Diff for /imach/src/imach.c between versions 1.41 and 1.112

version 1.41, 2002/05/07 15:53:01 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.
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.108  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 "wgnuplot"    This is the basic analysis of mortality and should be done before any
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    other analysis, in order to test if the mortality estimated from the
 #define FILENAMELENGTH 80    cross-longitudinal survey is different from the mortality estimated
 /*#define DEBUG*/    from other sources like vital statistic data.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    The same imach parameter file can be used but the option for mle should be -3.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Agnès, who wrote this part of the code, tried to keep most of the
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    former routines in order to include the new code within the former code.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     The output is very simple: only an estimate of the intercept and of
 #define NINTERVMAX 8    the slope with 95% confident intervals.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Current limitations:
 #define NCOVMAX 8 /* Maximum number of covariates */    A) Even if you enter covariates, i.e. with the
 #define MAXN 20000    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define YEARM 12. /* Number of months per year */    B) There is no computation of Life Expectancy nor Life Table.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 int erreur; /* Error number */  
 int nvar;    Revision 1.96  2003/07/15 15:38:55  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 int npar=NPARMAX;    rewritten within the same printf. Workaround: many printfs.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.95  2003/07/08 07:54:34  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Repository):
 int popbased=0;    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.94  2003/06/27 13:00:02  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    Just cleaning
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.93  2003/06/25 16:33:55  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): On windows (cygwin) function asctime_r doesn't
 double jmean; /* Mean space between 2 waves */    exist so I changed back to asctime which exists.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Version 0.96b
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.92  2003/06/25 16:30:45  brouard
 FILE *ficgp,*ficresprob,*ficpop;    (Module): On windows (cygwin) function asctime_r doesn't
 FILE *ficreseij;    exist so I changed back to asctime which exists.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.91  2003/06/25 15:30:29  brouard
   char fileresv[FILENAMELENGTH];    * imach.c (Repository): Duplicated warning errors corrected.
  FILE  *ficresvpl;    (Repository): Elapsed time after each iteration is now output. It
   char fileresvpl[FILENAMELENGTH];    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 #define NR_END 1    concerning matrix of covariance. It has extension -cov.htm.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 #define NRANSI    mle=-1 a template is output in file "or"mypar.txt with the design
 #define ITMAX 200    of the covariance matrix to be input.
   
 #define TOL 2.0e-4    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 #define CGOLD 0.3819660    mle=-1 a template is output in file "or"mypar.txt with the design
 #define ZEPS 1.0e-10    of the covariance matrix to be input.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.88  2003/06/23 17:54:56  brouard
 #define GOLD 1.618034    * 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 GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.86  2003/06/17 20:04:08  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Change position of html and gnuplot routines and added
      routine fileappend.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 static double sqrarg;    current date of interview. It may happen when the death was just
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    prior to the death. In this case, dh was negative and likelihood
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 int imx;    interview.
 int stepm;    (Repository): Because some people have very long ID (first column)
 /* Stepm, step in month: minimum step interpolation*/    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 int estepm;    truncation)
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (Repository): No more line truncation errors.
   
 int m,nb;    Revision 1.84  2003/06/13 21:44:43  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    * imach.c (Repository): Replace "freqsummary" at a correct
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    place. It differs from routine "prevalence" which may be called
 double **pmmij, ***probs, ***mobaverage;    many times. Probs is memory consuming and must be used with
 double dateintmean=0;    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 double *weight;  
 int **s; /* Status */    Revision 1.83  2003/06/10 13:39:11  lievre
 double *agedc, **covar, idx;    *** empty log message ***
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.82  2003/06/05 15:57:20  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Add log in  imach.c and  fullversion number is now printed.
 double ftolhess; /* Tolerance for computing hessian */  
   */
 /**************** split *************************/  /*
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )     Interpolated Markov Chain
 {  
    char *s;                             /* pointer */    Short summary of the programme:
    int  l1, l2;                         /* length counters */    
     This program computes Healthy Life Expectancies from
    l1 = strlen( path );                 /* length of path */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    first survey ("cross") where individuals from different ages are
 #ifdef windows    interviewed on their health status or degree of disability (in the
    s = strrchr( path, '\\' );           /* find last / */    case of a health survey which is our main interest) -2- at least a
 #else    second wave of interviews ("longitudinal") which measure each change
    s = strrchr( path, '/' );            /* find last / */    (if any) in individual health status.  Health expectancies are
 #endif    computed from the time spent in each health state according to a
    if ( s == NULL ) {                   /* no directory, so use current */    model. More health states you consider, more time is necessary to reach the
 #if     defined(__bsd__)                /* get current working directory */    Maximum Likelihood of the parameters involved in the model.  The
       extern char       *getwd( );    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
       if ( getwd( dirc ) == NULL ) {    conditional to be observed in state i at the first wave. Therefore
 #else    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       extern char       *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
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    where the markup *Covariates have to be included here again* invites
 #endif    you to do it.  More covariates you add, slower the
          return( GLOCK_ERROR_GETCWD );    convergence.
       }  
       strcpy( name, path );             /* we've got it */    The advantage of this computer programme, compared to a simple
    } else {                             /* strip direcotry from path */    multinomial logistic model, is clear when the delay between waves is not
       s++;                              /* after this, the filename */    identical for each individual. Also, if a individual missed an
       l2 = strlen( s );                 /* length of filename */    intermediate interview, the information is lost, but taken into
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    account using an interpolation or extrapolation.  
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    hPijx is the probability to be observed in state i at age x+h
       dirc[l1-l2] = 0;                  /* add zero */    conditional to the observed state i at age x. The delay 'h' can be
    }    split into an exact number (nh*stepm) of unobserved intermediate
    l1 = strlen( dirc );                 /* length of directory */    states. This elementary transition (by month, quarter,
 #ifdef windows    semester or year) is modelled as a multinomial logistic.  The hPx
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    matrix is simply the matrix product of nh*stepm elementary matrices
 #else    and the contribution of each individual to the likelihood is simply
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    hPijx.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Also this programme outputs the covariance matrix of the parameters but also
    s++;    of the life expectancies. It also computes the stable prevalence. 
    strcpy(ext,s);                       /* save extension */    
    l1= strlen( name);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    l2= strlen( s)+1;             Institut national d'études démographiques, Paris.
    strncpy( finame, name, l1-l2);    This software have been partly granted by Euro-REVES, a concerted action
    finame[l1-l2]= 0;    from the European Union.
    return( 0 );                         /* we're done */    It is copyrighted identically to a GNU software product, ie programme and
 }    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
   
 /******************************************/    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 void replace(char *s, char*t)    
 {    **********************************************************************/
   int i;  /*
   int lg=20;    main
   i=0;    read parameterfile
   lg=strlen(t);    read datafile
   for(i=0; i<= lg; i++) {    concatwav
     (s[i] = t[i]);    freqsummary
     if (t[i]== '\\') s[i]='/';    if (mle >= 1)
   }      mlikeli
 }    print results files
     if mle==1 
 int nbocc(char *s, char occ)       computes hessian
 {    read end of parameter file: agemin, agemax, bage, fage, estepm
   int i,j=0;        begin-prev-date,...
   int lg=20;    open gnuplot file
   i=0;    open html file
   lg=strlen(s);    stable prevalence
   for(i=0; i<= lg; i++) {     for age prevalim()
   if  (s[i] == occ ) j++;    h Pij x
   }    variance of p varprob
   return j;    forecasting if prevfcast==1 prevforecast call prevalence()
 }    health expectancies
     Variance-covariance of DFLE
 void cutv(char *u,char *v, char*t, char occ)    prevalence()
 {     movingaverage()
   int i,lg,j,p=0;    varevsij() 
   i=0;    if popbased==1 varevsij(,popbased)
   for(j=0; j<=strlen(t)-1; j++) {    total life expectancies
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Variance of stable prevalence
   }   end
   */
   lg=strlen(t);  
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  
   }   
      u[p]='\0';  #include <math.h>
   #include <stdio.h>
    for(j=0; j<= lg; j++) {  #include <stdlib.h>
     if (j>=(p+1))(v[j-p-1] = t[j]);  #include <string.h>
   }  #include <unistd.h>
 }  
   #include <limits.h>
 /********************** nrerror ********************/  #include <sys/types.h>
   #include <sys/stat.h>
 void nrerror(char error_text[])  #include <errno.h>
 {  extern int errno;
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  /* #include <sys/time.h> */
   exit(1);  #include <time.h>
 }  #include "timeval.h"
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define MAXLINE 256
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   int *v;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define NCOVMAX 8 /* Maximum number of covariates */
   if (!v) nrerror("allocation failure in ivector");  #define MAXN 20000
   return v-nl+NR_END;  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 /******************free ivector **************************/  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 void free_ivector(int *v, long nl, long nh)  #ifdef UNIX
 {  #define DIRSEPARATOR '/'
   free((FREE_ARG)(v+nl-NR_END));  #define CHARSEPARATOR "/"
 }  #define ODIRSEPARATOR '\\'
   #else
 /******************* 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 '/'
 {  #endif
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  /* $Id$ */
    /* $State$ */
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
   if (!m) nrerror("allocation failure 1 in matrix()");  char fullversion[]="$Revision$ $Date$"; 
   m += NR_END;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   m -= nrl;  int nvar;
    int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    int npar=NPARMAX;
   /* allocate rows and set pointers to them */  int nlstate=2; /* Number of live states */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int ndeath=1; /* Number of dead states */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m[nrl] += NR_END;  int popbased=0;
   m[nrl] -= ncl;  
    int *wav; /* Number of waves for this individuual 0 is possible */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int maxwav; /* Maxim number of waves */
    int jmin, jmax; /* min, max spacing between 2 waves */
   /* return pointer to array of pointers to rows */  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   return m;  int gipmx, gsw; /* Global variables on the number of contributions 
 }                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
 /****************** free_imatrix *************************/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 void free_imatrix(m,nrl,nrh,ncl,nch)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       int **m;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       long nch,ncl,nrh,nrl;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
      /* free an int matrix allocated by imatrix() */  double jmean; /* Mean space between 2 waves */
 {  double **oldm, **newm, **savm; /* Working pointers to matrices */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   free((FREE_ARG) (m+nrl-NR_END));  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 }  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
 /******************* matrix *******************************/  double fretone; /* Only one call to likelihood */
 double **matrix(long nrl, long nrh, long ncl, long nch)  long ipmx; /* Number of contributions */
 {  double sw; /* Sum of weights */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char filerespow[FILENAMELENGTH];
   double **m;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *ficresprobmorprev;
   m += NR_END;  FILE *fichtm, *fichtmcov; /* Html File */
   m -= nrl;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  FILE  *ficresvij;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char fileresv[FILENAMELENGTH];
   m[nrl] += NR_END;  FILE  *ficresvpl;
   m[nrl] -= ncl;  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   return m;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
 /*************************free matrix ************************/  int  outcmd=0;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  char filelog[FILENAMELENGTH]; /* Log file */
 }  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 /******************* ma3x *******************************/  char popfile[FILENAMELENGTH];
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  extern int gettimeofday();
   if (!m) nrerror("allocation failure 1 in matrix()");  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   m += NR_END;  long time_value;
   m -= nrl;  extern long time();
   char strcurr[80], strfor[80];
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char *endptr;
   m[nrl] += NR_END;  long lval;
   m[nrl] -= ncl;  
   #define NR_END 1
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define FREE_ARG char*
   #define FTOL 1.0e-10
   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 NRANSI 
   m[nrl][ncl] += NR_END;  #define ITMAX 200 
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  #define TOL 2.0e-4 
     m[nrl][j]=m[nrl][j-1]+nlay;  
    #define CGOLD 0.3819660 
   for (i=nrl+1; i<=nrh; i++) {  #define ZEPS 1.0e-10 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define GOLD 1.618034 
   }  #define GLIMIT 100.0 
   return m;  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /*************************free ma3x ************************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define rint(a) floor(a+0.5)
   free((FREE_ARG)(m+nrl-NR_END));  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /***************** f1dim *************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 extern int ncom;  int agegomp= AGEGOMP;
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  int imx; 
    int stepm=1;
 double f1dim(double x)  /* Stepm, step in month: minimum step interpolation*/
 {  
   int j;  int estepm;
   double f;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   double *xt;  
    int m,nb;
   xt=vector(1,ncom);  long *num;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   f=(*nrfunc)(xt);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   free_vector(xt,1,ncom);  double **pmmij, ***probs;
   return f;  double *ageexmed,*agecens;
 }  double dateintmean=0;
   
 /*****************brent *************************/  double *weight;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int **s; /* Status */
 {  double *agedc, **covar, idx;
   int iter;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double a,b,d,etemp;  double *lsurv, *lpop, *tpop;
   double fu,fv,fw,fx;  
   double ftemp;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double ftolhess; /* Tolerance for computing hessian */
   double e=0.0;  
    /**************** split *************************/
   a=(ax < cx ? ax : cx);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   fw=fv=fx=(*f)(x);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   for (iter=1;iter<=ITMAX;iter++) {    */ 
     xm=0.5*(a+b);    char  *ss;                            /* pointer */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    int   l1, l2;                         /* length counters */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    l1 = strlen(path );                   /* length of path */
 #ifdef DEBUG    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     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);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    if ( ss == NULL ) {                   /* no directory, so determine current directory */
 #endif      strcpy( name, path );               /* we got the fullname name because no directory */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       *xmin=x;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       return fx;      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
     ftemp=fu;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     if (fabs(e) > tol1) {        return( GLOCK_ERROR_GETCWD );
       r=(x-w)*(fx-fv);      }
       q=(x-v)*(fx-fw);      /* got dirc from getcwd*/
       p=(x-v)*q-(x-w)*r;      printf(" DIRC = %s \n",dirc);
       q=2.0*(q-r);    } else {                              /* strip direcotry from path */
       if (q > 0.0) p = -p;      ss++;                               /* after this, the filename */
       q=fabs(q);      l2 = strlen( ss );                  /* length of filename */
       etemp=e;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       e=d;      strcpy( name, ss );         /* save file name */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      dirc[l1-l2] = 0;                    /* add zero */
       else {      printf(" DIRC2 = %s \n",dirc);
         d=p/q;    }
         u=x+d;    /* We add a separator at the end of dirc if not exists */
         if (u-a < tol2 || b-u < tol2)    l1 = strlen( dirc );                  /* length of directory */
           d=SIGN(tol1,xm-x);    if( dirc[l1-1] != DIRSEPARATOR ){
       }      dirc[l1] =  DIRSEPARATOR;
     } else {      dirc[l1+1] = 0; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      printf(" DIRC3 = %s \n",dirc);
     }    }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    ss = strrchr( name, '.' );            /* find last / */
     fu=(*f)(u);    if (ss >0){
     if (fu <= fx) {      ss++;
       if (u >= x) a=x; else b=x;      strcpy(ext,ss);                     /* save extension */
       SHFT(v,w,x,u)      l1= strlen( name);
         SHFT(fv,fw,fx,fu)      l2= strlen(ss)+1;
         } else {      strncpy( finame, name, l1-l2);
           if (u < x) a=u; else b=u;      finame[l1-l2]= 0;
           if (fu <= fw || w == x) {    }
             v=w;  
             w=u;    return( 0 );                          /* we're done */
             fv=fw;  }
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /******************************************/
             fv=fu;  
           }  void replace_back_to_slash(char *s, char*t)
         }  {
   }    int i;
   nrerror("Too many iterations in brent");    int lg=0;
   *xmin=x;    i=0;
   return fx;    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /****************** mnbrak ***********************/      if (t[i]== '\\') s[i]='/';
     }
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  }
             double (*func)(double))  
 {  int nbocc(char *s, char occ)
   double ulim,u,r,q, dum;  {
   double fu;    int i,j=0;
      int lg=20;
   *fa=(*func)(*ax);    i=0;
   *fb=(*func)(*bx);    lg=strlen(s);
   if (*fb > *fa) {    for(i=0; i<= lg; i++) {
     SHFT(dum,*ax,*bx,dum)    if  (s[i] == occ ) j++;
       SHFT(dum,*fb,*fa,dum)    }
       }    return j;
   *cx=(*bx)+GOLD*(*bx-*ax);  }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  void cutv(char *u,char *v, char*t, char occ)
     r=(*bx-*ax)*(*fb-*fc);  {
     q=(*bx-*cx)*(*fb-*fa);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));       gives u="abcedf" and v="ghi2j" */
     ulim=(*bx)+GLIMIT*(*cx-*bx);    int i,lg,j,p=0;
     if ((*bx-u)*(u-*cx) > 0.0) {    i=0;
       fu=(*func)(u);    for(j=0; j<=strlen(t)-1; j++) {
     } else if ((*cx-u)*(u-ulim) > 0.0) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       fu=(*func)(u);    }
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    lg=strlen(t);
           SHFT(*fb,*fc,fu,(*func)(u))    for(j=0; j<p; j++) {
           }      (u[j] = t[j]);
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    }
       u=ulim;       u[p]='\0';
       fu=(*func)(u);  
     } else {     for(j=0; j<= lg; j++) {
       u=(*cx)+GOLD*(*cx-*bx);      if (j>=(p+1))(v[j-p-1] = t[j]);
       fu=(*func)(u);    }
     }  }
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  /********************** nrerror ********************/
       }  
 }  void nrerror(char error_text[])
   {
 /*************** linmin ************************/    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 int ncom;    exit(EXIT_FAILURE);
 double *pcom,*xicom;  }
 double (*nrfunc)(double []);  /*********************** vector *******************/
    double *vector(int nl, int nh)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  {
 {    double *v;
   double brent(double ax, double bx, double cx,    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
                double (*f)(double), double tol, double *xmin);    if (!v) nrerror("allocation failure in vector");
   double f1dim(double x);    return v-nl+NR_END;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  }
               double *fc, double (*func)(double));  
   int j;  /************************ free vector ******************/
   double xx,xmin,bx,ax;  void free_vector(double*v, int nl, int nh)
   double fx,fb,fa;  {
      free((FREE_ARG)(v+nl-NR_END));
   ncom=n;  }
   pcom=vector(1,n);  
   xicom=vector(1,n);  /************************ivector *******************************/
   nrfunc=func;  int *ivector(long nl,long nh)
   for (j=1;j<=n;j++) {  {
     pcom[j]=p[j];    int *v;
     xicom[j]=xi[j];    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   }    if (!v) nrerror("allocation failure in ivector");
   ax=0.0;    return v-nl+NR_END;
   xx=1.0;  }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /******************free ivector **************************/
 #ifdef DEBUG  void free_ivector(int *v, long nl, long nh)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
   for (j=1;j<=n;j++) {  }
     xi[j] *= xmin;  
     p[j] += xi[j];  /************************lvector *******************************/
   }  long *lvector(long nl,long nh)
   free_vector(xicom,1,n);  {
   free_vector(pcom,1,n);    long *v;
 }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
 /*************** powell ************************/    return v-nl+NR_END;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  
 {  /******************free lvector **************************/
   void linmin(double p[], double xi[], int n, double *fret,  void free_lvector(long *v, long nl, long nh)
               double (*func)(double []));  {
   int i,ibig,j;    free((FREE_ARG)(v+nl-NR_END));
   double del,t,*pt,*ptt,*xit;  }
   double fp,fptt;  
   double *xits;  /******************* imatrix *******************************/
   pt=vector(1,n);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   ptt=vector(1,n);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   xit=vector(1,n);  { 
   xits=vector(1,n);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   *fret=(*func)(p);    int **m; 
   for (j=1;j<=n;j++) pt[j]=p[j];    
   for (*iter=1;;++(*iter)) {    /* allocate pointers to rows */ 
     fp=(*fret);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     ibig=0;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     del=0.0;    m += NR_END; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    m -= nrl; 
     for (i=1;i<=n;i++)    
       printf(" %d %.12f",i, p[i]);    
     printf("\n");    /* allocate rows and set pointers to them */ 
     for (i=1;i<=n;i++) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       fptt=(*fret);    m[nrl] += NR_END; 
 #ifdef DEBUG    m[nrl] -= ncl; 
       printf("fret=%lf \n",*fret);    
 #endif    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       printf("%d",i);fflush(stdout);    
       linmin(p,xit,n,fret,func);    /* return pointer to array of pointers to rows */ 
       if (fabs(fptt-(*fret)) > del) {    return m; 
         del=fabs(fptt-(*fret));  } 
         ibig=i;  
       }  /****************** free_imatrix *************************/
 #ifdef DEBUG  void free_imatrix(m,nrl,nrh,ncl,nch)
       printf("%d %.12e",i,(*fret));        int **m;
       for (j=1;j<=n;j++) {        long nch,ncl,nrh,nrl; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);       /* free an int matrix allocated by imatrix() */ 
         printf(" x(%d)=%.12e",j,xit[j]);  { 
       }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for(j=1;j<=n;j++)    free((FREE_ARG) (m+nrl-NR_END)); 
         printf(" p=%.12e",p[j]);  } 
       printf("\n");  
 #endif  /******************* matrix *******************************/
     }  double **matrix(long nrl, long nrh, long ncl, long nch)
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  {
 #ifdef DEBUG    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       int k[2],l;    double **m;
       k[0]=1;  
       k[1]=-1;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       printf("Max: %.12e",(*func)(p));    if (!m) nrerror("allocation failure 1 in matrix()");
       for (j=1;j<=n;j++)    m += NR_END;
         printf(" %.12e",p[j]);    m -= nrl;
       printf("\n");  
       for(l=0;l<=1;l++) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    m[nrl] += NR_END;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    m[nrl] -= ncl;
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }    return m;
 #endif    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
   }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /*************************free matrix ************************/
       free_vector(ptt,1,n);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       free_vector(pt,1,n);  {
       return;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  /******************* ma3x *******************************/
       xit[j]=p[j]-pt[j];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       pt[j]=p[j];  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     fptt=(*func)(ptt);    double ***m;
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       if (t < 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()");
         linmin(p,xit,n,fret,func);    m += NR_END;
         for (j=1;j<=n;j++) {    m -= nrl;
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 #ifdef DEBUG    m[nrl] += NR_END;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    m[nrl] -= ncl;
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         printf("\n");  
 #endif    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
   }    m[nrl][ncl] -= nll;
 }    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
 /**** Prevalence limit ****************/    
     for (i=nrl+1; i<=nrh; i++) {
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 {      for (j=ncl+1; j<=nch; j++) 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        m[i][j]=m[i][j-1]+nlay;
      matrix by transitions matrix until convergence is reached */    }
     return m; 
   int i, ii,j,k;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   double min, max, maxmin, maxmax,sumnew=0.;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double **matprod2();    */
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   for (ii=1;ii<=nlstate+ndeath;ii++)  {
     for (j=1;j<=nlstate+ndeath;j++){    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
   }
    cov[1]=1.;  
    /*************** function subdirf ***********/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char *subdirf(char fileres[])
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  {
     newm=savm;    /* Caution optionfilefiname is hidden */
     /* Covariates have to be included here again */    strcpy(tmpout,optionfilefiname);
      cov[2]=agefin;    strcat(tmpout,"/"); /* Add to the right */
      strcat(tmpout,fileres);
       for (k=1; k<=cptcovn;k++) {    return tmpout;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[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]]);*/  
       }  /*************** function subdirf2 ***********/
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char *subdirf2(char fileres[], char *preop)
       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]]];    
     /* Caution optionfilefiname is hidden */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    strcpy(tmpout,optionfilefiname);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    strcat(tmpout,"/");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    strcat(tmpout,preop);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    strcat(tmpout,fileres);
     return tmpout;
     savm=oldm;  }
     oldm=newm;  
     maxmax=0.;  /*************** function subdirf3 ***********/
     for(j=1;j<=nlstate;j++){  char *subdirf3(char fileres[], char *preop, char *preop2)
       min=1.;  {
       max=0.;    
       for(i=1; i<=nlstate; i++) {    /* Caution optionfilefiname is hidden */
         sumnew=0;    strcpy(tmpout,optionfilefiname);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    strcat(tmpout,"/");
         prlim[i][j]= newm[i][j]/(1-sumnew);    strcat(tmpout,preop);
         max=FMAX(max,prlim[i][j]);    strcat(tmpout,preop2);
         min=FMIN(min,prlim[i][j]);    strcat(tmpout,fileres);
       }    return tmpout;
       maxmin=max-min;  }
       maxmax=FMAX(maxmax,maxmin);  
     }  /***************** f1dim *************************/
     if(maxmax < ftolpl){  extern int ncom; 
       return prlim;  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
   }   
 }  double f1dim(double x) 
   { 
 /*************** transition probabilities ***************/    int j; 
     double f;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    double *xt; 
 {   
   double s1, s2;    xt=vector(1,ncom); 
   /*double t34;*/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   int i,j,j1, nc, ii, jj;    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
     for(i=1; i<= nlstate; i++){    return f; 
     for(j=1; j<i;j++){  } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /*****************brent *************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  { 
       }    int iter; 
       ps[i][j]=s2;    double a,b,d,etemp;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double fu,fv,fw,fx;
     }    double ftemp;
     for(j=i+1; j<=nlstate+ndeath;j++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double e=0.0; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];   
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    a=(ax < cx ? ax : cx); 
       }    b=(ax > cx ? ax : cx); 
       ps[i][j]=s2;    x=w=v=bx; 
     }    fw=fv=fx=(*f)(x); 
   }    for (iter=1;iter<=ITMAX;iter++) { 
     /*ps[3][2]=1;*/      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for(i=1; i<= nlstate; i++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      s1=0;      printf(".");fflush(stdout);
     for(j=1; j<i; j++)      fprintf(ficlog,".");fflush(ficlog);
       s1+=exp(ps[i][j]);  #ifdef DEBUG
     for(j=i+1; j<=nlstate+ndeath; 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);
       s1+=exp(ps[i][j]);      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);
     ps[i][i]=1./(s1+1.);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(j=1; j<i; j++)  #endif
       ps[i][j]= exp(ps[i][j])*ps[i][i];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for(j=i+1; j<=nlstate+ndeath; j++)        *xmin=x; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        return fx; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      } 
   } /* end i */      ftemp=fu;
       if (fabs(e) > tol1) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        r=(x-w)*(fx-fv); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        q=(x-v)*(fx-fw); 
       ps[ii][jj]=0;        p=(x-v)*q-(x-w)*r; 
       ps[ii][ii]=1;        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
   }        q=fabs(q); 
         etemp=e; 
         e=d; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for(jj=1; jj<= nlstate+ndeath; jj++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      printf("%lf ",ps[ii][jj]);        else { 
    }          d=p/q; 
     printf("\n ");          u=x+d; 
     }          if (u-a < tol2 || b-u < tol2) 
     printf("\n ");printf("%lf ",cov[2]);*/            d=SIGN(tol1,xm-x); 
 /*        } 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      } else { 
   goto end;*/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     return ps;      } 
 }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 /**************** Product of 2 matrices ******************/      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        SHFT(v,w,x,u) 
 {          SHFT(fv,fw,fx,fu) 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          } else { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */            if (u < x) a=u; else b=u; 
   /* in, b, out are matrice of pointers which should have been initialized            if (fu <= fw || w == x) { 
      before: only the contents of out is modified. The function returns              v=w; 
      a pointer to pointers identical to out */              w=u; 
   long i, j, k;              fv=fw; 
   for(i=nrl; i<= nrh; i++)              fw=fu; 
     for(k=ncolol; k<=ncoloh; k++)            } else if (fu <= fv || v == x || v == w) { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)              v=u; 
         out[i][k] +=in[i][j]*b[j][k];              fv=fu; 
             } 
   return out;          } 
 }    } 
     nrerror("Too many iterations in brent"); 
     *xmin=x; 
 /************* Higher Matrix Product ***************/    return fx; 
   } 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {  /****************** mnbrak ***********************/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.              double (*func)(double)) 
      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).    double ulim,u,r,q, dum;
      Model is determined by parameters x and covariates have to be    double fu; 
      included manually here.   
     *fa=(*func)(*ax); 
      */    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
   int i, j, d, h, k;      SHFT(dum,*ax,*bx,dum) 
   double **out, cov[NCOVMAX];        SHFT(dum,*fb,*fa,dum) 
   double **newm;        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
   /* Hstepm could be zero and should return the unit matrix */    *fc=(*func)(*cx); 
   for (i=1;i<=nlstate+ndeath;i++)    while (*fb > *fc) { 
     for (j=1;j<=nlstate+ndeath;j++){      r=(*bx-*ax)*(*fb-*fc); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      q=(*bx-*cx)*(*fb-*fa); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for(h=1; h <=nhstepm; h++){      if ((*bx-u)*(u-*cx) > 0.0) { 
     for(d=1; d <=hstepm; d++){        fu=(*func)(u); 
       newm=savm;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       /* Covariates have to be included here again */        fu=(*func)(u); 
       cov[1]=1.;        if (fu < *fc) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            SHFT(*fb,*fc,fu,(*func)(u)) 
       for (k=1; k<=cptcovage;k++)            } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for (k=1; k<=cptcovprod;k++)        u=ulim; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fu=(*func)(u); 
       } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
       /*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]);*/      } 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      SHFT(*ax,*bx,*cx,u) 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        SHFT(*fa,*fb,*fc,fu) 
       savm=oldm;        } 
       oldm=newm;  } 
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /*************** linmin ************************/
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  int ncom; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  double *pcom,*xicom;
          */  double (*nrfunc)(double []); 
       }   
   } /* end h */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   return po;  { 
 }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 /*************** log-likelihood *************/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 double func( double *x)                double *fc, double (*func)(double)); 
 {    int j; 
   int i, ii, j, k, mi, d, kk;    double xx,xmin,bx,ax; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double fx,fb,fa;
   double **out;   
   double sw; /* Sum of weights */    ncom=n; 
   double lli; /* Individual log likelihood */    pcom=vector(1,n); 
   long ipmx;    xicom=vector(1,n); 
   /*extern weight */    nrfunc=func; 
   /* We are differentiating ll according to initial status */    for (j=1;j<=n;j++) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      pcom[j]=p[j]; 
   /*for(i=1;i<imx;i++)      xicom[j]=xi[j]; 
     printf(" %d\n",s[4][i]);    } 
   */    ax=0.0; 
   cov[1]=1.;    xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  #ifdef DEBUG
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(mi=1; mi<= wav[i]-1; mi++){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for (ii=1;ii<=nlstate+ndeath;ii++)  #endif
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for (j=1;j<=n;j++) { 
       for(d=0; d<dh[mi][i]; d++){      xi[j] *= xmin; 
         newm=savm;      p[j] += xi[j]; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    } 
         for (kk=1; kk<=cptcovage;kk++) {    free_vector(xicom,1,n); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    free_vector(pcom,1,n); 
         }  } 
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  char *asc_diff_time(long time_sec, char ascdiff[])
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  {
         savm=oldm;    long sec_left, days, hours, minutes;
         oldm=newm;    days = (time_sec) / (60*60*24);
            sec_left = (time_sec) % (60*60*24);
            hours = (sec_left) / (60*60) ;
       } /* end mult */    sec_left = (sec_left) %(60*60);
          minutes = (sec_left) /60;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    sec_left = (sec_left) % (60);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       ipmx +=1;    return ascdiff;
       sw += weight[i];  }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  /*************** powell ************************/
   } /* end of individual */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    void linmin(double p[], double xi[], int n, 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;    int i,ibig,j; 
 }    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
     double *xits;
 /*********** Maximum Likelihood Estimation ***************/    int niterf, itmp;
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    pt=vector(1,n); 
 {    ptt=vector(1,n); 
   int i,j, iter;    xit=vector(1,n); 
   double **xi,*delti;    xits=vector(1,n); 
   double fret;    *fret=(*func)(p); 
   xi=matrix(1,npar,1,npar);    for (j=1;j<=n;j++) pt[j]=p[j]; 
   for (i=1;i<=npar;i++)    for (*iter=1;;++(*iter)) { 
     for (j=1;j<=npar;j++)      fp=(*fret); 
       xi[i][j]=(i==j ? 1.0 : 0.0);      ibig=0; 
   printf("Powell\n");      del=0.0; 
   powell(p,xi,npar,ftol,&iter,&fret,func);      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      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(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      /*    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);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 }      */
      for (i=1;i<=n;i++) {
 /**** Computes Hessian and covariance matrix ***/        printf(" %d %.12f",i, p[i]);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        fprintf(ficlog," %d %.12lf",i, p[i]);
 {        fprintf(ficrespow," %.12lf", p[i]);
   double  **a,**y,*x,pd;      }
   double **hess;      printf("\n");
   int i, j,jk;      fprintf(ficlog,"\n");
   int *indx;      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   double hessii(double p[], double delta, int theta, double delti[]);        tm = *localtime(&curr_time.tv_sec);
   double hessij(double p[], double delti[], int i, int j);        strcpy(strcurr,asctime(&tm));
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /*       asctime_r(&tm,strcurr); */
   void ludcmp(double **a, int npar, int *indx, double *d) ;        forecast_time=curr_time; 
         itmp = strlen(strcurr);
   hess=matrix(1,npar,1,npar);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
   printf("\nCalculation of the hessian matrix. Wait...\n");        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   for (i=1;i<=npar;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("%d",i);fflush(stdout);        for(niterf=10;niterf<=30;niterf+=10){
     hess[i][i]=hessii(p,ftolhess,i,delti);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     /*printf(" %f ",p[i]);*/          tmf = *localtime(&forecast_time.tv_sec);
     /*printf(" %lf ",hess[i][i]);*/  /*      asctime_r(&tmf,strfor); */
   }          strcpy(strfor,asctime(&tmf));
            itmp = strlen(strfor);
   for (i=1;i<=npar;i++) {          if(strfor[itmp-1]=='\n')
     for (j=1;j<=npar;j++)  {          strfor[itmp-1]='\0';
       if (j>i) {          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         printf(".%d%d",i,j);fflush(stdout);          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);
         hess[i][j]=hessij(p,delti,i,j);        }
         hess[j][i]=hess[i][j];          }
         /*printf(" %lf ",hess[i][j]);*/      for (i=1;i<=n;i++) { 
       }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     }        fptt=(*fret); 
   }  #ifdef DEBUG
   printf("\n");        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  #endif
          printf("%d",i);fflush(stdout);
   a=matrix(1,npar,1,npar);        fprintf(ficlog,"%d",i);fflush(ficlog);
   y=matrix(1,npar,1,npar);        linmin(p,xit,n,fret,func); 
   x=vector(1,npar);        if (fabs(fptt-(*fret)) > del) { 
   indx=ivector(1,npar);          del=fabs(fptt-(*fret)); 
   for (i=1;i<=npar;i++)          ibig=i; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        } 
   ludcmp(a,npar,indx,&pd);  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   for (j=1;j<=npar;j++) {        fprintf(ficlog,"%d %.12e",i,(*fret));
     for (i=1;i<=npar;i++) x[i]=0;        for (j=1;j<=n;j++) {
     x[j]=1;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     lubksb(a,npar,indx,x);          printf(" x(%d)=%.12e",j,xit[j]);
     for (i=1;i<=npar;i++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       matcov[i][j]=x[i];        }
     }        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
   printf("\n#Hessian matrix#\n");        }
   for (i=1;i<=npar;i++) {        printf("\n");
     for (j=1;j<=npar;j++) {        fprintf(ficlog,"\n");
       printf("%.3e ",hess[i][j]);  #endif
     }      } 
     printf("\n");      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   }  #ifdef DEBUG
         int k[2],l;
   /* Recompute Inverse */        k[0]=1;
   for (i=1;i<=npar;i++)        k[1]=-1;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        printf("Max: %.12e",(*func)(p));
   ludcmp(a,npar,indx,&pd);        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   /*  printf("\n#Hessian matrix recomputed#\n");          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
   for (j=1;j<=npar;j++) {        }
     for (i=1;i<=npar;i++) x[i]=0;        printf("\n");
     x[j]=1;        fprintf(ficlog,"\n");
     lubksb(a,npar,indx,x);        for(l=0;l<=1;l++) {
     for (i=1;i<=npar;i++){          for (j=1;j<=n;j++) {
       y[i][j]=x[i];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       printf("%.3e ",y[i][j]);            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]);
     printf("\n");          }
   }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   free_matrix(a,1,npar,1,npar);  #endif
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);        free_vector(xit,1,n); 
   free_matrix(hess,1,npar,1,npar);        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 }        return; 
       } 
 /*************** hessian matrix ****************/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 double hessii( double x[], double delta, int theta, double delti[])      for (j=1;j<=n;j++) { 
 {        ptt[j]=2.0*p[j]-pt[j]; 
   int i;        xit[j]=p[j]-pt[j]; 
   int l=1, lmax=20;        pt[j]=p[j]; 
   double k1,k2;      } 
   double p2[NPARMAX+1];      fptt=(*func)(ptt); 
   double res;      if (fptt < fp) { 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double fx;        if (t < 0.0) { 
   int k=0,kmax=10;          linmin(p,xit,n,fret,func); 
   double l1;          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
   fx=func(x);            xi[j][n]=xit[j]; 
   for (i=1;i<=npar;i++) p2[i]=x[i];          }
   for(l=0 ; l <=lmax; l++){  #ifdef DEBUG
     l1=pow(10,l);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     delts=delt;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(k=1 ; k <kmax; k=k+1){          for(j=1;j<=n;j++){
       delt = delta*(l1*k);            printf(" %.12e",xit[j]);
       p2[theta]=x[theta] +delt;            fprintf(ficlog," %.12e",xit[j]);
       k1=func(p2)-fx;          }
       p2[theta]=x[theta]-delt;          printf("\n");
       k2=func(p2)-fx;          fprintf(ficlog,"\n");
       /*res= (k1-2.0*fx+k2)/delt/delt; */  #endif
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        }
            } 
 #ifdef DEBUG    } 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  } 
 #endif  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  /**** Prevalence limit (stable prevalence)  ****************/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         k=kmax; l=lmax*10.;       matrix by transitions matrix until convergence is reached */
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    int i, ii,j,k;
         delts=delt;    double min, max, maxmin, maxmax,sumnew=0.;
       }    double **matprod2();
     }    double **out, cov[NCOVMAX], **pmij();
   }    double **newm;
   delti[theta]=delts;    double agefin, delaymax=50 ; /* Max number of years to converge */
   return res;  
      for (ii=1;ii<=nlstate+ndeath;ii++)
 }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 double hessij( double x[], double delti[], int thetai,int thetaj)      }
 {  
   int i;     cov[1]=1.;
   int l=1, l1, lmax=20;   
   double k1,k2,k3,k4,res,fx;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double p2[NPARMAX+1];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   int k;      newm=savm;
       /* Covariates have to be included here again */
   fx=func(x);       cov[2]=agefin;
   for (k=1; k<=2; k++) {    
     for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovn;k++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     k1=func(p2)-fx;        }
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     p2[thetai]=x[thetai]+delti[thetai]/k;        for (k=1; k<=cptcovprod;k++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     k2=func(p2)-fx;  
          /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     p2[thetai]=x[thetai]-delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     k3=func(p2)-fx;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
    
     p2[thetai]=x[thetai]-delti[thetai]/k;      savm=oldm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      oldm=newm;
     k4=func(p2)-fx;      maxmax=0.;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      for(j=1;j<=nlstate;j++){
 #ifdef DEBUG        min=1.;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        max=0.;
 #endif        for(i=1; i<=nlstate; i++) {
   }          sumnew=0;
   return res;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 }          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
 /************** Inverse of matrix **************/          min=FMIN(min,prlim[i][j]);
 void ludcmp(double **a, int n, int *indx, double *d)        }
 {        maxmin=max-min;
   int i,imax,j,k;        maxmax=FMAX(maxmax,maxmin);
   double big,dum,sum,temp;      }
   double *vv;      if(maxmax < ftolpl){
          return prlim;
   vv=vector(1,n);      }
   *d=1.0;    }
   for (i=1;i<=n;i++) {  }
     big=0.0;  
     for (j=1;j<=n;j++)  /*************** transition probabilities ***************/ 
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     vv[i]=1.0/big;  {
   }    double s1, s2;
   for (j=1;j<=n;j++) {    /*double t34;*/
     for (i=1;i<j;i++) {    int i,j,j1, nc, ii, jj;
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      for(i=1; i<= nlstate; i++){
       a[i][j]=sum;        for(j=1; j<i;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     big=0.0;            /*s2 += param[i][j][nc]*cov[nc];*/
     for (i=j;i<=n;i++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       sum=a[i][j];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       for (k=1;k<j;k++)          }
         sum -= a[i][k]*a[k][j];          ps[i][j]=s2;
       a[i][j]=sum;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       if ( (dum=vv[i]*fabs(sum)) >= big) {        }
         big=dum;        for(j=i+1; j<=nlstate+ndeath;j++){
         imax=i;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       }            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     if (j != imax) {          }
       for (k=1;k<=n;k++) {          ps[i][j]=s2;
         dum=a[imax][k];        }
         a[imax][k]=a[j][k];      }
         a[j][k]=dum;      /*ps[3][2]=1;*/
       }      
       *d = -(*d);      for(i=1; i<= nlstate; i++){
       vv[imax]=vv[j];        s1=0;
     }        for(j=1; j<i; j++)
     indx[j]=imax;          s1+=exp(ps[i][j]);
     if (a[j][j] == 0.0) a[j][j]=TINY;        for(j=i+1; j<=nlstate+ndeath; j++)
     if (j != n) {          s1+=exp(ps[i][j]);
       dum=1.0/(a[j][j]);        ps[i][i]=1./(s1+1.);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(j=1; j<i; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
   }        for(j=i+1; j<=nlstate+ndeath; j++)
   free_vector(vv,1,n);  /* Doesn't work */          ps[i][j]= exp(ps[i][j])*ps[i][i];
 ;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 }      } /* end i */
       
 void lubksb(double **a, int n, int *indx, double b[])      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 {        for(jj=1; jj<= nlstate+ndeath; jj++){
   int i,ii=0,ip,j;          ps[ii][jj]=0;
   double sum;          ps[ii][ii]=1;
          }
   for (i=1;i<=n;i++) {      }
     ip=indx[i];      
     sum=b[ip];  
     b[ip]=b[i];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     if (ii)  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /*         printf("ddd %lf ",ps[ii][jj]); */
     else if (sum) ii=i;  /*       } */
     b[i]=sum;  /*       printf("\n "); */
   }  /*        } */
   for (i=n;i>=1;i--) {  /*        printf("\n ");printf("%lf ",cov[2]); */
     sum=b[i];         /*
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     b[i]=sum/a[i][i];        goto end;*/
   }      return ps;
 }  }
   
 /************ Frequencies ********************/  /**************** Product of 2 matrices ******************/
 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 */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
    {
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double ***freq; /* Frequencies */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double *pp;    /* in, b, out are matrice of pointers which should have been initialized 
   double pos, k2, dateintsum=0,k2cpt=0;       before: only the contents of out is modified. The function returns
   FILE *ficresp;       a pointer to pointers identical to out */
   char fileresp[FILENAMELENGTH];    long i, j, k;
      for(i=nrl; i<= nrh; i++)
   pp=vector(1,nlstate);      for(k=ncolol; k<=ncoloh; k++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   strcpy(fileresp,"p");          out[i][k] +=in[i][j]*b[j][k];
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {    return out;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  }
     exit(0);  
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /************* Higher Matrix Product ***************/
   j1=0;  
    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   j=cptcoveff;  {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
   for(k1=1; k1<=j;k1++){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     for(i1=1; i1<=ncodemax[k1];i1++){       nhstepm*hstepm matrices. 
       j1++;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);       (typically every 2 years instead of every month which is too big 
         scanf("%d", i);*/       for the memory).
       for (i=-1; i<=nlstate+ndeath; i++)         Model is determined by parameters x and covariates have to be 
         for (jk=-1; jk<=nlstate+ndeath; jk++)         included manually here. 
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;       */
        
       dateintsum=0;    int i, j, d, h, k;
       k2cpt=0;    double **out, cov[NCOVMAX];
       for (i=1; i<=imx; i++) {    double **newm;
         bool=1;  
         if  (cptcovn>0) {    /* Hstepm could be zero and should return the unit matrix */
           for (z1=1; z1<=cptcoveff; z1++)    for (i=1;i<=nlstate+ndeath;i++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for (j=1;j<=nlstate+ndeath;j++){
               bool=0;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         }        po[i][j][0]=(i==j ? 1.0 : 0.0);
         if (bool==1) {      }
           for(m=firstpass; m<=lastpass; m++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             k2=anint[m][i]+(mint[m][i]/12.);    for(h=1; h <=nhstepm; h++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for(d=1; d <=hstepm; d++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;        newm=savm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;        /* Covariates have to be included here again */
               if (m<lastpass) {        cov[1]=1.;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        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];
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        for (k=1; k<=cptcovprod;k++)
                 dateintsum=dateintsum+k2;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                 k2cpt++;  
               }  
             }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
           }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        oldm=newm;
       }
       if  (cptcovn>0) {      for(i=1; i<=nlstate+ndeath; i++)
         fprintf(ficresp, "\n#********** Variable ");        for(j=1;j<=nlstate+ndeath;j++) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          po[i][j][h]=newm[i][j];
         fprintf(ficresp, "**********\n#");          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       }           */
       for(i=1; i<=nlstate;i++)        }
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    } /* end h */
       fprintf(ficresp, "\n");    return po;
        }
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3)  
           printf("Total");  /*************** log-likelihood *************/
         else  double func( double *x)
           printf("Age %d", i);  {
         for(jk=1; jk <=nlstate ; jk++){    int i, ii, j, k, mi, d, kk;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
             pp[jk] += freq[jk][m][i];    double **out;
         }    double sw; /* Sum of weights */
         for(jk=1; jk <=nlstate ; jk++){    double lli; /* Individual log likelihood */
           for(m=-1, pos=0; m <=0 ; m++)    int s1, s2;
             pos += freq[jk][m][i];    double bbh, survp;
           if(pp[jk]>=1.e-10)    long ipmx;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /*extern weight */
           else    /* We are differentiating ll according to initial status */
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    /*  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; jk <=nlstate ; jk++){    */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    cov[1]=1.;
             pp[jk] += freq[jk][m][i];  
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
         for(jk=1,pos=0; jk <=nlstate ; jk++)    if(mle==1){
           pos += pp[jk];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1; jk <=nlstate ; jk++){        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++){
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          for (ii=1;ii<=nlstate+ndeath;ii++)
           else            for (j=1;j<=nlstate+ndeath;j++){
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if( i <= (int) agemax){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             if(pos>=1.e-5){            }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          for(d=0; d<dh[mi][i]; d++){
               probs[i][jk][j1]= pp[jk]/pos;            newm=savm;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             }            for (kk=1; kk<=cptcovage;kk++) {
             else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            }
           }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                    savm=oldm;
         for(jk=-1; jk <=nlstate+ndeath; jk++)            oldm=newm;
           for(m=-1; m <=nlstate+ndeath; m++)          } /* end mult */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        
         if(i <= (int) agemax)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           fprintf(ficresp,"\n");          /* But now since version 0.9 we anticipate for bias at large stepm.
         printf("\n");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   dateintmean=dateintsum/k2cpt;           * (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
   fclose(ficresp);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * -stepm/2 to stepm/2 .
   free_vector(pp,1,nlstate);           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
   /* End of Freq */           */
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /************ Prevalence ********************/          bbh=(double)bh[mi][i]/(double)stepm; 
 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)          /* bias bh is positive if real duration
 {  /* Some frequencies */           * is higher than the multiple of stepm and negative otherwise.
             */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double ***freq; /* Frequencies */          if( s2 > nlstate){ 
   double *pp;            /* i.e. if s2 is a death state and if the date of death is known 
   double pos, k2;               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
   pp=vector(1,nlstate);               which is also equal to probability to die before dh 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);               minus probability to die before dh-stepm . 
                 In version up to 0.92 likelihood was computed
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          as if date of death was unknown. Death was treated as any other
   j1=0;          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
   j=cptcoveff;          to consider that at each interview the state was recorded
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          (healthy, disable or death) and IMaCh was corrected; but when we
            introduced the exact date of death then we should have modified
  for(k1=1; k1<=j;k1++){          the contribution of an exact death to the likelihood. This new
     for(i1=1; i1<=ncodemax[k1];i1++){          contribution is smaller and very dependent of the step unit
       j1++;          stepm. It is no more the probability to die between last interview
            and month of death but the probability to survive from last
       for (i=-1; i<=nlstate+ndeath; i++)            interview up to one month before death multiplied by the
         for (jk=-1; jk<=nlstate+ndeath; jk++)            probability to die within a month. Thanks to Chris
           for(m=agemin; m <= agemax+3; m++)          Jackson for correcting this bug.  Former versions increased
             freq[i][jk][m]=0;          mortality artificially. The bad side is that we add another loop
                which slows down the processing. The difference can be up to 10%
       for (i=1; i<=imx; i++) {          lower mortality.
         bool=1;            */
         if  (cptcovn>0) {            lli=log(out[s1][s2] - savm[s1][s2]);
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;          } else if  (s2==-2) {
         }            for (j=1,survp=0. ; j<=nlstate; j++) 
         if (bool==1) {              survp += out[s1][j];
           for(m=firstpass; m<=lastpass; m++){            lli= survp;
             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==-4) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=3,survp=0. ; j<=nlstate; j++) 
               if (m<lastpass)              survp += out[s1][j];
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            lli= survp;
               else          }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          else if  (s2==-5) {
             }            for (j=1,survp=0. ; j<=2; j++) 
           }              survp += out[s1][j];
         }            lli= survp;
       }          }
         for(i=(int)agemin; i <= (int)agemax+3; i++){  
           for(jk=1; jk <=nlstate ; jk++){  
             for(m=-1, 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; jk <=nlstate ; jk++){          } 
             for(m=-1, pos=0; m <=0 ; m++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
             pos += freq[jk][m][i];          /*if(lli ==000.0)*/
         }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                  ipmx +=1;
          for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              pp[jk] += freq[jk][m][i];        } /* end of wave */
          }      } /* end of individual */
              }  else if(mle==2){
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(jk=1; jk <=nlstate ; jk++){                  for(mi=1; mi<= wav[i]-1; mi++){
            if( i <= (int) agemax){          for (ii=1;ii<=nlstate+ndeath;ii++)
              if(pos>=1.e-5){            for (j=1;j<=nlstate+ndeath;j++){
                probs[i][jk][j1]= pp[jk]/pos;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }            }
          }          for(d=0; d<=dh[mi][i]; d++){
                      newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(pp,1,nlstate);            savm=oldm;
              oldm=newm;
 }  /* End of Freq */          } /* end mult */
         
 /************* Waves Concatenation ***************/          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          bbh=(double)bh[mi][i]/(double)stepm; 
 {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          ipmx +=1;
      Death is a valid wave (if date is known).          sw += weight[i];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        } /* end of wave */
      and mw[mi+1][i]. dh depends on stepm.      } /* end of individual */
      */    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, mi, m;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for(mi=1; mi<= wav[i]-1; mi++){
      double sum=0., jmean=0.;*/          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   int j, k=0,jk, ju, jl;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double sum=0.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmin=1e+5;            }
   jmax=-1;          for(d=0; d<dh[mi][i]; d++){
   jmean=0.;            newm=savm;
   for(i=1; i<=imx; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     mi=0;            for (kk=1; kk<=cptcovage;kk++) {
     m=firstpass;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     while(s[m][i] <= nlstate){            }
       if(s[m][i]>=1)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         mw[++mi][i]=m;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(m >=lastpass)            savm=oldm;
         break;            oldm=newm;
       else          } /* end mult */
         m++;        
     }/* end while */          s1=s[mw[mi][i]][i];
     if (s[m][i] > nlstate){          s2=s[mw[mi+1][i]][i];
       mi++;     /* Death is another wave */          bbh=(double)bh[mi][i]/(double)stepm; 
       /* if(mi==0)  never been interviewed correctly before death */          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 */
          /* Only death is a correct wave */          ipmx +=1;
       mw[mi][i]=m;          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     wav[i]=mi;      } /* end of individual */
     if(mi==0)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   for(i=1; i<=imx; i++){          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(mi=1; mi<wav[i];mi++){            for (j=1;j<=nlstate+ndeath;j++){
       if (stepm <=0)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         dh[mi][i]=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else{            }
         if (s[mw[mi+1][i]][i] > nlstate) {          for(d=0; d<dh[mi][i]; d++){
           if (agedc[i] < 2*AGESUP) {            newm=savm;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           if(j==0) j=1;  /* Survives at least one month after exam */            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;            }
           if (j <= jmin) jmin=j;          
           sum=sum+j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }            savm=oldm;
         }            oldm=newm;
         else{          } /* end mult */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        
           k=k+1;          s1=s[mw[mi][i]][i];
           if (j >= jmax) jmax=j;          s2=s[mw[mi+1][i]][i];
           else if (j <= jmin)jmin=j;          if( s2 > nlstate){ 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            lli=log(out[s1][s2] - savm[s1][s2]);
           sum=sum+j;          }else{
         }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         jk= j/stepm;          }
         jl= j -jk*stepm;          ipmx +=1;
         ju= j -(jk+1)*stepm;          sw += weight[i];
         if(jl <= -ju)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           dh[mi][i]=jk;  /*      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]); */
         else        } /* end of wave */
           dh[mi][i]=jk+1;      } /* end of individual */
         if(dh[mi][i]==0)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           dh[mi][i]=1; /* At least one step */      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++)
   jmean=sum/k;            for (j=1;j<=nlstate+ndeath;j++){
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /*********** Tricode ****************************/            }
 void tricode(int *Tvar, int **nbcode, int imx)          for(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   int Ndum[20],ij=1, k, j, i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int cptcode=0;            for (kk=1; kk<=cptcovage;kk++) {
   cptcoveff=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   for (k=0; k<19; k++) Ndum[k]=0;          
   for (k=1; k<=7; k++) ncodemax[k]=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            savm=oldm;
     for (i=1; i<=imx; i++) {            oldm=newm;
       ij=(int)(covar[Tvar[j]][i]);          } /* end mult */
       Ndum[ij]++;        
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          s1=s[mw[mi][i]][i];
       if (ij > cptcode) cptcode=ij;          s2=s[mw[mi+1][i]][i];
     }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
     for (i=0; i<=cptcode; i++) {          sw += weight[i];
       if(Ndum[i]!=0) ncodemax[j]++;          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]);*/
     ij=1;        } /* end of wave */
       } /* end of individual */
     } /* End of if */
     for (i=1; i<=ncodemax[j]; i++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for (k=0; k<=19; k++) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         if (Ndum[k] != 0) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           nbcode[Tvar[j]][ij]=k;    return -l;
            }
           ij++;  
         }  /*************** log-likelihood *************/
         if (ij > ncodemax[j]) break;  double funcone( double *x)
       }    {
     }    /* Same as likeli but slower because of a lot of printf and if */
   }      int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
  for (k=0; k<19; k++) Ndum[k]=0;    double **out;
     double lli; /* Individual log likelihood */
  for (i=1; i<=ncovmodel-2; i++) {    double llt;
       ij=Tvar[i];    int s1, s2;
       Ndum[ij]++;    double bbh, survp;
     }    /*extern weight */
     /* We are differentiating ll according to initial status */
  ij=1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
  for (i=1; i<=10; i++) {    /*for(i=1;i<imx;i++) 
    if((Ndum[i]!=0) && (i<=ncovcol)){      printf(" %d\n",s[4][i]);
      Tvaraff[ij]=i;    */
      ij++;    cov[1]=1.;
    }  
  }    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
     cptcoveff=ij-1;    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++){
 /*********** Health Expectancies ****************/        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
 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 )            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {          }
   /* Health expectancies */        for(d=0; d<dh[mi][i]; d++){
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          newm=savm;
   double age, agelim, hf;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***p3mat,***varhe;          for (kk=1; kk<=cptcovage;kk++) {
   double **dnewm,**doldm;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *xp;          }
   double **gp, **gm;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***gradg, ***trgradg;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int theta;          savm=oldm;
           oldm=newm;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        } /* end mult */
   xp=vector(1,npar);        
   dnewm=matrix(1,nlstate*2,1,npar);        s1=s[mw[mi][i]][i];
   doldm=matrix(1,nlstate*2,1,nlstate*2);        s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficreseij,"# Health expectancies\n");        /* bias is positive if real duration
   fprintf(ficreseij,"# Age");         * 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 */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficreseij,"\n");        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   if(estepm < stepm){        } else if(mle==2){
     printf ("Problem %d lower than %d\n",estepm, stepm);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   }        } else if(mle==3){  /* exponential inter-extrapolation */
   else  hstepm=estepm;            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 */
   /* We compute the life expectancy from trapezoids spaced every estepm months        } else if (mle==4){  /* mle=4 no inter-extrapolation */
    * This is mainly to measure the difference between two models: for example          lli=log(out[s1][s2]); /* Original formula */
    * if stepm=24 months pijx are given only every 2 years and by summing them        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
    * we are calculating an estimate of the Life Expectancy assuming a linear          lli=log(out[s1][s2]); /* Original formula */
    * progression inbetween and thus overestimating or underestimating according        } /* End of if */
    * to the curvature of the survival function. If, for the same date, we        ipmx +=1;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        sw += weight[i];
    * to compare the new estimate of Life expectancy with the same linear        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    * hypothesis. A more precise result, taking into account a more precise  /*       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]); */
    * curvature will be obtained if estepm is as small as stepm. */        if(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   /* For example we decided to compute the life expectancy with the smallest unit */   %10.6f %10.6f %10.6f ", \
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      nhstepm is the number of hstepm from age to agelim                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
      nstepm is the number of stepm from age to agelin.          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
      Look at hpijx to understand the reason of that which relies in memory size            llt +=ll[k]*gipmx/gsw;
      and note for a fixed period like estepm months */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   /* 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          fprintf(ficresilk," %10.6f\n", -llt);
      means that if the survival funtion is printed only each two years of age and if        }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      } /* end of wave */
      results. So we changed our mind and took the option of the best precision.    } /* end of individual */
   */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   agelim=AGESUP;    if(globpr==0){ /* First time we count the contributions and weights */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      gipmx=ipmx;
     /* nhstepm age range expressed in number of stepm */      gsw=sw;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    return -l;
     /* if (stepm >= YEARM) hstepm=1;*/  }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);  /*************** function likelione ***********/
     gp=matrix(0,nhstepm,1,nlstate*2);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     gm=matrix(0,nhstepm,1,nlstate*2);  {
     /* This routine should help understanding what is done with 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored       the selection of individuals/waves and
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */       to check the exact contribution to the likelihood.
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);         Plotting could be done.
       */
     int k;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     if(*globpri !=0){ /* Just counts and sums, no printings */
     /* Computing Variances of health expectancies */      strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
      for(theta=1; theta <=npar; theta++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(i=1; i<=npar; i++){        printf("Problem with resultfile: %s\n", fileresilk);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }      }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       cptj=0;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(j=1; j<= nlstate; j++){      for(k=1; k<=nlstate; k++) 
         for(i=1; i<=nlstate; i++){        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           cptj=cptj+1;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
       }      fclose(ficresilk);
            fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
            fflush(fichtm); 
       for(i=1; i<=npar; i++)    } 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    }
        
       cptj=0;  
       for(j=1; j<= nlstate; j++){  /*********** Maximum Likelihood Estimation ***************/
         for(i=1;i<=nlstate;i++){  
           cptj=cptj+1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  {
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int i,j, iter;
           }    double **xi;
         }    double fret;
       }    double fretone; /* Only one call to likelihood */
          /*  char filerespow[FILENAMELENGTH];*/
        xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
       for(j=1; j<= nlstate*2; j++)      for (j=1;j<=npar;j++)
         for(h=0; h<=nhstepm-1; h++){        xi[i][j]=(i==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         }    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
      }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", filerespow);
 /* End theta */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
      for(h=0; h<=nhstepm-1; h++)      for(j=1;j<=nlstate+ndeath;j++)
       for(j=1; j<=nlstate*2;j++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         for(theta=1; theta <=npar; theta++)    fprintf(ficrespow,"\n");
         trgradg[h][j][theta]=gradg[h][theta][j];  
     powell(p,xi,npar,ftol,&iter,&fret,func);
   
      for(i=1;i<=nlstate*2;i++)    fclose(ficrespow);
       for(j=1;j<=nlstate*2;j++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         varhe[i][j][(int)age] =0.;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(h=0;h<=nhstepm-1;h++){  
       for(k=0;k<=nhstepm-1;k++){  }
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  /**** Computes Hessian and covariance matrix ***/
         for(i=1;i<=nlstate*2;i++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           for(j=1;j<=nlstate*2;j++)  {
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    double  **a,**y,*x,pd;
       }    double **hess;
     }    int i, j,jk;
     int *indx;
        
     /* Computing expectancies */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       for(j=1; j<=nlstate;j++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    double gompertz(double p[]);
              hess=matrix(1,npar,1,npar);
 /* 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]);*/  
     printf("\nCalculation of the hessian matrix. Wait...\n");
         }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
     fprintf(ficreseij,"%3.0f",age );      printf("%d",i);fflush(stdout);
     cptj=0;      fprintf(ficlog,"%d",i);fflush(ficlog);
     for(i=1; i<=nlstate;i++)     
       for(j=1; j<=nlstate;j++){       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         cptj++;      
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      /*  printf(" %f ",p[i]);
       }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     fprintf(ficreseij,"\n");    }
        
     free_matrix(gm,0,nhstepm,1,nlstate*2);    for (i=1;i<=npar;i++) {
     free_matrix(gp,0,nhstepm,1,nlstate*2);      for (j=1;j<=npar;j++)  {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        if (j>i) { 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          printf(".%d%d",i,j);fflush(stdout);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   }          hess[i][j]=hessij(p,delti,i,j,func,npar);
   free_vector(xp,1,npar);          
   free_matrix(dnewm,1,nlstate*2,1,npar);          hess[j][i]=hess[i][j];    
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          /*printf(" %lf ",hess[i][j]);*/
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        }
 }      }
     }
 /************ Variance ******************/    printf("\n");
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    fprintf(ficlog,"\n");
 {  
   /* Variance of health expectancies */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **newm;    
   double **dnewm,**doldm;    a=matrix(1,npar,1,npar);
   int i, j, nhstepm, hstepm, h, nstepm ;    y=matrix(1,npar,1,npar);
   int k, cptcode;    x=vector(1,npar);
   double *xp;    indx=ivector(1,npar);
   double **gp, **gm;    for (i=1;i<=npar;i++)
   double ***gradg, ***trgradg;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double ***p3mat;    ludcmp(a,npar,indx,&pd);
   double age,agelim, hf;  
   int theta;    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
    fprintf(ficresvij,"# Covariances of life expectancies\n");      x[j]=1;
   fprintf(ficresvij,"# Age");      lubksb(a,npar,indx,x);
   for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
     for(j=1; j<=nlstate;j++)        matcov[i][j]=x[i];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      }
   fprintf(ficresvij,"\n");    }
   
   xp=vector(1,npar);    printf("\n#Hessian matrix#\n");
   dnewm=matrix(1,nlstate,1,npar);    fprintf(ficlog,"\n#Hessian matrix#\n");
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1;i<=npar;i++) { 
        for (j=1;j<=npar;j++) { 
   if(estepm < stepm){        printf("%.3e ",hess[i][j]);
     printf ("Problem %d lower than %d\n",estepm, stepm);        fprintf(ficlog,"%.3e ",hess[i][j]);
   }      }
   else  hstepm=estepm;        printf("\n");
   /* For example we decided to compute the life expectancy with the smallest unit */      fprintf(ficlog,"\n");
   /* 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  
      nstepm is the number of stepm from age to agelin.    /* Recompute Inverse */
      Look at hpijx to understand the reason of that which relies in memory size    for (i=1;i<=npar;i++)
      and note for a fixed period like k years */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    ludcmp(a,npar,indx,&pd);
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    /*  printf("\n#Hessian matrix recomputed#\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.    for (j=1;j<=npar;j++) {
   */      for (i=1;i<=npar;i++) x[i]=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      x[j]=1;
   agelim = AGESUP;      lubksb(a,npar,indx,x);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1;i<=npar;i++){ 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        y[i][j]=x[i];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        printf("%.3e ",y[i][j]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficlog,"%.3e ",y[i][j]);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      }
     gp=matrix(0,nhstepm,1,nlstate);      printf("\n");
     gm=matrix(0,nhstepm,1,nlstate);      fprintf(ficlog,"\n");
     }
     for(theta=1; theta <=npar; theta++){    */
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    free_matrix(a,1,npar,1,npar);
       }    free_matrix(y,1,npar,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      free_vector(x,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  }
       }  
    /*************** hessian matrix ****************/
       for(j=1; j<= nlstate; j++){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         for(h=0; h<=nhstepm; h++){  {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int i;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    int l=1, lmax=20;
         }    double k1,k2;
       }    double p2[NPARMAX+1];
        double res;
       for(i=1; i<=npar; i++) /* Computes gradient */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int k=0,kmax=10;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double l1;
    
       if (popbased==1) {    fx=func(x);
         for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
           prlim[i][i]=probs[(int)age][i][ij];    for(l=0 ; l <=lmax; l++){
       }      l1=pow(10,l);
       delts=delt;
       for(j=1; j<= nlstate; j++){      for(k=1 ; k <kmax; k=k+1){
         for(h=0; h<=nhstepm; h++){        delt = delta*(l1*k);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        p2[theta]=x[theta] +delt;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        k1=func(p2)-fx;
         }        p2[theta]=x[theta]-delt;
       }        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(j=1; j<= nlstate; j++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for(h=0; h<=nhstepm; h++){        
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  #ifdef DEBUG
         }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     } /* End theta */        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
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for(h=0; h<=nhstepm; h++)          k=kmax;
       for(j=1; j<=nlstate;j++)        }
         for(theta=1; theta <=npar; theta++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           trgradg[h][j][theta]=gradg[h][theta][j];          k=kmax; l=lmax*10.;
         }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for(i=1;i<=nlstate;i++)          delts=delt;
       for(j=1;j<=nlstate;j++)        }
         vareij[i][j][(int)age] =0.;      }
     }
     for(h=0;h<=nhstepm;h++){    delti[theta]=delts;
       for(k=0;k<=nhstepm;k++){    return res; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  }
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  {
       }    int i;
     }    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     fprintf(ficresvij,"%.0f ",age );    double p2[NPARMAX+1];
     for(i=1; i<=nlstate;i++)    int k;
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    fx=func(x);
       }    for (k=1; k<=2; k++) {
     fprintf(ficresvij,"\n");      for (i=1;i<=npar;i++) p2[i]=x[i];
     free_matrix(gp,0,nhstepm,1,nlstate);      p2[thetai]=x[thetai]+delti[thetai]/k;
     free_matrix(gm,0,nhstepm,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      k1=func(p2)-fx;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetai]=x[thetai]+delti[thetai]/k;
   } /* End age */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);      p2[thetai]=x[thetai]-delti[thetai]/k;
   free_matrix(dnewm,1,nlstate,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
 }    
       p2[thetai]=x[thetai]-delti[thetai]/k;
 /************ Variance of prevlim ******************/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      k4=func(p2)-fx;
 {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   /* Variance of prevalence limit */  #ifdef DEBUG
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   double **newm;      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);
   double **dnewm,**doldm;  #endif
   int i, j, nhstepm, hstepm;    }
   int k, cptcode;    return res;
   double *xp;  }
   double *gp, *gm;  
   double **gradg, **trgradg;  /************** Inverse of matrix **************/
   double age,agelim;  void ludcmp(double **a, int n, int *indx, double *d) 
   int theta;  { 
        int i,imax,j,k; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    double big,dum,sum,temp; 
   fprintf(ficresvpl,"# Age");    double *vv; 
   for(i=1; i<=nlstate;i++)   
       fprintf(ficresvpl," %1d-%1d",i,i);    vv=vector(1,n); 
   fprintf(ficresvpl,"\n");    *d=1.0; 
     for (i=1;i<=n;i++) { 
   xp=vector(1,npar);      big=0.0; 
   dnewm=matrix(1,nlstate,1,npar);      for (j=1;j<=n;j++) 
   doldm=matrix(1,nlstate,1,nlstate);        if ((temp=fabs(a[i][j])) > big) big=temp; 
        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   hstepm=1*YEARM; /* Every year of age */      vv[i]=1.0/big; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    } 
   agelim = AGESUP;    for (j=1;j<=n;j++) { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1;i<j;i++) { 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        sum=a[i][j]; 
     if (stepm >= YEARM) hstepm=1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        a[i][j]=sum; 
     gradg=matrix(1,npar,1,nlstate);      } 
     gp=vector(1,nlstate);      big=0.0; 
     gm=vector(1,nlstate);      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
     for(theta=1; theta <=npar; theta++){        for (k=1;k<j;k++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */          sum -= a[i][k]*a[k][j]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        a[i][j]=sum; 
       }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          big=dum; 
       for(i=1;i<=nlstate;i++)          imax=i; 
         gp[i] = prlim[i][i];        } 
          } 
       for(i=1; i<=npar; i++) /* Computes gradient */      if (j != imax) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (k=1;k<=n;k++) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          dum=a[imax][k]; 
       for(i=1;i<=nlstate;i++)          a[imax][k]=a[j][k]; 
         gm[i] = prlim[i][i];          a[j][k]=dum; 
         } 
       for(i=1;i<=nlstate;i++)        *d = -(*d); 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        vv[imax]=vv[j]; 
     } /* End theta */      } 
       indx[j]=imax; 
     trgradg =matrix(1,nlstate,1,npar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
     for(j=1; j<=nlstate;j++)        dum=1.0/(a[j][j]); 
       for(theta=1; theta <=npar; theta++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         trgradg[j][theta]=gradg[theta][j];      } 
     } 
     for(i=1;i<=nlstate;i++)    free_vector(vv,1,n);  /* Doesn't work */
       varpl[i][(int)age] =0.;  ;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  } 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)  void lubksb(double **a, int n, int *indx, double b[]) 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  { 
     int i,ii=0,ip,j; 
     fprintf(ficresvpl,"%.0f ",age );    double sum; 
     for(i=1; i<=nlstate;i++)   
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    for (i=1;i<=n;i++) { 
     fprintf(ficresvpl,"\n");      ip=indx[i]; 
     free_vector(gp,1,nlstate);      sum=b[ip]; 
     free_vector(gm,1,nlstate);      b[ip]=b[i]; 
     free_matrix(gradg,1,npar,1,nlstate);      if (ii) 
     free_matrix(trgradg,1,nlstate,1,npar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   } /* End age */      else if (sum) ii=i; 
       b[i]=sum; 
   free_vector(xp,1,npar);    } 
   free_matrix(doldm,1,nlstate,1,npar);    for (i=n;i>=1;i--) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 }      b[i]=sum/a[i][i]; 
     } 
 /************ Variance of one-step probabilities  ******************/  } 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  
 {  /************ Frequencies ********************/
   int i, j, i1, k1, j1, z1;  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[])
   int k=0, cptcode;  {  /* Some frequencies */
   double **dnewm,**doldm;    
   double *xp;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double *gp, *gm;    int first;
   double **gradg, **trgradg;    double ***freq; /* Frequencies */
   double age,agelim, cov[NCOVMAX];    double *pp, **prop;
   int theta;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   char fileresprob[FILENAMELENGTH];    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
   strcpy(fileresprob,"prob");    
   strcat(fileresprob,fileres);    pp=vector(1,nlstate);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
     printf("Problem with resultfile: %s\n", fileresprob);    strcpy(fileresp,"p");
   }    strcat(fileresp,fileres);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    if((ficresp=fopen(fileresp,"w"))==NULL) {
        printf("Problem with prevalence resultfile: %s\n", fileresp);
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   fprintf(ficresprob,"# Age");      exit(0);
   for(i=1; i<=nlstate;i++)    }
     for(j=1; j<=(nlstate+ndeath);j++)    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    j1=0;
     
     j=cptcoveff;
   fprintf(ficresprob,"\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
     first=1;
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for(k1=1; k1<=j;k1++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
   cov[1]=1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   j=cptcoveff;          scanf("%d", i);*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for (i=-5; i<=nlstate+ndeath; i++)  
   j1=0;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   for(k1=1; k1<=1;k1++){            for(m=iagemin; m <= iagemax+3; m++)
     for(i1=1; i1<=ncodemax[k1];i1++){              freq[i][jk][m]=0;
     j1++;  
       for (i=1; i<=nlstate; i++)  
     if  (cptcovn>0) {        for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficresprob, "\n#********** Variable ");          prop[i][m]=0;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        
       fprintf(ficresprob, "**********\n#");        dateintsum=0;
     }        k2cpt=0;
            for (i=1; i<=imx; i++) {
       for (age=bage; age<=fage; age ++){          bool=1;
         cov[2]=age;          if  (cptcovn>0) {
         for (k=1; k<=cptcovn;k++) {            for (z1=1; z1<=cptcoveff; z1++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                          bool=0;
         }          }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          if (bool==1){
         for (k=1; k<=cptcovprod;k++)            for(m=firstpass; m<=lastpass; m++){
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              k2=anint[m][i]+(mint[m][i]/12.);
                      /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         gradg=matrix(1,npar,1,9);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         trgradg=matrix(1,9,1,npar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                if (m<lastpass) {
                      freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         for(theta=1; theta <=npar; theta++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           for(i=1; i<=npar; i++)                }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);                
                          if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                  dateintsum=dateintsum+k2;
                            k2cpt++;
           k=0;                }
           for(i=1; i<= (nlstate+ndeath); i++){                /*}*/
             for(j=1; j<=(nlstate+ndeath);j++){            }
               k=k+1;          }
               gp[k]=pmmij[i][j];        }
             }         
           }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
            fprintf(ficresp, "#Local time at start: %s", strstart);
           for(i=1; i<=npar; i++)        if  (cptcovn>0) {
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficresp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          fprintf(ficresp, "**********\n#");
           k=0;        }
           for(i=1; i<=(nlstate+ndeath); i++){        for(i=1; i<=nlstate;i++) 
             for(j=1; j<=(nlstate+ndeath);j++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
               k=k+1;        fprintf(ficresp, "\n");
               gm[k]=pmmij[i][j];        
             }        for(i=iagemin; i <= iagemax+3; i++){
           }          if(i==iagemax+3){
                  fprintf(ficlog,"Total");
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          }else{
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              if(first==1){
         }              first=0;
               printf("See log file for details...\n");
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            }
           for(theta=1; theta <=npar; theta++)            fprintf(ficlog,"Age %d", i);
             trgradg[j][theta]=gradg[theta][j];          }
                  for(jk=1; jk <=nlstate ; jk++){
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              pp[jk] += freq[jk][m][i]; 
                  }
         pmij(pmmij,cov,ncovmodel,x,nlstate);          for(jk=1; jk <=nlstate ; jk++){
                    for(m=-1, pos=0; m <=0 ; m++)
         k=0;              pos += freq[jk][m][i];
         for(i=1; i<=(nlstate+ndeath); i++){            if(pp[jk]>=1.e-10){
           for(j=1; j<=(nlstate+ndeath);j++){              if(first==1){
             k=k+1;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             gm[k]=pmmij[i][j];              }
           }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }            }else{
                    if(first==1)
      /*printf("\n%d ",(int)age);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            }
      }*/          }
   
         fprintf(ficresprob,"\n%d ",(int)age);          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)              pp[jk] += freq[jk][m][i];
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));          }       
            for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       }            pos += pp[jk];
     }            posprop += prop[jk][i];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            if(pos>=1.e-5){
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              if(first==1)
   }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   free_vector(xp,1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   fclose(ficresprob);            }else{
                if(first==1)
 }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /******************* Printing html file ***********/            }
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \            if( i <= iagemax){
  int lastpass, int stepm, int weightopt, char model[],\              if(pos>=1.e-5){
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\                /*probs[i][jk][j1]= pp[jk]/pos;*/
  char version[], int popforecast, int estepm ){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int jj1, k1, i1, cpt;              }
   FILE *fichtm;              else
   /*char optionfilehtm[FILENAMELENGTH];*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
   strcpy(optionfilehtm,optionfile);          }
   strcat(optionfilehtm,".htm");          
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for(jk=-1; jk <=nlstate+ndeath; jk++)
     printf("Problem with %s \n",optionfilehtm), exit(0);            for(m=-1; m <=nlstate+ndeath; m++)
   }              if(freq[jk][m][i] !=0 ) {
               if(first==1)
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 \n              }
 Total number of observations=%d <br>\n          if(i <= iagemax)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            fprintf(ficresp,"\n");
 <hr  size=\"2\" color=\"#EC5E5E\">          if(first==1)
  <ul><li>Outputs files<br>\n            printf("Others in log...\n");
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          fprintf(ficlog,"\n");
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n        }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      }
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    }
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    dateintmean=dateintsum/k2cpt; 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);   
     fclose(ficresp);
  fprintf(fichtm,"\n    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    free_vector(pp,1,nlstate);
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    /* End of Freq */
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n  }
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  
   /************ Prevalence ********************/
  if(popforecast==1) fprintf(fichtm,"\n  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  {  
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         <br>",fileres,fileres,fileres,fileres);       in each health status at the date of interview (if between dateprev1 and dateprev2).
  else       We still use firstpass and lastpass as another selection.
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    */
 fprintf(fichtm," <li>Graphs</li><p>");   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
  m=cptcoveff;    double ***freq; /* Frequencies */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double *pp, **prop;
     double pos,posprop; 
  jj1=0;    double  y2; /* in fractional years */
  for(k1=1; k1<=m;k1++){    int iagemin, iagemax;
    for(i1=1; i1<=ncodemax[k1];i1++){  
        jj1++;    iagemin= (int) agemin;
        if (cptcovn > 0) {    iagemax= (int) agemax;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    /*pp=vector(1,nlstate);*/
          for (cpt=1; cpt<=cptcoveff;cpt++)    prop=matrix(1,nlstate,iagemin,iagemax+3); 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    j1=0;
        }    
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    j=cptcoveff;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        if (cptcovn<1) {j=1;ncodemax[1]=1;}
        for(cpt=1; cpt<nlstate;cpt++){    
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    for(k1=1; k1<=j;k1++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for(i1=1; i1<=ncodemax[k1];i1++){
        }        j1++;
     for(cpt=1; cpt<=nlstate;cpt++) {        
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        for (i=1; i<=nlstate; i++)  
 interval) in state (%d): v%s%d%d.gif <br>          for(m=iagemin; m <= iagemax+3; m++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              prop[i][m]=0.0;
      }       
      for(cpt=1; cpt<=nlstate;cpt++) {        for (i=1; i<=imx; i++) { /* Each individual */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          bool=1;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          if  (cptcovn>0) {
      }            for (z1=1; z1<=cptcoveff; z1++) 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 health expectancies in states (1) and (2): e%s%d.gif<br>                bool=0;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          } 
 fprintf(fichtm,"\n</body>");          if (bool==1) { 
    }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
    }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 fclose(fichtm);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
 /******************* Gnuplot file **************/                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); 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
   strcpy(optionfilegnuplot,optionfilefiname);                } 
   strcat(optionfilegnuplot,".gp.txt");              }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            } /* end selection of waves */
     printf("Problem with file %s",optionfilegnuplot);          }
   }        }
         for(i=iagemin; i <= iagemax+3; i++){  
 #ifdef windows          
     fprintf(ficgp,"cd \"%s\" \n",pathc);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 #endif            posprop += prop[jk][i]; 
 m=pow(2,cptcoveff);          } 
    
  /* 1eme*/          for(jk=1; jk <=nlstate ; jk++){     
   for (cpt=1; cpt<= nlstate ; cpt ++) {            if( i <=  iagemax){ 
    for (k1=1; k1<= m ; k1 ++) {              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
 #ifdef windows              } 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            } 
 #endif          }/* end jk */ 
 #ifdef unix        }/* end i */ 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      } /* end i1 */
 #endif    } /* end k1 */
     
 for (i=1; i<= nlstate ; i ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*free_vector(pp,1,nlstate);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 }  }  /* End of prevalence */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {  /************* Waves Concatenation ***************/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 }  {
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
      for (i=1; i<= nlstate ; i ++) {       Death is a valid wave (if date is known).
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   else fprintf(ficgp," \%%*lf (\%%*lf)");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 }         and mw[mi+1][i]. dh depends on stepm.
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       */
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");    int i, mi, m;
 #endif    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       double sum=0., jmean=0.;*/
    }    int first;
   }    int j, k=0,jk, ju, jl;
   /*2 eme*/    double sum=0.;
     first=0;
   for (k1=1; k1<= m ; k1 ++) {    jmin=1e+5;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    jmax=-1;
        jmean=0.;
     for (i=1; i<= nlstate+1 ; i ++) {    for(i=1; i<=imx; i++){
       k=2*i;      mi=0;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      m=firstpass;
       for (j=1; j<= nlstate+1 ; j ++) {      while(s[m][i] <= nlstate){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          mw[++mi][i]=m;
 }          if(m >=lastpass)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          break;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        else
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          m++;
       for (j=1; j<= nlstate+1 ; j ++) {      }/* end while */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      if (s[m][i] > nlstate){
         else fprintf(ficgp," \%%*lf (\%%*lf)");        mi++;     /* Death is another wave */
 }          /* if(mi==0)  never been interviewed correctly before death */
       fprintf(ficgp,"\" t\"\" w l 0,");           /* Only death is a correct wave */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        mw[mi][i]=m;
       for (j=1; j<= nlstate+1 ; j ++) {      }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      wav[i]=mi;
 }        if(mi==0){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        nbwarn++;
       else fprintf(ficgp,"\" t\"\" w l 0,");        if(first==0){
     }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          first=1;
   }        }
          if(first==1){
   /*3eme*/          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
   for (k1=1; k1<= m ; k1 ++) {      } /* end mi==0 */
     for (cpt=1; cpt<= nlstate ; cpt ++) {    } /* End individuals */
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    for(i=1; i<=imx; i++){
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      for(mi=1; mi<wav[i];mi++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        if (stepm <=0)
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          dh[mi][i]=1;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        else{
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
 */              if(j==0) j=1;  /* Survives at least one month after exam */
       for (i=1; i< nlstate ; i ++) {              else if(j<0){
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);                nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       }                j=1; /* Temporary Dangerous patch */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                }
   /* CV preval stat */              k=k+1;
     for (k1=1; k1<= m ; k1 ++) {              if (j >= jmax){
     for (cpt=1; cpt<nlstate ; cpt ++) {                jmax=j;
       k=3;                ijmax=i;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              }
               if (j <= jmin){
       for (i=1; i< nlstate ; i ++)                jmin=j;
         fprintf(ficgp,"+$%d",k+i+1);                ijmin=i;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              }
                    sum=sum+j;
       l=3+(nlstate+ndeath)*cpt;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for (i=1; i< nlstate ; i ++) {            }
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }            k=k+1;
   }              if (j >= jmax) {
                jmax=j;
   /* proba elementaires */              ijmax=i;
    for(i=1,jk=1; i <=nlstate; i++){            }
     for(k=1; k <=(nlstate+ndeath); k++){            else if (j <= jmin){
       if (k != i) {              jmin=j;
         for(j=1; j <=ncovmodel; j++){              ijmin=i;
                    }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           jk++;            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           fprintf(ficgp,"\n");            if(j<0){
         }              nberr++;
       }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }            }
             sum=sum+j;
     for(jk=1; jk <=m; jk++) {          }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          jk= j/stepm;
    i=1;          jl= j -jk*stepm;
    for(k2=1; k2<=nlstate; k2++) {          ju= j -(jk+1)*stepm;
      k3=i;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
      for(k=1; k<=(nlstate+ndeath); k++) {            if(jl==0){
        if (k != k2){              dh[mi][i]=jk;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              bh[mi][i]=0;
 ij=1;            }else{ /* We want a negative bias in order to only have interpolation ie
         for(j=3; j <=ncovmodel; j++) {                    * at the price of an extra matrix product in likelihood */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              dh[mi][i]=jk+1;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              bh[mi][i]=ju;
             ij++;            }
           }          }else{
           else            if(jl <= -ju){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              dh[mi][i]=jk;
         }              bh[mi][i]=jl;       /* bias is positive if real duration
           fprintf(ficgp,")/(1");                                   * is higher than the multiple of stepm and negative otherwise.
                                           */
         for(k1=1; k1 <=nlstate; k1++){              }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            else{
 ij=1;              dh[mi][i]=jk+1;
           for(j=3; j <=ncovmodel; j++){              bh[mi][i]=ju;
           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]]]);            if(dh[mi][i]==0){
             ij++;              dh[mi][i]=1; /* At least one step */
           }              bh[mi][i]=ju; /* At least one step */
           else              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            }
           }          } /* end if mle */
           fprintf(ficgp,")");        }
         }      } /* end wave */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    jmean=sum/k;
         i=i+ncovmodel;    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);
      }   }
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  /*********** Tricode ****************************/
    }  void tricode(int *Tvar, int **nbcode, int imx)
      {
   fclose(ficgp);    
 }  /* end gnuplot */    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
     cptcoveff=0; 
 /*************** Moving average **************/   
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=nlstate;i++)      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                                 modality*/ 
           mobaverage[(int)agedeb][i][cptcod]=0.;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            Ndum[ij]++; /*store the modality */
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       for (i=1; i<=nlstate;i++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                                         Tvar[j]. If V=sex and male is 0 and 
           for (cpt=0;cpt<=4;cpt++){                                         female is 1, then  cptcode=1.*/
             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;      for (i=0; i<=cptcode; i++) {
         }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       }      }
     }  
          ij=1; 
 }      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
 /************** Forecasting ******************/            nbcode[Tvar[j]][ij]=k; 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
              
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            ij++;
   int *popage;          }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          if (ij > ncodemax[j]) break; 
   double *popeffectif,*popcount;        }  
   double ***p3mat;      } 
   char fileresf[FILENAMELENGTH];    }  
   
  agelim=AGESUP;   for (k=0; k< maxncov; k++) Ndum[k]=0;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
    for (i=1; i<=ncovmodel-2; i++) { 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     /* 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];
       Ndum[ij]++;
   strcpy(fileresf,"f");   }
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {   ij=1;
     printf("Problem with forecast resultfile: %s\n", fileresf);   for (i=1; i<= maxncov; i++) {
   }     if((Ndum[i]!=0) && (i<=ncovcol)){
   printf("Computing forecasting: result on file '%s' \n", fileresf);       Tvaraff[ij]=i; /*For printing */
        ij++;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;     }
    }
   if (mobilav==1) {   
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   cptcoveff=ij-1; /*Number of simple covariates*/
     movingaverage(agedeb, fage, ageminpar, mobaverage);  }
   }  
   /*********** Health Expectancies ****************/
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
    
   agelim=AGESUP;  {
      /* Health expectancies */
   hstepm=1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   hstepm=hstepm/stepm;    double age, agelim, hf;
   yp1=modf(dateintmean,&yp);    double ***p3mat,***varhe;
   anprojmean=yp;    double **dnewm,**doldm;
   yp2=modf((yp1*12),&yp);    double *xp;
   mprojmean=yp;    double **gp, **gm;
   yp1=modf((yp2*30.5),&yp);    double ***gradg, ***trgradg;
   jprojmean=yp;    int theta;
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      xp=vector(1,npar);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    dnewm=matrix(1,nlstate*nlstate,1,npar);
      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   for(cptcov=1;cptcov<=i2;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficreseij,"# Local time at start: %s", strstart);
       k=k+1;    fprintf(ficreseij,"# Health expectancies\n");
       fprintf(ficresf,"\n#******");    fprintf(ficreseij,"# Age");
       for(j=1;j<=cptcoveff;j++) {    for(i=1; i<=nlstate;i++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=1; j<=nlstate;j++)
       }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       fprintf(ficresf,"******\n");    fprintf(ficreseij,"\n");
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    if(estepm < stepm){
            printf ("Problem %d lower than %d\n",estepm, stepm);
          }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    else  hstepm=estepm;   
         fprintf(ficresf,"\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);       * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     * we are calculating an estimate of the Life Expectancy assuming a linear 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * progression in between and thus overestimating or underestimating according
           nhstepm = nhstepm/hstepm;     * to the curvature of the survival function. If, for the same date, we 
               * estimate the model with stepm=1 month, we can keep estepm to 24 months
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * to compare the new estimate of Life expectancy with the same linear 
           oldm=oldms;savm=savms;     * hypothesis. A more precise result, taking into account a more precise
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * curvature will be obtained if estepm is as small as stepm. */
          
           for (h=0; h<=nhstepm; h++){    /* For example we decided to compute the life expectancy with the smallest unit */
             if (h==(int) (calagedate+YEARM*cpt)) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       nhstepm is the number of hstepm from age to agelim 
             }       nstepm is the number of stepm from age to agelin. 
             for(j=1; j<=nlstate+ndeath;j++) {       Look at hpijx to understand the reason of that which relies in memory size
               kk1=0.;kk2=0;       and note for a fixed period like estepm months */
               for(i=1; i<=nlstate;i++) {                  /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                 if (mobilav==1)       survival function given by stepm (the optimization length). Unfortunately it
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];       means that if the survival funtion is printed only each two years of age and if
                 else {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       results. So we changed our mind and took the option of the best precision.
                 }    */
                    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               }  
               if (h==(int)(calagedate+12*cpt)){    agelim=AGESUP;
                 fprintf(ficresf," %.3f", kk1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                              /* nhstepm age range expressed in number of stepm */
               }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
             }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           }      /* if (stepm >= YEARM) hstepm=1;*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   fclose(ficresf);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 }   
 /************** Forecasting ******************/  
 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){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      /* Computing  Variances of health expectancies */
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;       for(theta=1; theta <=npar; theta++){
   double *popeffectif,*popcount;        for(i=1; i<=npar; i++){ 
   double ***p3mat,***tabpop,***tabpopprev;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char filerespop[FILENAMELENGTH];        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        cptj=0;
   agelim=AGESUP;        for(j=1; j<= nlstate; j++){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
              }
   strcpy(filerespop,"pop");          }
   strcat(filerespop,fileres);        }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {       
     printf("Problem with forecast resultfile: %s\n", filerespop);       
   }        for(i=1; i<=npar; i++) 
   printf("Computing forecasting: result on file '%s' \n", filerespop);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        
         cptj=0;
   if (mobilav==1) {        for(j=1; j<= nlstate; j++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1;i<=nlstate;i++){
     movingaverage(agedeb, fage, ageminpar, mobaverage);            cptj=cptj+1;
   }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if (stepm<=12) stepsize=1;            }
            }
   agelim=AGESUP;        }
          for(j=1; j<= nlstate*nlstate; j++)
   hstepm=1;          for(h=0; h<=nhstepm-1; h++){
   hstepm=hstepm/stepm;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   if (popforecast==1) {       } 
     if((ficpop=fopen(popfile,"r"))==NULL) {     
       printf("Problem with population file : %s\n",popfile);exit(0);  /* End theta */
     }  
     popage=ivector(0,AGESUP);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);       for(h=0; h<=nhstepm-1; h++)
            for(j=1; j<=nlstate*nlstate;j++)
     i=1;            for(theta=1; theta <=npar; theta++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            trgradg[h][j][theta]=gradg[h][theta][j];
           
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       for(i=1;i<=nlstate*nlstate;i++)
   }        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       printf("%d|",(int)age);fflush(stdout);
       k=k+1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficrespop,"\n#******");       for(h=0;h<=nhstepm-1;h++){
       for(j=1;j<=cptcoveff;j++) {        for(k=0;k<=nhstepm-1;k++){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficrespop,"******\n");          for(i=1;i<=nlstate*nlstate;i++)
       fprintf(ficrespop,"# Age");            for(j=1;j<=nlstate*nlstate;j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       if (popforecast==1)  fprintf(ficrespop," [Population]");        }
            }
       for (cpt=0; cpt<=0;cpt++) {      /* Computing expectancies */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           nhstepm = nhstepm/hstepm;            
            /* 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]);*/
           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(ficreseij,"%3.0f",age );
           for (h=0; h<=nhstepm; h++){      cptj=0;
             if (h==(int) (calagedate+YEARM*cpt)) {      for(i=1; i<=nlstate;i++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(j=1; j<=nlstate;j++){
             }          cptj++;
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
               kk1=0.;kk2=0;        }
               for(i=1; i<=nlstate;i++) {                    fprintf(ficreseij,"\n");
                 if (mobilav==1)     
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                 else {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      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);
               if (h==(int)(calagedate+12*cpt)){    }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    printf("\n");
                   /*fprintf(ficrespop," %.3f", kk1);    fprintf(ficlog,"\n");
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }    free_vector(xp,1,npar);
             }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             for(i=1; i<=nlstate;i++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
               kk1=0.;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                 for(j=1; j<=nlstate;j++){  }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }  /************ Variance ******************/
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
             }  {
     /* Variance of health expectancies */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    /* double **newm;*/
           }    double **dnewm,**doldm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewmp,**doldmp;
         }    int i, j, nhstepm, hstepm, h, nstepm ;
       }    int k, cptcode;
      double *xp;
   /******/    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    double **gradgp, **trgradgp; /* for var p point j */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double *gpp, *gmp; /* for var p point j */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double ***p3mat;
           nhstepm = nhstepm/hstepm;    double age,agelim, hf;
              double ***mobaverage;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int theta;
           oldm=oldms;savm=savms;    char digit[4];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      char digitp[25];
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    char fileresprobmorprev[FILENAMELENGTH];
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    if(popbased==1){
             for(j=1; j<=nlstate+ndeath;j++) {      if(mobilav!=0)
               kk1=0.;kk2=0;        strcpy(digitp,"-populbased-mobilav-");
               for(i=1; i<=nlstate;i++) {                    else strcpy(digitp,"-populbased-nomobil-");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        }
               }    else 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      strcpy(digitp,"-stablbased-");
             }  
           }    if (mobilav!=0) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      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);
   }      }
      }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     strcpy(fileresprobmorprev,"prmorprev"); 
   if (popforecast==1) {    sprintf(digit,"%-d",ij);
     free_ivector(popage,0,AGESUP);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     free_vector(popeffectif,0,AGESUP);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     free_vector(popcount,0,AGESUP);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   }    strcat(fileresprobmorprev,fileres);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   fclose(ficrespop);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 }    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 /***********************************************/   
 /**************** Main Program *****************/    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);
     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);
 int main(int argc, char *argv[])    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      for(i=1; i<=nlstate;i++)
   double agedeb, agefin,hf;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    }  
     fprintf(ficresprobmorprev,"\n");
   double fret;    fprintf(ficgp,"\n# Routine varevsij");
   double **xi,tmp,delta;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   double dum; /* Dummy variable */    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   double ***p3mat;  /*   } */
   int *indx;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char line[MAXLINE], linepar[MAXLINE];   fprintf(ficresvij, "#Local time at start: %s", strstart);
   char title[MAXLINE];    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");
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    fprintf(ficresvij,"# Age");
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fprintf(ficresvij,"\n");
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    xp=vector(1,npar);
   char popfile[FILENAMELENGTH];    dnewm=matrix(1,nlstate,1,npar);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    doldm=matrix(1,nlstate,1,nlstate);
   int firstobs=1, lastobs=10;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   int sdeb, sfin; /* Status at beginning and end */    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   int c,  h , cpt,l;  
   int ju,jl, mi;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    gpp=vector(nlstate+1,nlstate+ndeath);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    gmp=vector(nlstate+1,nlstate+ndeath);
   int mobilav=0,popforecast=0;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   int hstepm, nhstepm;    
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   double bage, fage, age, agelim, agebase;    }
   double ftolpl=FTOL;    else  hstepm=estepm;   
   double **prlim;    /* For example we decided to compute the life expectancy with the smallest unit */
   double *severity;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double ***param; /* Matrix of parameters */       nhstepm is the number of hstepm from age to agelim 
   double  *p;       nstepm is the number of stepm from age to agelin. 
   double **matcov; /* Matrix of covariance */       Look at hpijx to understand the reason of that which relies in memory size
   double ***delti3; /* Scale */       and note for a fixed period like k years */
   double *delti; /* Scale */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double ***eij, ***vareij;       survival function given by stepm (the optimization length). Unfortunately it
   double **varpl; /* Variances of prevalence limits by age */       means that if the survival funtion is printed every two years of age and if
   double *epj, vepp;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double kk1, kk2;       results. So we changed our mind and took the option of the best precision.
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char *alph[]={"a","a","b","c","d","e"}, str[4];      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char z[1]="c", occ;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 #include <sys/time.h>      gp=matrix(0,nhstepm,1,nlstate);
 #include <time.h>      gm=matrix(0,nhstepm,1,nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
    
   /* long total_usecs;      for(theta=1; theta <=npar; theta++){
   struct timeval start_time, end_time;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
   getcwd(pathcd, size);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("\n%s",version);  
   if(argc <=1){        if (popbased==1) {
     printf("\nEnter the parameter file name: ");          if(mobilav ==0){
     scanf("%s",pathtot);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
   else{          }else{ /* mobilav */ 
     strcpy(pathtot,argv[1]);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          }
   /*cygwin_split_path(pathtot,path,optionfile);        }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    
   /* cutv(path,optionfile,pathtot,'\\');*/        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   chdir(path);          }
   replace(pathc,path);        }
         /* This for computing probability of death (h=1 means
 /*-------- arguments in the command line --------*/           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   strcpy(fileres,"r");        */
   strcat(fileres, optionfilefiname);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcat(fileres,".txt");    /* Other files have txt extension */          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
   /*---------arguments file --------*/        }    
         /* end probability of death */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     goto end;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcpy(filereso,"o");   
   strcat(filereso,fileres);        if (popbased==1) {
   if((ficparo=fopen(filereso,"w"))==NULL) {          if(mobilav ==0){
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   /* Reads comments: lines beginning with '#' */            for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              prlim[i][i]=mobaverage[(int)age][i][ij];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);  
     fputs(line,ficparo);        for(j=1; j<= nlstate; j++){
   }          for(h=0; h<=nhstepm; h++){
   ungetc(c,ficpar);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);        }
   fprintf(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);        /* This for computing probability of death (h=1 means
 while((c=getc(ficpar))=='#' && c!= EOF){           computed over hstepm matrices product = hstepm*stepm months) 
     ungetc(c,ficpar);           as a weighted average of prlim.
     fgets(line, MAXLINE, ficpar);        */
     puts(line);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   ungetc(c,ficpar);        }    
          /* end probability of death */
      
   covar=matrix(0,NCOVMAX,1,n);        for(j=1; j<= nlstate; j++) /* vareij */
   cptcovn=0;          for(h=0; h<=nhstepm; h++){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   /* Read guess parameters */        }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* End theta */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     puts(line);  
     fputs(line,ficparo);      for(h=0; h<=nhstepm; h++) /* veij */
   }        for(j=1; j<=nlstate;j++)
   ungetc(c,ficpar);          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     for(j=1; j <=nlstate+ndeath-1; j++){        for(theta=1; theta <=npar; theta++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);          trgradgp[j][theta]=gradgp[theta][j];
       fprintf(ficparo,"%1d%1d",i1,j1);    
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fscanf(ficpar," %lf",&param[i][j][k]);      for(i=1;i<=nlstate;i++)
         printf(" %lf",param[i][j][k]);        for(j=1;j<=nlstate;j++)
         fprintf(ficparo," %lf",param[i][j][k]);          vareij[i][j][(int)age] =0.;
       }  
       fscanf(ficpar,"\n");      for(h=0;h<=nhstepm;h++){
       printf("\n");        for(k=0;k<=nhstepm;k++){
       fprintf(ficparo,"\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
            for(i=1;i<=nlstate;i++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   p=param[1][1];        }
        }
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){      /* pptj */
     ungetc(c,ficpar);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     fgets(line, MAXLINE, ficpar);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     puts(line);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     fputs(line,ficparo);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   }          varppt[j][i]=doldmp[j][i];
   ungetc(c,ficpar);      /* end ppptj */
       /*  x centered again */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   for(i=1; i <=nlstate; i++){   
     for(j=1; j <=nlstate+ndeath-1; j++){      if (popbased==1) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);        if(mobilav ==0){
       printf("%1d%1d",i,j);          for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);            prlim[i][i]=probs[(int)age][i][ij];
       for(k=1; k<=ncovmodel;k++){        }else{ /* mobilav */ 
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for(i=1; i<=nlstate;i++)
         printf(" %le",delti3[i][j][k]);            prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficparo," %le",delti3[i][j][k]);        }
       }      }
       fscanf(ficpar,"\n");               
       printf("\n");      /* This for computing probability of death (h=1 means
       fprintf(ficparo,"\n");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     }         as a weighted average of prlim.
   }      */
   delti=delti3[1][1];      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   /* Reads comments: lines beginning with '#' */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   while((c=getc(ficpar))=='#' && c!= EOF){      }    
     ungetc(c,ficpar);      /* end probability of death */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     fputs(line,ficparo);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   ungetc(c,ficpar);        for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   matcov=matrix(1,npar,1,npar);        }
   for(i=1; i <=npar; i++){      } 
     fscanf(ficpar,"%s",&str);      fprintf(ficresprobmorprev,"\n");
     printf("%s",str);  
     fprintf(ficparo,"%s",str);      fprintf(ficresvij,"%.0f ",age );
     for(j=1; j <=i; j++){      for(i=1; i<=nlstate;i++)
       fscanf(ficpar," %le",&matcov[i][j]);        for(j=1; j<=nlstate;j++){
       printf(" %.5le",matcov[i][j]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficparo," %.5le",matcov[i][j]);        }
     }      fprintf(ficresvij,"\n");
     fscanf(ficpar,"\n");      free_matrix(gp,0,nhstepm,1,nlstate);
     printf("\n");      free_matrix(gm,0,nhstepm,1,nlstate);
     fprintf(ficparo,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   for(i=1; i <=npar; i++)      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(j=i+1;j<=npar;j++)    } /* End age */
       matcov[i][j]=matcov[j][i];    free_vector(gpp,nlstate+1,nlstate+ndeath);
        free_vector(gmp,nlstate+1,nlstate+ndeath);
   printf("\n");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /*-------- Rewriting paramater file ----------*/    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      strcpy(rfileres,"r");    /* "Rparameterfile */    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      strcat(rfileres,".");    /* */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     if((ficres =fopen(rfileres,"w"))==NULL) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficres,"#%s\n",version);    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);
     /*-------- data file ----------*/    /*  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);
     if((fic=fopen(datafile,"r"))==NULL)    {  */
       printf("Problem with datafile: %s\n", datafile);goto end;  /*   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);
   
     n= lastobs;    free_vector(xp,1,npar);
     severity = vector(1,maxwav);    free_matrix(doldm,1,nlstate,1,nlstate);
     outcome=imatrix(1,maxwav+1,1,n);    free_matrix(dnewm,1,nlstate,1,npar);
     num=ivector(1,n);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     moisnais=vector(1,n);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     annais=vector(1,n);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     moisdc=vector(1,n);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     andc=vector(1,n);    fclose(ficresprobmorprev);
     agedc=vector(1,n);    fflush(ficgp);
     cod=ivector(1,n);    fflush(fichtm); 
     weight=vector(1,n);  }  /* end varevsij */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  
     mint=matrix(1,maxwav,1,n);  /************ Variance of prevlim ******************/
     anint=matrix(1,maxwav,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[])
     s=imatrix(1,maxwav+1,1,n);  {
     adl=imatrix(1,maxwav+1,1,n);        /* Variance of prevalence limit */
     tab=ivector(1,NCOVMAX);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     ncodemax=ivector(1,8);    double **newm;
     double **dnewm,**doldm;
     i=1;    int i, j, nhstepm, hstepm;
     while (fgets(line, MAXLINE, fic) != NULL)    {    int k, cptcode;
       if ((i >= firstobs) && (i <=lastobs)) {    double *xp;
            double *gp, *gm;
         for (j=maxwav;j>=1;j--){    double **gradg, **trgradg;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double age,agelim;
           strcpy(line,stra);    int theta;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         }    fprintf(ficresvpl,"# Age");
            for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresvpl," %1d-%1d",i,i);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl,"\n");
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    xp=vector(1,npar);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    
         for (j=ncovcol;j>=1;j--){    hstepm=1*YEARM; /* Every year of age */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         }    agelim = AGESUP;
         num[i]=atol(stra);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      if (stepm >= YEARM) hstepm=1;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
         i=i+1;      gp=vector(1,nlstate);
       }      gm=vector(1,nlstate);
     }  
     /* printf("ii=%d", ij);      for(theta=1; theta <=npar; theta++){
        scanf("%d",i);*/        for(i=1; i<=npar; i++){ /* Computes gradient */
   imx=i-1; /* Number of individuals */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   /* for (i=1; i<=imx; i++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        for(i=1;i<=nlstate;i++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          gp[i] = prlim[i][i];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      
     }*/        for(i=1; i<=npar; i++) /* Computes gradient */
    /*  for (i=1; i<=imx; i++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      if (s[4][i]==9)  s[4][i]=-1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      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]));}*/        for(i=1;i<=nlstate;i++)
            gm[i] = prlim[i][i];
    
   /* Calculation of the number of parameter from char model*/        for(i=1;i<=nlstate;i++)
   Tvar=ivector(1,15);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   Tprod=ivector(1,15);      } /* End theta */
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);      trgradg =matrix(1,nlstate,1,npar);
   Tage=ivector(1,15);        
          for(j=1; j<=nlstate;j++)
   if (strlen(model) >1){        for(theta=1; theta <=npar; theta++)
     j=0, j1=0, k1=1, k2=1;          trgradg[j][theta]=gradg[theta][j];
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');      for(i=1;i<=nlstate;i++)
     cptcovn=j+1;        varpl[i][(int)age] =0.;
     cptcovprod=j1;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     strcpy(modelsav,model);      for(i=1;i<=nlstate;i++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       printf("Error. Non available option model=%s ",model);  
       goto end;      fprintf(ficresvpl,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
            fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     for(i=(j+1); i>=1;i--){      fprintf(ficresvpl,"\n");
       cutv(stra,strb,modelsav,'+');      free_vector(gp,1,nlstate);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      free_vector(gm,1,nlstate);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      free_matrix(gradg,1,npar,1,nlstate);
       /*scanf("%d",i);*/      free_matrix(trgradg,1,nlstate,1,npar);
       if (strchr(strb,'*')) {    } /* End age */
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {    free_vector(xp,1,npar);
           cptcovprod--;    free_matrix(doldm,1,nlstate,1,npar);
           cutv(strb,stre,strd,'V');    free_matrix(dnewm,1,nlstate,1,nlstate);
           Tvar[i]=atoi(stre);  
           cptcovage++;  }
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/  /************ Variance of one-step probabilities  ******************/
         }  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[])
         else if (strcmp(strd,"age")==0) {  {
           cptcovprod--;    int i, j=0,  i1, k1, l1, t, tj;
           cutv(strb,stre,strc,'V');    int k2, l2, j1,  z1;
           Tvar[i]=atoi(stre);    int k=0,l, cptcode;
           cptcovage++;    int first=1, first1;
           Tage[cptcovage]=i;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         }    double **dnewm,**doldm;
         else {    double *xp;
           cutv(strb,stre,strc,'V');    double *gp, *gm;
           Tvar[i]=ncovcol+k1;    double **gradg, **trgradg;
           cutv(strb,strc,strd,'V');    double **mu;
           Tprod[k1]=i;    double age,agelim, cov[NCOVMAX];
           Tvard[k1][1]=atoi(strc);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           Tvard[k1][2]=atoi(stre);    int theta;
           Tvar[cptcovn+k2]=Tvard[k1][1];    char fileresprob[FILENAMELENGTH];
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    char fileresprobcov[FILENAMELENGTH];
           for (k=1; k<=lastobs;k++)    char fileresprobcor[FILENAMELENGTH];
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    double ***varpij;
           k2=k2+2;  
         }    strcpy(fileresprob,"prob"); 
       }    strcat(fileresprob,fileres);
       else {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      printf("Problem with resultfile: %s\n", fileresprob);
        /*  scanf("%d",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       cutv(strd,strc,strb,'V');    }
       Tvar[i]=atoi(strc);    strcpy(fileresprobcov,"probcov"); 
       }    strcat(fileresprobcov,fileres);
       strcpy(modelsav,stra);      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      printf("Problem with resultfile: %s\n", fileresprobcov);
         scanf("%d",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }    }
 }    strcpy(fileresprobcor,"probcor"); 
      strcat(fileresprobcor,fileres);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   printf("cptcovprod=%d ", cptcovprod);      printf("Problem with resultfile: %s\n", fileresprobcor);
   scanf("%d ",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     fclose(fic);    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     /*  if(mle==1){*/    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     if (weightopt != 1) { /* Maximisation without weights*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     }    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     agev=matrix(1,maxwav,1,imx);    fprintf(ficresprob, "#Local time at start: %s", strstart);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     for (i=1; i<=imx; i++) {    fprintf(ficresprob,"# Age");
       for(m=2; (m<= maxwav); m++) {    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
          anint[m][i]=9999;    fprintf(ficresprobcov,"# Age");
          s[m][i]=-1;    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
        }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    fprintf(ficresprobcov,"# Age");
       }  
     }  
     for(i=1; i<=nlstate;i++)
     for (i=1; i<=imx; i++)  {      for(j=1; j<=(nlstate+ndeath);j++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       for(m=1; (m<= maxwav); m++){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         if(s[m][i] >0){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           if (s[m][i] >= nlstate+1) {      }  
             if(agedc[i]>0)   /* fprintf(ficresprob,"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficresprobcov,"\n");
                 agev[m][i]=agedc[i];    fprintf(ficresprobcor,"\n");
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/   */
            else {   xp=vector(1,npar);
               if (andc[i]!=9999){    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               agev[m][i]=-1;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               }    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
             }    first=1;
           }    fprintf(ficgp,"\n# Routine varprob");
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fprintf(fichtm,"\n");
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
             else if(agev[m][i] <agemin){    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
               agemin=agev[m][i];    file %s<br>\n",optionfilehtmcov);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
             }  and drawn. It helps understanding how is the covariance between two incidences.\
             else if(agev[m][i] >agemax){   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
               agemax=agev[m][i];    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
             }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
             /*agev[m][i]=anint[m][i]-annais[i];*/  standard deviations wide on each axis. <br>\
             /*   agev[m][i] = age[i]+2*m;*/   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
           }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
           else { /* =9 */  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
             agev[m][i]=1;  
             s[m][i]=-1;    cov[1]=1;
           }    tj=cptcoveff;
         }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         else /*= 0 Unknown */    j1=0;
           agev[m][i]=1;    for(t=1; t<=tj;t++){
       }      for(i1=1; i1<=ncodemax[t];i1++){ 
            j1++;
     }        if  (cptcovn>0) {
     for (i=1; i<=imx; i++)  {          fprintf(ficresprob, "\n#********** Variable "); 
       for(m=1; (m<= maxwav); m++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(ficresprob, "**********\n#\n");
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficresprobcov, "\n#********** Variable "); 
           goto end;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprobcov, "**********\n#\n");
       }          
     }          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          fprintf(ficgp, "**********\n#\n");
           
     free_vector(severity,1,maxwav);          
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     free_vector(moisnais,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(annais,1,n);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     /* free_matrix(mint,1,maxwav,1,n);          
        free_matrix(anint,1,maxwav,1,n);*/          fprintf(ficresprobcor, "\n#********** Variable ");    
     free_vector(moisdc,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(andc,1,n);          fprintf(ficresprobcor, "**********\n#");    
         }
            
     wav=ivector(1,imx);        for (age=bage; age<=fage; age ++){ 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          cov[2]=age;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for (k=1; k<=cptcovn;k++) {
                cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     /* Concatenates waves */          }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          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]]];
       Tcode=ivector(1,100);          
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       ncodemax[1]=1;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          gp=vector(1,(nlstate)*(nlstate+ndeath));
                gm=vector(1,(nlstate)*(nlstate+ndeath));
    codtab=imatrix(1,100,1,10);      
    h=0;          for(theta=1; theta <=npar; theta++){
    m=pow(2,cptcoveff);            for(i=1; i<=npar; i++)
                xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
    for(k=1;k<=cptcoveff; k++){            
      for(i=1; i <=(m/pow(2,k));i++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
        for(j=1; j <= ncodemax[k]; j++){            
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            k=0;
            h++;            for(i=1; i<= (nlstate); i++){
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              for(j=1; j<=(nlstate+ndeath);j++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                k=k+1;
          }                gp[k]=pmmij[i][j];
        }              }
      }            }
    }            
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            for(i=1; i<=npar; i++)
       codtab[1][2]=1;codtab[2][2]=2; */              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    /* for(i=1; i <=m ;i++){      
       for(k=1; k <=cptcovn; k++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            k=0;
       }            for(i=1; i<=(nlstate); i++){
       printf("\n");              for(j=1; j<=(nlstate+ndeath);j++){
       }                k=k+1;
       scanf("%d",i);*/                gm[k]=pmmij[i][j];
                  }
    /* Calculates basic frequencies. Computes observed prevalence at single age            }
        and prints on file fileres'p'. */       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                  gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
              }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(theta=1; theta <=npar; theta++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              trgradg[j][theta]=gradg[theta][j];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          
                matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     /* For Powell, parameters are in a vector p[] starting at p[1]          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     if(mle==1){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }          pmij(pmmij,cov,ncovmodel,x,nlstate);
              
     /*--------- results files --------------*/          k=0;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);          for(i=1; i<=(nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
    jk=1;              mu[k][(int) age]=pmmij[i][j];
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            }
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          }
    for(i=1,jk=1; i <=nlstate; i++){          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
      for(k=1; k <=(nlstate+ndeath); k++){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
        if (k != i)              varpij[i][j][(int)age] = doldm[i][j];
          {  
            printf("%d%d ",i,k);          /*printf("\n%d ",(int)age);
            fprintf(ficres,"%1d%1d ",i,k);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            for(j=1; j <=ncovmodel; j++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              printf("%f ",p[jk]);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              fprintf(ficres,"%f ",p[jk]);            }*/
              jk++;  
            }          fprintf(ficresprob,"\n%d ",(int)age);
            printf("\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficres,"\n");          fprintf(ficresprobcor,"\n%d ",(int)age);
          }  
      }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
    }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
  if(mle==1){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     /* Computing hessian and covariance matrix */            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     ftolhess=ftol; /* Usually correct */            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     hesscov(matcov, p, npar, delti, ftolhess, func);          }
  }          i=0;
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");          for (k=1; k<=(nlstate);k++){
     printf("# Scales (for hessian or gradient estimation)\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
      for(i=1,jk=1; i <=nlstate; i++){              i=i++;
       for(j=1; j <=nlstate+ndeath; j++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         if (j!=i) {              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
           fprintf(ficres,"%1d%1d",i,j);              for (j=1; j<=i;j++){
           printf("%1d%1d",i,j);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           for(k=1; k<=ncovmodel;k++){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
             printf(" %.5e",delti[jk]);              }
             fprintf(ficres," %.5e",delti[jk]);            }
             jk++;          }/* end of loop for state */
           }        } /* end of loop for age */
           printf("\n");  
           fprintf(ficres,"\n");        /* Confidence intervalle of pij  */
         }        /*
       }          fprintf(ficgp,"\nset noparametric;unset label");
      }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
              fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     k=1;          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     fprintf(ficres,"# 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(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     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(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     for(i=1;i<=npar;i++){          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       /*  if (k>nlstate) k=1;        */
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/        first1=1;
       fprintf(ficres,"%3d",i);        for (k2=1; k2<=(nlstate);k2++){
       printf("%3d",i);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       for(j=1; j<=i;j++){            if(l2==k2) continue;
         fprintf(ficres," %.5e",matcov[i][j]);            j=(k2-1)*(nlstate+ndeath)+l2;
         printf(" %.5e",matcov[i][j]);            for (k1=1; k1<=(nlstate);k1++){
       }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       fprintf(ficres,"\n");                if(l1==k1) continue;
       printf("\n");                i=(k1-1)*(nlstate+ndeath)+l1;
       k++;                if(i<=j) continue;
     }                for (age=bage; age<=fage; age ++){ 
                      if ((int)age %5==0){
     while((c=getc(ficpar))=='#' && c!= EOF){                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       ungetc(c,ficpar);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       fgets(line, MAXLINE, ficpar);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       puts(line);                    mu1=mu[i][(int) age]/stepm*YEARM ;
       fputs(line,ficparo);                    mu2=mu[j][(int) age]/stepm*YEARM;
     }                    c12=cv12/sqrt(v1*v2);
     ungetc(c,ficpar);                    /* Computing eigen value of matrix of covariance */
     estepm=0;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     if (estepm==0 || estepm < stepm) estepm=stepm;                    /* Eigen vectors */
     if (fage <= 2) {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       bage = ageminpar;                    /*v21=sqrt(1.-v11*v11); *//* error */
       fage = agemaxpar;                    v21=(lc1-v1)/cv12*v11;
     }                    v12=-v21;
                        v22=v11;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    tnalp=v21/v11;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    if(first1==1){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                      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);
     while((c=getc(ficpar))=='#' && c!= EOF){                    }
     ungetc(c,ficpar);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     fgets(line, MAXLINE, ficpar);                    /*printf(fignu*/
     puts(line);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fputs(line,ficparo);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   }                    if(first==1){
   ungetc(c,ficpar);                      first=0;
                        fprintf(ficgp,"\nset parametric;unset label");
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                      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(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
         :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   while((c=getc(ficpar))=='#' && c!= EOF){  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     ungetc(c,ficpar);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     fgets(line, MAXLINE, ficpar);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     puts(line);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     fputs(line,ficparo);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   }                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   ungetc(c,ficpar);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
   fscanf(ficpar,"pop_based=%d\n",&popbased);                      first=0;
   fprintf(ficparo,"pop_based=%d\n",popbased);                        fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   fprintf(ficres,"pop_based=%d\n",popbased);                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     ungetc(c,ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fgets(line, MAXLINE, ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     puts(line);                    }/* if first */
     fputs(line,ficparo);                  } /* age mod 5 */
   }                } /* end loop age */
   ungetc(c,ficpar);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);              } /*l12 */
 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);            } /* k12 */
 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);          } /*l1 */
         }/* k1 */
       } /* loop covariates */
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     fgets(line, MAXLINE, ficpar);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     puts(line);    free_vector(xp,1,npar);
     fputs(line,ficparo);    fclose(ficresprob);
   }    fclose(ficresprobcov);
   ungetc(c,ficpar);    fclose(ficresprobcor);
     fflush(ficgp);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    fflush(fichtmcov);
   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(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);  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 /*------------ gnuplot -------------*/                    int lastpass, int stepm, int weightopt, char model[],\
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                      int popforecast, int estepm ,\
 /*------------ free_vector  -------------*/                    double jprev1, double mprev1,double anprev1, \
  chdir(path);                    double jprev2, double mprev2,double anprev2){
      int jj1, k1, i1, cpt;
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
  free_ivector(num,1,n);  </ul>");
  free_vector(agedc,1,n);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
  fclose(ficparo);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
  fclose(ficres);     fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
 /*--------- index.htm --------*/             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       fprintf(fichtm,"\
   /*--------------- Prevalence limit --------------*/   - Life expectancies by age and initial health status (estepm=%2d months): \
       <a href=\"%s\">%s</a> <br>\n</li>",
   strcpy(filerespl,"pl");             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }   m=cptcoveff;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");   jj1=0;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);   for(k1=1; k1<=m;k1++){
   fprintf(ficrespl,"\n");     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   prlim=matrix(1,nlstate,1,nlstate);       if (cptcovn > 0) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for (cpt=1; cpt<=cptcoveff;cpt++) 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       }
   k=0;       /* Pij */
   agebase=ageminpar;       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> \
   agelim=agemaxpar;  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   ftolpl=1.e-10;       /* Quasi-incidences */
   i1=cptcoveff;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   if (cptcovn < 1){i1=1;}   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   for(cptcov=1;cptcov<=i1;cptcov++){         /* Stable prevalence in each health state */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         for(cpt=1; cpt<nlstate;cpt++){
         k=k+1;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         fprintf(ficrespl,"\n#******");         }
         for(j=1;j<=cptcoveff;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         fprintf(ficrespl,"******\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
               }
         for (age=agebase; age<=agelim; age++){     } /* end i1 */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   }/* End k1 */
           fprintf(ficrespl,"%.0f",age );   fprintf(fichtm,"</ul>");
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");   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);
     }  
   fclose(ficrespl);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
   /*------------- h Pij x at various ages ------------*/   fprintf(fichtm,"\
     - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   fprintf(fichtm,"\
   }   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   printf("Computing pij: result on file '%s' \n", filerespij);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     fprintf(fichtm,"\
   stepsize=(int) (stepm+YEARM-1)/YEARM;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   /*if (stepm<=24) stepsize=2;*/           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
   agelim=AGESUP;   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   hstepm=stepsize*YEARM; /* Every year of age */           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   fprintf(fichtm,"\
     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   k=0;           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*  if(popforecast==1) fprintf(fichtm,"\n */
       k=k+1;  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
         fprintf(ficrespij,"\n#****** ");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
         for(j=1;j<=cptcoveff;j++)  /*      <br>",fileres,fileres,fileres,fileres); */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*  else  */
         fprintf(ficrespij,"******\n");  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
           fflush(fichtm);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   m=cptcoveff;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     jj1=0;
           fprintf(ficrespij,"# Age");   for(k1=1; k1<=m;k1++){
           for(i=1; i<=nlstate;i++)     for(i1=1; i1<=ncodemax[k1];i1++){
             for(j=1; j<=nlstate+ndeath;j++)       jj1++;
               fprintf(ficrespij," %1d-%1d",i,j);       if (cptcovn > 0) {
           fprintf(ficrespij,"\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
            for (h=0; h<=nhstepm; h++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             for(i=1; i<=nlstate;i++)         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               for(j=1; j<=nlstate+ndeath;j++)       }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);       for(cpt=1; cpt<=nlstate;cpt++) {
             fprintf(ficrespij,"\n");         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
              }  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           fprintf(ficrespij,"\n");       }
         }       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 */
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);   }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(ficrespij);   fflush(fichtm);
   }
   
   /*---------- Forecasting ------------------*/  /******************* Gnuplot file **************/
   if((stepm == 1) && (strcmp(model,".")==0)){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    char dirfileres[132],optfileres[132];
   }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   else{    int ng;
     erreur=108;  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     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);  /*     printf("Problem with file %s",optionfilegnuplot); */
   }  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
    /*   } */
   
   /*---------- Health expectancies and variances ------------*/    /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
   strcpy(filerest,"t");      /*#endif */
   strcat(filerest,fileres);    m=pow(2,cptcoveff);
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    strcpy(dirfileres,optionfilefiname);
   }    strcpy(optfileres,"vpl");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
   strcpy(filerese,"e");       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   strcat(filerese,fileres);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   if((ficreseij=fopen(filerese,"w"))==NULL) {       fprintf(ficgp,"set xlabel \"Age\" \n\
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  set ylabel \"Probability\" \n\
   }  set ter png small\n\
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  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);
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);       for (i=1; i<= nlstate ; i ++) {
   if((ficresvij=fopen(fileresv,"w"))==NULL) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       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);
   calagedate=-1;       for (i=1; i<= nlstate ; i ++) {
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   k=0;       } 
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       for (i=1; i<= nlstate ; i ++) {
       k=k+1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficrest,"\n#****** ");         else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(j=1;j<=cptcoveff;j++)       }  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       fprintf(ficrest,"******\n");     }
     }
       fprintf(ficreseij,"\n#****** ");    /*2 eme*/
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficreseij,"******\n");      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       fprintf(ficresvij,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)      for (i=1; i<= nlstate+1 ; i ++) {
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        k=2*i;
       fprintf(ficresvij,"******\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       oldm=oldms;savm=savms;          else fprintf(ficgp," \%%*lf (\%%*lf)");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          }   
          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       oldm=oldms;savm=savms;        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        fprintf(ficgp,"\" t\"\" w l 0,");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficrest,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       epj=vector(1,nlstate+1);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(age=bage; age <=fage ;age++){        }   
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         if (popbased==1) {        else fprintf(ficgp,"\" t\"\" w l 0,");
           for(i=1; i<=nlstate;i++)      }
             prlim[i][i]=probs[(int)age][i][k];    }
         }    
            /*3eme*/
         fprintf(ficrest," %4.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    for (k1=1; k1<= m ; k1 ++) { 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        k=2+nlstate*(2*cpt-2);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
           }        fprintf(ficgp,"set ter png small\n\
           epj[nlstate+1] +=epj[j];  set size 0.65,0.65\n\
         }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for(i=1, vepp=0.;i <=nlstate;i++)          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           for(j=1;j <=nlstate;j++)          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             vepp += vareij[i][j][(int)age];          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         for(j=1;j <=nlstate;j++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          
         }        */
         fprintf(ficrest,"\n");        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);
     }          
   }        } 
 free_matrix(mint,1,maxwav,1,n);      }
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    }
     free_vector(weight,1,n);    
   fclose(ficreseij);    /* CV preval stable (period) */
   fclose(ficresvij);    for (k1=1; k1<= m ; k1 ++) { 
   fclose(ficrest);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   fclose(ficpar);        k=3;
   free_vector(epj,1,nlstate+1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   /*------- Variance limit prevalence------*/    set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   strcpy(fileresvpl,"vpl");  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   strcat(fileresvpl,fileres);        
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        for (i=1; i< nlstate ; i ++)
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          fprintf(ficgp,"+$%d",k+i+1);
     exit(0);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   }        
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   k=0;        for (i=1; i< nlstate ; i ++) {
   for(cptcov=1;cptcov<=i1;cptcov++){          l=3+(nlstate+ndeath)*cpt;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficgp,"+$%d",l+i+1);
       k=k+1;        }
       fprintf(ficresvpl,"\n#****** ");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       for(j=1;j<=cptcoveff;j++)      } 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }  
       fprintf(ficresvpl,"******\n");    
          /* proba elementaires */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    for(i=1,jk=1; i <=nlstate; i++){
       oldm=oldms;savm=savms;      for(k=1; k <=(nlstate+ndeath); k++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        if (k != i) {
     }          for(j=1; j <=ncovmodel; j++){
  }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
   fclose(ficresvpl);            fprintf(ficgp,"\n");
           }
   /*---------- End : free ----------------*/        }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      }
       }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);     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); 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);         if (ng==2)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);         else
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);           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);
   free_matrix(matcov,1,npar,1,npar);         i=1;
   free_vector(delti,1,npar);         for(k2=1; k2<=nlstate; k2++) {
   free_matrix(agev,1,maxwav,1,imx);           k3=i;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);           for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
   if(erreur >0)               if(ng==2)
     printf("End of Imach with error or warning %d\n",erreur);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   else   printf("End of Imach\n");               else
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                 ij=1;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/               for(j=3; j <=ncovmodel; j++) {
   /*printf("Total time was %d uSec.\n", total_usecs);*/                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   /*------ End -----------*/                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
  end:                 else
 #ifdef windows                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   /* chdir(pathcd);*/               }
 #endif               fprintf(ficgp,")/(1");
  /*system("wgnuplot graph.plt");*/               
  /*system("../gp37mgw/wgnuplot graph.plt");*/               for(k1=1; k1 <=nlstate; k1++){   
  /*system("cd ../gp37mgw");*/                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                 ij=1;
  strcpy(plotcmd,GNUPLOTPROGRAM);                 for(j=3; j <=ncovmodel; j++){
  strcat(plotcmd," ");                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  strcat(plotcmd,optionfilegnuplot);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  system(plotcmd);                     ij++;
                    }
 #ifdef windows                   else
   while (z[0] != 'q') {                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     /* chdir(path); */                 }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                 fprintf(ficgp,")");
     scanf("%s",z);               }
     if (z[0] == 'c') system("./imach");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     else if (z[0] == 'e') system(optionfilehtm);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     else if (z[0] == 'g') system(plotcmd);               i=i+ncovmodel;
     else if (z[0] == 'q') exit(0);             }
   }           } /* end k */
 #endif         } /* 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.1.41  
changed lines
  Added in v.1.112


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