*cpt)){              k=k+1;
                 fprintf(ficresf," %.3f", kk1);              if (j >= jmax){
                                        jmax=j;
               }                ijmax=i;
             }              }
           }              if (j <= jmin){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                jmin=j;
         }                ijmin=i;
       }              }
     }              sum=sum+j;
   }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                      /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
           }
   fclose(ficresf);          else{
 }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 /************** Forecasting ******************/  /*        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]); */
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  
              k=k+1;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            if (j >= jmax) {
   int *popage;              jmax=j;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              ijmax=i;
   double *popeffectif,*popcount;            }
   double ***p3mat,***tabpop,***tabpopprev;            else if (j <= jmin){
   char filerespop[FILENAMELENGTH];              jmin=j;
               ijmin=i;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   agelim=AGESUP;            /*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]);*/
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            if(j<0){
                nberr++;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              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]);
              }
   strcpy(filerespop,"pop");            sum=sum+j;
   strcat(filerespop,fileres);          }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          jk= j/stepm;
     printf("Problem with forecast resultfile: %s\n", filerespop);          jl= j -jk*stepm;
   }          ju= j -(jk+1)*stepm;
   printf("Computing forecasting: result on file '%s' \n", filerespop);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              dh[mi][i]=jk;
               bh[mi][i]=0;
   if (mobilav==1) {            }else{ /* We want a negative bias in order to only have interpolation ie
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    * at the price of an extra matrix product in likelihood */
     movingaverage(agedeb, fage, agemin, mobaverage);              dh[mi][i]=jk+1;
   }              bh[mi][i]=ju;
             }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }else{
   if (stepm<=12) stepsize=1;            if(jl <= -ju){
                dh[mi][i]=jk;
   agelim=AGESUP;              bh[mi][i]=jl;       /* bias is positive if real duration
                                     * is higher than the multiple of stepm and negative otherwise.
   hstepm=1;                                   */
   hstepm=hstepm/stepm;            }
              else{
   if (popforecast==1) {              dh[mi][i]=jk+1;
     if((ficpop=fopen(popfile,"r"))==NULL) {              bh[mi][i]=ju;
       printf("Problem with population file : %s\n",popfile);exit(0);            }
     }            if(dh[mi][i]==0){
     popage=ivector(0,AGESUP);              dh[mi][i]=1; /* At least one step */
     popeffectif=vector(0,AGESUP);              bh[mi][i]=ju; /* At least one step */
     popcount=vector(0,AGESUP);              /*  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);*/
                }
     i=1;            } /* end if mle */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        }
          } /* end wave */
     imx=i;    }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    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);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   for(cptcov=1;cptcov<=i2;cptcov++){   }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  /*********** Tricode ****************************/
       fprintf(ficrespop,"\n#******");  void tricode(int *Tvar, int **nbcode, int imx)
       for(j=1;j<=cptcoveff;j++) {  {
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       }    int Ndum[20],ij=1, k, j, i, maxncov=19;
       fprintf(ficrespop,"******\n");    int cptcode=0;
       fprintf(ficrespop,"# Age");    cptcoveff=0; 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);   
       if (popforecast==1)  fprintf(ficrespop," [Population]");    for (k=0; k<maxncov; k++) Ndum[k]=0;
          for (k=1; k<=7; k++) ncodemax[k]=0;
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
              for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){                                 modality*/ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           nhstepm = nhstepm/hstepm;        Ndum[ij]++; /*store the modality */
                  /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           oldm=oldms;savm=savms;                                         Tvar[j]. If V=sex and male is 0 and 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                                           female is 1, then  cptcode=1.*/
              }
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {      for (i=0; i<=cptcode; i++) {
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        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(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;      ij=1; 
               for(i=1; i<=nlstate;i++) {                    for (i=1; i<=ncodemax[j]; i++) {
                 if (mobilav==1)        for (k=0; k<= maxncov; k++) {
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          if (Ndum[k] != 0) {
                 else {            nbcode[Tvar[j]][ij]=k; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            /* 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 (h==(int)(calagedate+12*cpt)){          }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          if (ij > ncodemax[j]) break; 
                   /*fprintf(ficrespop," %.3f", kk1);        }  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      } 
               }    }  
             }  
             for(i=1; i<=nlstate;i++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){   for (i=1; i<=ncovmodel-2; i++) { 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                 }     ij=Tvar[i];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];     Ndum[ij]++;
             }   }
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)   ij=1;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);   for (i=1; i<= maxncov; i++) {
           }     if((Ndum[i]!=0) && (i<=ncovcol)){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       Tvaraff[ij]=i; /*For printing */
         }       ij++;
       }     }
     }
   /******/   
    cptcoveff=ij-1; /*Number of simple covariates*/
       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)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  /*********** Health Expectancies ****************/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  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[] )
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
           oldm=oldms;savm=savms;    /* Health expectancies */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
           for (h=0; h<=nhstepm; h++){    double age, agelim, hf;
             if (h==(int) (calagedate+YEARM*cpt)) {    double ***p3mat,***varhe;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double **dnewm,**doldm;
             }    double *xp;
             for(j=1; j<=nlstate+ndeath;j++) {    double **gp, **gm;
               kk1=0.;kk2=0;    double ***gradg, ***trgradg;
               for(i=1; i<=nlstate;i++) {                  int theta;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    xp=vector(1,npar);
             }    dnewm=matrix(1,nlstate*nlstate,1,npar);
           }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
         }    fprintf(ficreseij,"# Local time at start: %s", strstart);
       }    fprintf(ficreseij,"# Health expectancies\n");
    }    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);    if(estepm < stepm){
     free_vector(popeffectif,0,AGESUP);      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_vector(popcount,0,AGESUP);    }
   }    else  hstepm=estepm;   
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* We compute the life expectancy from trapezoids spaced every estepm months
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * This is mainly to measure the difference between two models: for example
   fclose(ficrespop);     * if stepm=24 months pijx are given only every 2 years and by summing them
 }     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
 /***********************************************/     * to the curvature of the survival function. If, for the same date, we 
 /**************** Main Program *****************/     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 /***********************************************/     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 int main(int argc, char *argv[])     * curvature will be obtained if estepm is as small as stepm. */
 {  
     /* For example we decided to compute the life expectancy with the smallest unit */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double agedeb, agefin,hf;       nhstepm is the number of hstepm from age to agelim 
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   double fret;       and note for a fixed period like estepm months */
   double **xi,tmp,delta;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   double dum; /* Dummy variable */       means that if the survival funtion is printed only each two years of age and if
   double ***p3mat;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   int *indx;       results. So we changed our mind and took the option of the best precision.
   char line[MAXLINE], linepar[MAXLINE];    */
   char title[MAXLINE];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    agelim=AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   char filerest[FILENAMELENGTH];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   char fileregp[FILENAMELENGTH];      /* if (stepm >= YEARM) hstepm=1;*/
   char popfile[FILENAMELENGTH];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int firstobs=1, lastobs=10;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   int sdeb, sfin; /* Status at beginning and end */      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   int c,  h , cpt,l;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   int mobilav=0,popforecast=0;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   int hstepm, nhstepm;   
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;      /* Computing  Variances of health expectancies */
   double **prlim;  
   double *severity;       for(theta=1; theta <=npar; theta++){
   double ***param; /* Matrix of parameters */        for(i=1; i<=npar; i++){ 
   double  *p;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double **matcov; /* Matrix of covariance */        }
   double ***delti3; /* Scale */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double *delti; /* Scale */    
   double ***eij, ***vareij;        cptj=0;
   double **varpl; /* Variances of prevalence limits by age */        for(j=1; j<= nlstate; j++){
   double *epj, vepp;          for(i=1; i<=nlstate; i++){
   double kk1, kk2;            cptj=cptj+1;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";          }
   char *alph[]={"a","a","b","c","d","e"}, str[4];        }
        
        
   char z[1]="c", occ;        for(i=1; i<=npar; i++) 
 #include <sys/time.h>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 #include <time.h>        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        
          cptj=0;
   /* long total_usecs;        for(j=1; j<= nlstate; j++){
   struct timeval start_time, end_time;          for(i=1;i<=nlstate;i++){
              cptj=cptj+1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   printf("\n%s",version);            }
   if(argc <=1){          }
     printf("\nEnter the parameter file name: ");        }
     scanf("%s",pathtot);        for(j=1; j<= nlstate*nlstate; j++)
   }          for(h=0; h<=nhstepm-1; h++){
   else{            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     strcpy(pathtot,argv[1]);          }
   }       } 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/     
   /*cygwin_split_path(pathtot,path,optionfile);  /* End theta */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);       for(h=0; h<=nhstepm-1; h++)
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for(j=1; j<=nlstate*nlstate;j++)
   chdir(path);          for(theta=1; theta <=npar; theta++)
   replace(pathc,path);            trgradg[h][j][theta]=gradg[h][theta][j];
        
 /*-------- arguments in the command line --------*/  
        for(i=1;i<=nlstate*nlstate;i++)
   strcpy(fileres,"r");        for(j=1;j<=nlstate*nlstate;j++)
   strcat(fileres, optionfilefiname);          varhe[i][j][(int)age] =0.;
   strcat(fileres,".txt");    /* Other files have txt extension */  
        printf("%d|",(int)age);fflush(stdout);
   /*---------arguments file --------*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for(k=0;k<=nhstepm-1;k++){
     printf("Problem with optionfile %s\n",optionfile);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     goto end;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   }          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1;j<=nlstate*nlstate;j++)
   strcpy(filereso,"o");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   strcat(filereso,fileres);        }
   if((ficparo=fopen(filereso,"w"))==NULL) {      }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      /* Computing expectancies */
   }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);  /* 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]);*/
     puts(line);  
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
   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);      for(i=1; i<=nlstate;i++)
   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);        for(j=1; j<=nlstate;j++){
   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);          cptj++;
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      fprintf(ficreseij,"\n");
     puts(line);     
     fputs(line,ficparo);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   ungetc(c,ficpar);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   covar=matrix(0,NCOVMAX,1,n);    }
   cptcovn=0;    printf("\n");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fprintf(ficlog,"\n");
   
   ncovmodel=2+cptcovn;    free_vector(xp,1,npar);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   /* Read guess parameters */    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   /* Reads comments: lines beginning with '#' */  }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /************ Variance ******************/
     fgets(line, MAXLINE, ficpar);  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[])
     puts(line);  {
     fputs(line,ficparo);    /* Variance of health expectancies */
   }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   ungetc(c,ficpar);    /* double **newm;*/
      double **dnewm,**doldm;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double **dnewmp,**doldmp;
     for(i=1; i <=nlstate; i++)    int i, j, nhstepm, hstepm, h, nstepm ;
     for(j=1; j <=nlstate+ndeath-1; j++){    int k, cptcode;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double *xp;
       fprintf(ficparo,"%1d%1d",i1,j1);    double **gp, **gm;  /* for var eij */
       printf("%1d%1d",i,j);    double ***gradg, ***trgradg; /*for var eij */
       for(k=1; k<=ncovmodel;k++){    double **gradgp, **trgradgp; /* for var p point j */
         fscanf(ficpar," %lf",&param[i][j][k]);    double *gpp, *gmp; /* for var p point j */
         printf(" %lf",param[i][j][k]);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         fprintf(ficparo," %lf",param[i][j][k]);    double ***p3mat;
       }    double age,agelim, hf;
       fscanf(ficpar,"\n");    double ***mobaverage;
       printf("\n");    int theta;
       fprintf(ficparo,"\n");    char digit[4];
     }    char digitp[25];
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    char fileresprobmorprev[FILENAMELENGTH];
   
   p=param[1][1];    if(popbased==1){
        if(mobilav!=0)
   /* Reads comments: lines beginning with '#' */        strcpy(digitp,"-populbased-mobilav-");
   while((c=getc(ficpar))=='#' && c!= EOF){      else strcpy(digitp,"-populbased-nomobil-");
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    else 
     puts(line);      strcpy(digitp,"-stablbased-");
     fputs(line,ficparo);  
   }    if (mobilav!=0) {
   ungetc(c,ficpar);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   for(i=1; i <=nlstate; i++){      }
     for(j=1; j <=nlstate+ndeath-1; j++){    }
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    strcpy(fileresprobmorprev,"prmorprev"); 
       fprintf(ficparo,"%1d%1d",i1,j1);    sprintf(digit,"%-d",ij);
       for(k=1; k<=ncovmodel;k++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         fscanf(ficpar,"%le",&delti3[i][j][k]);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         printf(" %le",delti3[i][j][k]);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         fprintf(ficparo," %le",delti3[i][j][k]);    strcat(fileresprobmorprev,fileres);
       }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fscanf(ficpar,"\n");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       printf("\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficparo,"\n");    }
     }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   }   
   delti=delti3[1][1];    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   /* Reads comments: lines beginning with '#' */    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);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     ungetc(c,ficpar);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fgets(line, MAXLINE, ficpar);      fprintf(ficresprobmorprev," p.%-d SE",j);
     puts(line);      for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   }    }  
   ungetc(c,ficpar);    fprintf(ficresprobmorprev,"\n");
      fprintf(ficgp,"\n# Routine varevsij");
   matcov=matrix(1,npar,1,npar);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   for(i=1; i <=npar; 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");
     fscanf(ficpar,"%s",&str);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     printf("%s",str);  /*   } */
     fprintf(ficparo,"%s",str);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(j=1; j <=i; j++){   fprintf(ficresvij, "#Local time at start: %s", strstart);
       fscanf(ficpar," %le",&matcov[i][j]);    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");
       printf(" %.5le",matcov[i][j]);    fprintf(ficresvij,"# Age");
       fprintf(ficparo," %.5le",matcov[i][j]);    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     fscanf(ficpar,"\n");        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     printf("\n");    fprintf(ficresvij,"\n");
     fprintf(ficparo,"\n");  
   }    xp=vector(1,npar);
   for(i=1; i <=npar; i++)    dnewm=matrix(1,nlstate,1,npar);
     for(j=i+1;j<=npar;j++)    doldm=matrix(1,nlstate,1,nlstate);
       matcov[i][j]=matcov[j][i];    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
        doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("\n");  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     /*-------- Rewriting paramater file ----------*/    gmp=vector(nlstate+1,nlstate+ndeath);
      strcpy(rfileres,"r");    /* "Rparameterfile */    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    
      strcat(rfileres,".");    /* */    if(estepm < stepm){
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      printf ("Problem %d lower than %d\n",estepm, stepm);
     if((ficres =fopen(rfileres,"w"))==NULL) {    }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    else  hstepm=estepm;   
     }    /* For example we decided to compute the life expectancy with the smallest unit */
     fprintf(ficres,"#%s\n",version);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm is the number of hstepm from age to agelim 
     /*-------- data file ----------*/       nstepm is the number of stepm from age to agelin. 
     if((fic=fopen(datafile,"r"))==NULL)    {       Look at hpijx to understand the reason of that which relies in memory size
       printf("Problem with datafile: %s\n", datafile);goto end;       and note for a fixed period like k years */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
     n= lastobs;       means that if the survival funtion is printed every two years of age and if
     severity = vector(1,maxwav);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     outcome=imatrix(1,maxwav+1,1,n);       results. So we changed our mind and took the option of the best precision.
     num=ivector(1,n);    */
     moisnais=vector(1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     annais=vector(1,n);    agelim = AGESUP;
     moisdc=vector(1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     andc=vector(1,n);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     agedc=vector(1,n);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     cod=ivector(1,n);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     weight=vector(1,n);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      gp=matrix(0,nhstepm,1,nlstate);
     mint=matrix(1,maxwav,1,n);      gm=matrix(0,nhstepm,1,nlstate);
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);          for(theta=1; theta <=npar; theta++){
     tab=ivector(1,NCOVMAX);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     ncodemax=ivector(1,8);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
     i=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     while (fgets(line, MAXLINE, fic) != NULL)    {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       if ((i >= firstobs) && (i <=lastobs)) {  
                if (popbased==1) {
         for (j=maxwav;j>=1;j--){          if(mobilav ==0){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            for(i=1; i<=nlstate;i++)
           strcpy(line,stra);              prlim[i][i]=probs[(int)age][i][ij];
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }else{ /* mobilav */ 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=mobaverage[(int)age][i][ij];
                  }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    
         for(j=1; j<= nlstate; j++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          for(h=0; h<=nhstepm; h++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         for (j=ncov;j>=1;j--){        }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        /* This for computing probability of death (h=1 means
         }           computed over hstepm matrices product = hstepm*stepm months) 
         num[i]=atol(stra);           as a weighted average of prlim.
                */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           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;}*/          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         i=i+1;        }    
       }        /* end probability of death */
     }  
     /* printf("ii=%d", ij);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
        scanf("%d",i);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   imx=i-1; /* Number of individuals */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* for (i=1; i<=imx; i++){   
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        if (popbased==1) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          if(mobilav ==0){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
     for (i=1; i<=imx; i++)            for(i=1; i<=nlstate;i++)
     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]));*/              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);        for(j=1; j<= nlstate; j++){
   Tvaraff=ivector(1,15);          for(h=0; h<=nhstepm; h++){
   Tvard=imatrix(1,15,1,2);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   Tage=ivector(1,15);                    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
   if (strlen(model) >1){        }
     j=0, j1=0, k1=1, k2=1;        /* This for computing probability of death (h=1 means
     j=nbocc(model,'+');           computed over hstepm matrices product = hstepm*stepm months) 
     j1=nbocc(model,'*');           as a weighted average of prlim.
     cptcovn=j+1;        */
     cptcovprod=j1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gmp[j]=0.; i<= nlstate; i++)
               gmp[j] += prlim[i][i]*p3mat[i][j][1];
     strcpy(modelsav,model);        }    
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        /* end probability of death */
       printf("Error. Non available option model=%s ",model);  
       goto end;        for(j=1; j<= nlstate; j++) /* vareij */
     }          for(h=0; h<=nhstepm; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(i=(j+1); i>=1;i--){          }
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       /*scanf("%d",i);*/        }
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');      } /* End theta */
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);      for(h=0; h<=nhstepm; h++) /* veij */
           cptcovage++;        for(j=1; j<=nlstate;j++)
             Tage[cptcovage]=i;          for(theta=1; theta <=npar; theta++)
             /*printf("stre=%s ", stre);*/            trgradg[h][j][theta]=gradg[h][theta][j];
         }  
         else if (strcmp(strd,"age")==0) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           cptcovprod--;        for(theta=1; theta <=npar; theta++)
           cutv(strb,stre,strc,'V');          trgradgp[j][theta]=gradgp[theta][j];
           Tvar[i]=atoi(stre);    
           cptcovage++;  
           Tage[cptcovage]=i;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         }      for(i=1;i<=nlstate;i++)
         else {        for(j=1;j<=nlstate;j++)
           cutv(strb,stre,strc,'V');          vareij[i][j][(int)age] =0.;
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');      for(h=0;h<=nhstepm;h++){
           Tprod[k1]=i;        for(k=0;k<=nhstepm;k++){
           Tvard[k1][1]=atoi(strc);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           Tvard[k1][2]=atoi(stre);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           Tvar[cptcovn+k2]=Tvard[k1][1];          for(i=1;i<=nlstate;i++)
           Tvar[cptcovn+k2+1]=Tvard[k1][2];            for(j=1;j<=nlstate;j++)
           for (k=1; k<=lastobs;k++)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        }
           k1++;      }
           k2=k2+2;    
         }      /* pptj */
       }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       else {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      for(j=nlstate+1;j<=nlstate+ndeath;j++)
        /*  scanf("%d",i);*/        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       cutv(strd,strc,strb,'V');          varppt[j][i]=doldmp[j][i];
       Tvar[i]=atoi(strc);      /* end ppptj */
       }      /*  x centered again */
       strcpy(modelsav,stra);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         scanf("%d",i);*/   
     }      if (popbased==1) {
 }        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            prlim[i][i]=probs[(int)age][i][ij];
   printf("cptcovprod=%d ", cptcovprod);        }else{ /* mobilav */ 
   scanf("%d ",i);*/          for(i=1; i<=nlstate;i++)
     fclose(fic);            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
     /*  if(mle==1){*/      }
     if (weightopt != 1) { /* Maximisation without weights*/               
       for(i=1;i<=n;i++) weight[i]=1.0;      /* This for computing probability of death (h=1 means
     }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     /*-calculation of age at interview from date of interview and age at death -*/         as a weighted average of prlim.
     agev=matrix(1,maxwav,1,imx);      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
    for (i=1; i<=imx; i++)        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
      for(m=2; (m<= maxwav); m++)          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      }    
          anint[m][i]=9999;      /* end probability of death */
          s[m][i]=-1;  
        }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     for (i=1; i<=imx; i++)  {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(i=1; i<=nlstate;i++){
       for(m=1; (m<= maxwav); m++){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         if(s[m][i] >0){        }
           if (s[m][i] == nlstate+1) {      } 
             if(agedc[i]>0)      fprintf(ficresprobmorprev,"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)  
               agev[m][i]=agedc[i];      fprintf(ficresvij,"%.0f ",age );
             else {      for(i=1; i<=nlstate;i++)
               if (andc[i]!=9999){        for(j=1; j<=nlstate;j++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
               agev[m][i]=-1;        }
               }      fprintf(ficresvij,"\n");
             }      free_matrix(gp,0,nhstepm,1,nlstate);
           }      free_matrix(gm,0,nhstepm,1,nlstate);
           else if(s[m][i] !=9){ /* Should no more exist */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
             if(mint[m][i]==99 || anint[m][i]==9999)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               agev[m][i]=1;    } /* End age */
             else if(agev[m][i] <agemin){    free_vector(gpp,nlstate+1,nlstate+ndeath);
               agemin=agev[m][i];    free_vector(gmp,nlstate+1,nlstate+ndeath);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             else if(agev[m][i] >agemax){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
               agemax=agev[m][i];    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    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); */
             /*agev[m][i]=anint[m][i]-annais[i];*/  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
             /*   agev[m][i] = age[i]+2*m;*/  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           else { /* =9 */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
             agev[m][i]=1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
             s[m][i]=-1;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
         else /*= 0 Unknown */  */
           agev[m][i]=1;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      
     }    free_vector(xp,1,npar);
     for (i=1; i<=imx; i++)  {    free_matrix(doldm,1,nlstate,1,nlstate);
       for(m=1; (m<= maxwav); m++){    free_matrix(dnewm,1,nlstate,1,npar);
         if (s[m][i] > (nlstate+ndeath)) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           printf("Error: Wrong value in nlstate or ndeath\n");      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           goto end;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }    fclose(ficresprobmorprev);
     }    fflush(ficgp);
     fflush(fichtm); 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  }  /* end varevsij */
   
     free_vector(severity,1,maxwav);  /************ Variance of prevlim ******************/
     free_imatrix(outcome,1,maxwav+1,1,n);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
     free_vector(moisnais,1,n);  {
     free_vector(annais,1,n);    /* Variance of prevalence limit */
     /* free_matrix(mint,1,maxwav,1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
        free_matrix(anint,1,maxwav,1,n);*/    double **newm;
     free_vector(moisdc,1,n);    double **dnewm,**doldm;
     free_vector(andc,1,n);    int i, j, nhstepm, hstepm;
     int k, cptcode;
        double *xp;
     wav=ivector(1,imx);    double *gp, *gm;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double **gradg, **trgradg;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    double age,agelim;
        int theta;
     /* Concatenates waves */    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
       Tcode=ivector(1,100);        fprintf(ficresvpl," %1d-%1d",i,i);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    fprintf(ficresvpl,"\n");
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    xp=vector(1,npar);
          dnewm=matrix(1,nlstate,1,npar);
    codtab=imatrix(1,100,1,10);    doldm=matrix(1,nlstate,1,nlstate);
    h=0;    
    m=pow(2,cptcoveff);    hstepm=1*YEARM; /* Every year of age */
      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
    for(k=1;k<=cptcoveff; k++){    agelim = AGESUP;
      for(i=1; i <=(m/pow(2,k));i++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        for(j=1; j <= ncodemax[k]; j++){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      if (stepm >= YEARM) hstepm=1;
            h++;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
            if (h>m) h=1;codtab[h][k]=j;      gradg=matrix(1,npar,1,nlstate);
          }      gp=vector(1,nlstate);
        }      gm=vector(1,nlstate);
      }  
    }      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
    /*for(i=1; i <=m ;i++){        }
      for(k=1; k <=cptcovn; k++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        for(i=1;i<=nlstate;i++)
      }          gp[i] = prlim[i][i];
      printf("\n");      
    }        for(i=1; i<=npar; i++) /* Computes gradient */
    scanf("%d",i);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    /* Calculates basic frequencies. Computes observed prevalence at single age        for(i=1;i<=nlstate;i++)
        and prints on file fileres'p'. */          gm[i] = prlim[i][i];
   
            for(i=1;i<=nlstate;i++)
              gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      } /* End theta */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      trgradg =matrix(1,nlstate,1,npar);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
     /* For Powell, parameters are in a vector p[] starting at p[1]          trgradg[j][theta]=gradg[theta][j];
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
     if(mle==1){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     }      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     /*--------- 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= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);      fprintf(ficresvpl,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
    jk=1;      fprintf(ficresvpl,"\n");
    fprintf(ficres,"# Parameters\n");      free_vector(gp,1,nlstate);
    printf("# Parameters\n");      free_vector(gm,1,nlstate);
    for(i=1,jk=1; i <=nlstate; i++){      free_matrix(gradg,1,npar,1,nlstate);
      for(k=1; k <=(nlstate+ndeath); k++){      free_matrix(trgradg,1,nlstate,1,npar);
        if (k != i)    } /* End age */
          {  
            printf("%d%d ",i,k);    free_vector(xp,1,npar);
            fprintf(ficres,"%1d%1d ",i,k);    free_matrix(doldm,1,nlstate,1,npar);
            for(j=1; j <=ncovmodel; j++){    free_matrix(dnewm,1,nlstate,1,nlstate);
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);  }
              jk++;  
            }  /************ Variance of one-step probabilities  ******************/
            printf("\n");  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
            fprintf(ficres,"\n");  {
          }    int i, j=0,  i1, k1, l1, t, tj;
      }    int k2, l2, j1,  z1;
    }    int k=0,l, cptcode;
  if(mle==1){    int first=1, first1;
     /* Computing hessian and covariance matrix */    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     ftolhess=ftol; /* Usually correct */    double **dnewm,**doldm;
     hesscov(matcov, p, npar, delti, ftolhess, func);    double *xp;
  }    double *gp, *gm;
     fprintf(ficres,"# Scales\n");    double **gradg, **trgradg;
     printf("# Scales\n");    double **mu;
      for(i=1,jk=1; i <=nlstate; i++){    double age,agelim, cov[NCOVMAX];
       for(j=1; j <=nlstate+ndeath; j++){    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         if (j!=i) {    int theta;
           fprintf(ficres,"%1d%1d",i,j);    char fileresprob[FILENAMELENGTH];
           printf("%1d%1d",i,j);    char fileresprobcov[FILENAMELENGTH];
           for(k=1; k<=ncovmodel;k++){    char fileresprobcor[FILENAMELENGTH];
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);    double ***varpij;
             jk++;  
           }    strcpy(fileresprob,"prob"); 
           printf("\n");    strcat(fileresprob,fileres);
           fprintf(ficres,"\n");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", fileresprob);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }    }
        strcpy(fileresprobcov,"probcov"); 
     k=1;    strcat(fileresprobcov,fileres);
     fprintf(ficres,"# Covariance\n");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     printf("# Covariance\n");      printf("Problem with resultfile: %s\n", fileresprobcov);
     for(i=1;i<=npar;i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       /*  if (k>nlstate) k=1;    }
       i1=(i-1)/(ncovmodel*nlstate)+1;    strcpy(fileresprobcor,"probcor"); 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    strcat(fileresprobcor,fileres);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       fprintf(ficres,"%3d",i);      printf("Problem with resultfile: %s\n", fileresprobcor);
       printf("%3d",i);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       for(j=1; j<=i;j++){    }
         fprintf(ficres," %.5e",matcov[i][j]);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         printf(" %.5e",matcov[i][j]);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficres,"\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       printf("\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       k++;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     }    fprintf(ficresprob, "#Local time at start: %s", strstart);
        fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprob,"# Age");
       ungetc(c,ficpar);    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
       fgets(line, MAXLINE, ficpar);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       puts(line);    fprintf(ficresprobcov,"# Age");
       fputs(line,ficparo);    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     ungetc(c,ficpar);    fprintf(ficresprobcov,"# Age");
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);  
        for(i=1; i<=nlstate;i++)
     if (fage <= 2) {      for(j=1; j<=(nlstate+ndeath);j++){
       bage = agemin;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fage = agemaxpar;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
          }  
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");   /* fprintf(ficresprob,"\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    fprintf(ficresprobcov,"\n");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    fprintf(ficresprobcor,"\n");
     */
     while((c=getc(ficpar))=='#' && c!= EOF){   xp=vector(1,npar);
     ungetc(c,ficpar);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fgets(line, MAXLINE, ficpar);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     puts(line);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     fputs(line,ficparo);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   }    first=1;
   ungetc(c,ficpar);    fprintf(ficgp,"\n# Routine varprob");
      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    fprintf(fichtm,"\n");
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    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\
   while((c=getc(ficpar))=='#' && c!= EOF){    file %s<br>\n",optionfilehtmcov);
     ungetc(c,ficpar);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     fgets(line, MAXLINE, ficpar);  and drawn. It helps understanding how is the covariance between two incidences.\
     puts(line);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fputs(line,ficparo);    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   }  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   ungetc(c,ficpar);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
    standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    dateprev1=anprev1+mprev1/12.+jprev1/365.;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    cov[1]=1;
   fprintf(ficparo,"pop_based=%d\n",popbased);      tj=cptcoveff;
   fprintf(ficres,"pop_based=%d\n",popbased);      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      j1=0;
   while((c=getc(ficpar))=='#' && c!= EOF){    for(t=1; t<=tj;t++){
     ungetc(c,ficpar);      for(i1=1; i1<=ncodemax[t];i1++){ 
     fgets(line, MAXLINE, ficpar);        j1++;
     puts(line);        if  (cptcovn>0) {
     fputs(line,ficparo);          fprintf(ficresprob, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   ungetc(c,ficpar);          fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficresprobcov, "**********\n#\n");
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp, "**********\n#\n");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          
     puts(line);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     fputs(line,ficparo);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   ungetc(c,ficpar);          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          fprintf(ficresprobcor, "**********\n#");    
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
         
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
 /*------------ gnuplot -------------*/          for (k=1; k<=cptcovn;k++) {
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
            }
 /*------------ free_vector  -------------*/          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
  chdir(path);          for (k=1; k<=cptcovprod;k++)
              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
  free_ivector(wav,1,imx);          
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
  free_ivector(num,1,n);          gp=vector(1,(nlstate)*(nlstate+ndeath));
  free_vector(agedc,1,n);          gm=vector(1,(nlstate)*(nlstate+ndeath));
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      
  fclose(ficparo);          for(theta=1; theta <=npar; theta++){
  fclose(ficres);            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
 /*--------- index.htm --------*/            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);            
             k=0;
              for(i=1; i<= (nlstate); i++){
   /*--------------- Prevalence limit --------------*/              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   strcpy(filerespl,"pl");                gp[k]=pmmij[i][j];
   strcat(filerespl,fileres);              }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            
   }            for(i=1; i<=npar; i++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   fprintf(ficrespl,"#Prevalence limit\n");      
   fprintf(ficrespl,"#Age ");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            k=0;
   fprintf(ficrespl,"\n");            for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
   prlim=matrix(1,nlstate,1,nlstate);                k=k+1;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                gm[k]=pmmij[i][j];
   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(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   k=0;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   agebase=agemin;          }
   agelim=agemaxpar;  
   ftolpl=1.e-10;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   i1=cptcoveff;            for(theta=1; theta <=npar; theta++)
   if (cptcovn < 1){i1=1;}              trgradg[j][theta]=gradg[theta][j];
           
   for(cptcov=1;cptcov<=i1;cptcov++){          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         k=k+1;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficrespl,"\n#******");          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for(j=1;j<=cptcoveff;j++)          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");          pmij(pmmij,cov,ncovmodel,x,nlstate);
                  
         for (age=agebase; age<=agelim; age++){          k=0;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for(i=1; i<=(nlstate); i++){
           fprintf(ficrespl,"%.0f",age );            for(j=1; j<=(nlstate+ndeath);j++){
           for(i=1; i<=nlstate;i++)              k=k+1;
           fprintf(ficrespl," %.5f", prlim[i][i]);              mu[k][(int) age]=pmmij[i][j];
           fprintf(ficrespl,"\n");            }
         }          }
       }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   fclose(ficrespl);              varpij[i][j][(int)age] = doldm[i][j];
   
   /*------------- h Pij x at various ages ------------*/          /*printf("\n%d ",(int)age);
              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            }*/
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);          fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficresprobcov,"\n%d ",(int)age);
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficresprobcor,"\n%d ",(int)age);
   /*if (stepm<=24) stepsize=2;*/  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   agelim=AGESUP;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   hstepm=stepsize*YEARM; /* Every year of age */          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
              fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){          i=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (k=1; k<=(nlstate);k++){
       k=k+1;            for (l=1; l<=(nlstate+ndeath);l++){ 
         fprintf(ficrespij,"\n#****** ");              i=i++;
         for(j=1;j<=cptcoveff;j++)              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
         fprintf(ficrespij,"******\n");              for (j=1; j<=i;j++){
                        fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }/* end of loop for state */
           oldm=oldms;savm=savms;        } /* end of loop for age */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");        /* Confidence intervalle of pij  */
           for(i=1; i<=nlstate;i++)        /*
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp,"\nset noparametric;unset label");
               fprintf(ficrespij," %1d-%1d",i,j);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficrespij,"\n");          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           for (h=0; h<=nhstepm; h++){          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
             for(i=1; i<=nlstate;i++)          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
               for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        */
             fprintf(ficrespij,"\n");  
           }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        first1=1;
           fprintf(ficrespij,"\n");        for (k2=1; k2<=(nlstate);k2++){
         }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     }            if(l2==k2) continue;
   }            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
   fclose(ficrespij);                i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
   /*---------- Forecasting ------------------*/                  if ((int)age %5==0){
   if(stepm == 1) {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     free_matrix(mint,1,maxwav,1,n);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                    mu2=mu[j][(int) age]/stepm*YEARM;
     free_vector(weight,1,n);}                    c12=cv12/sqrt(v1*v2);
   else{                    /* Computing eigen value of matrix of covariance */
     erreur=108;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     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);                    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 */
   /*---------- Health expectancies and variances ------------*/                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
   strcpy(filerest,"t");                    v22=v11;
   strcat(filerest,fileres);                    tnalp=v21/v11;
   if((ficrest=fopen(filerest,"w"))==NULL) {                    if(first1==1){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                      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);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                    }
                     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*/
   strcpy(filerese,"e");                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   strcat(filerese,fileres);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   if((ficreseij=fopen(filerese,"w"))==NULL) {                    if(first==1){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                      first=0;
   }                      fprintf(ficgp,"\nset parametric;unset label");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                      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");
  strcpy(fileresv,"v");                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   strcat(fileresv,fileres);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   }                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                      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);
   k=0;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   for(cptcov=1;cptcov<=i1;cptcov++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       k=k+1;                      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",\
       fprintf(ficrest,"\n#****** ");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       for(j=1;j<=cptcoveff;j++)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    }else{
       fprintf(ficrest,"******\n");                      first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       fprintf(ficreseij,"\n#****** ");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
       fprintf(ficreseij,"******\n");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       fprintf(ficresvij,"\n#****** ");                    }/* if first */
       for(j=1;j<=cptcoveff;j++)                  } /* age mod 5 */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                } /* end loop age */
       fprintf(ficresvij,"******\n");                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              } /*l12 */
       oldm=oldms;savm=savms;            } /* k12 */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            } /*l1 */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }/* k1 */
       oldm=oldms;savm=savms;      } /* loop covariates */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    }
        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_vector(xp,1,npar);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fclose(ficresprob);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fclose(ficresprobcov);
       fprintf(ficrest,"\n");    fclose(ficresprobcor);
     fflush(ficgp);
       hf=1;    fflush(fichtmcov);
       if (stepm >= YEARM) hf=stepm/YEARM;  }
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  /******************* Printing html file ***********/
         if (popbased==1) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
           for(i=1; i<=nlstate;i++)                    int lastpass, int stepm, int weightopt, char model[],\
             prlim[i][i]=probs[(int)age][i][k];                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
         }                    int popforecast, int estepm ,\
                            double jprev1, double mprev1,double anprev1, \
         fprintf(ficrest," %.0f",age);                    double jprev2, double mprev2,double anprev2){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    int jj1, k1, i1, cpt;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];     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 \
           epj[nlstate+1] +=epj[j];  </ul>");
         }     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
         for(i=1, vepp=0.;i <=nlstate;i++)   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
           for(j=1;j <=nlstate;j++)             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
             vepp += vareij[i][j][(int)age];     fprintf(fichtm,"\
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
         for(j=1;j <=nlstate;j++){             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));     fprintf(fichtm,"\
         }   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficrest,"\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"));
   fclose(ficreseij);  
   fclose(ficresvij);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   fclose(ficrest);  
   fclose(ficpar);   m=cptcoveff;
   free_vector(epj,1,nlstate+1);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   /*------- Variance limit prevalence------*/     jj1=0;
    for(k1=1; k1<=m;k1++){
   strcpy(fileresvpl,"vpl");     for(i1=1; i1<=ncodemax[k1];i1++){
   strcat(fileresvpl,fileres);       jj1++;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {       if (cptcovn > 0) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     exit(0);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   k=0;       /* Pij */
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
       k=k+1;       /* Quasi-incidences */
       fprintf(ficresvpl,"\n#****** ");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       for(j=1;j<=cptcoveff;j++)   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       fprintf(ficresvpl,"******\n");         /* Stable prevalence in each health state */
               for(cpt=1; cpt<nlstate;cpt++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       oldm=oldms;savm=savms;  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         }
     }       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);
   fclose(ficresvpl);       }
      } /* end i1 */
   /*---------- End : free ----------------*/   }/* End k1 */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   fprintf(fichtm,"</ul>");
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   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);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   fprintf(fichtm,"\
     - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   free_matrix(matcov,1,npar,1,npar);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);   fprintf(fichtm,"\
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   if(erreur >0)   fprintf(fichtm,"\
     printf("End of Imach with error %d\n",erreur);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   else   printf("End of Imach\n");           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */   fprintf(fichtm,"\
     - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   /* 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);*/           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   /*printf("Total time was %d uSec.\n", total_usecs);*/   fprintf(fichtm,"\
   /*------ End -----------*/   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
  end:  /*  if(popforecast==1) fprintf(fichtm,"\n */
 #ifdef windows  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /* chdir(pathcd);*/  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
 #endif  /*      <br>",fileres,fileres,fileres,fileres); */
  /*system("wgnuplot graph.plt");*/  /*  else  */
  /*system("../gp37mgw/wgnuplot graph.plt");*/  /*    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); */
  /*system("cd ../gp37mgw");*/   fflush(fichtm);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");   m=cptcoveff;
  strcat(plotcmd,optionfilegnuplot);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  system(plotcmd);  
    jj1=0;
 #ifdef windows   for(k1=1; k1<=m;k1++){
   while (z[0] != 'q') {     for(i1=1; i1<=ncodemax[k1];i1++){
     chdir(path);       jj1++;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       if (cptcovn > 0) {
     scanf("%s",z);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     if (z[0] == 'c') system("./imach");         for (cpt=1; cpt<=cptcoveff;cpt++) 
     else if (z[0] == 'e') {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
       chdir(path);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       system(optionfilehtm);       }
     }       for(cpt=1; cpt<=nlstate;cpt++) {
     else if (z[0] == 'q') exit(0);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   }  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
 #endif  <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 */
     /* 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);
     fclose(fic);*/
   
       /*  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(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);
   
   
     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.1.29  
changed lines
  Added in v.1.112


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