Diff for /imach/src/imach.c between versions 1.41.2.1 and 1.116

version 1.41.2.1, 2003/06/12 10:43:20 version 1.116, 2006/03/06 10:29:27
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.116  2006/03/06 10:29:27  brouard
      (Module): Variance-covariance wrong links and
   This program computes Healthy Life Expectancies from    varian-covariance of ej. is needed (Saito).
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.115  2006/02/27 12:17:45  brouard
   interviewed on their health status or degree of disability (in the    (Module): One freematrix added in mlikeli! 0.98c
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.114  2006/02/26 12:57:58  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Some improvements in processing parameter
   computed from the time spent in each health state according to a    filename with strsep.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.113  2006/02/24 14:20:24  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): Memory leaks checks with valgrind and:
   probability to be observed in state j at the second wave    datafile was not closed, some imatrix were not freed and on matrix
   conditional to be observed in state i at the first wave. Therefore    allocation too.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.112  2006/01/30 09:55:26  brouard
   complex model than "constant and age", you should modify the program    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.111  2006/01/25 20:38:18  brouard
   convergence.    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
   The advantage of this computer programme, compared to a simple    can be a simple dot '.'.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.110  2006/01/25 00:51:50  brouard
   intermediate interview, the information is lost, but taken into    (Module): Lots of cleaning and bugs added (Gompertz)
   account using an interpolation or extrapolation.    
     Revision 1.109  2006/01/24 19:37:15  brouard
   hPijx is the probability to be observed in state i at age x+h    (Module): Comments (lines starting with a #) are allowed in data.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.108  2006/01/19 18:05:42  lievre
   states. This elementary transition (by month or quarter trimester,    Gnuplot problem appeared...
   semester or year) is model as a multinomial logistic.  The hPx    To be fixed
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.107  2006/01/19 16:20:37  brouard
   hPijx.    Test existence of gnuplot in imach path
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.106  2006/01/19 13:24:36  brouard
   of the life expectancies. It also computes the prevalence limits.    Some cleaning and links added in html output
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.105  2006/01/05 20:23:19  lievre
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.104  2005/09/30 16:11:43  lievre
   It is copyrighted identically to a GNU software product, ie programme and    (Module): sump fixed, loop imx fixed, and simplifications.
   software can be distributed freely for non commercial use. Latest version    (Module): If the status is missing at the last wave but we know
   can be accessed at http://euroreves.ined.fr/imach .    that the person is alive, then we can code his/her status as -2
   **********************************************************************/    (instead of missing=-1 in earlier versions) and his/her
      contributions to the likelihood is 1 - Prob of dying from last
 #include <math.h>    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #include <stdio.h>    the healthy state at last known wave). Version is 0.98
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "wgnuplot"    Revision 1.102  2004/09/15 17:31:30  brouard
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Add the possibility to read data file including tab characters.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 /*#define windows*/  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.100  2004/07/12 18:29:06  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Add version for Mac OS X. Just define UNIX in Makefile
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.99  2004/06/05 08:57:40  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    *** empty log message ***
   
 #define NINTERVMAX 8    Revision 1.98  2004/05/16 15:05:56  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    New version 0.97 . First attempt to estimate force of mortality
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    directly from the data i.e. without the need of knowing the health
 #define NCOVMAX 8 /* Maximum number of covariates */    state at each age, but using a Gompertz model: log u =a + b*age .
 #define MAXN 20000    This is the basic analysis of mortality and should be done before any
 #define YEARM 12. /* Number of months per year */    other analysis, in order to test if the mortality estimated from the
 #define AGESUP 130    cross-longitudinal survey is different from the mortality estimated
 #define AGEBASE 40    from other sources like vital statistic data.
   
     The same imach parameter file can be used but the option for mle should be -3.
 int erreur; /* Error number */  
 int nvar;    Agnès, who wrote this part of the code, tried to keep most of the
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    former routines in order to include the new code within the former code.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    The output is very simple: only an estimate of the intercept and of
 int ndeath=1; /* Number of dead states */    the slope with 95% confident intervals.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Current limitations:
     A) Even if you enter covariates, i.e. with the
 int *wav; /* Number of waves for this individuual 0 is possible */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int maxwav; /* Maxim number of waves */    B) There is no computation of Life Expectancy nor Life Table.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.97  2004/02/20 13:25:42  lievre
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Version 0.96d. Population forecasting command line is (temporarily)
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    suppressed.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.96  2003/07/15 15:38:55  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    rewritten within the same printf. Workaround: many printfs.
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.95  2003/07/08 07:54:34  brouard
   char filerese[FILENAMELENGTH];    * imach.c (Repository):
  FILE  *ficresvij;    (Repository): Using imachwizard code to output a more meaningful covariance
   char fileresv[FILENAMELENGTH];    matrix (cov(a12,c31) instead of numbers.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.93  2003/06/25 16:33:55  brouard
 #define FTOL 1.0e-10    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define NRANSI    (Module): Version 0.96b
 #define ITMAX 200  
     Revision 1.92  2003/06/25 16:30:45  brouard
 #define TOL 2.0e-4    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.91  2003/06/25 15:30:29  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 #define GOLD 1.618034    helps to forecast when convergence will be reached. Elapsed time
 #define GLIMIT 100.0    is stamped in powell.  We created a new html file for the graphs
 #define TINY 1.0e-20    concerning matrix of covariance. It has extension -cov.htm.
   
 static double maxarg1,maxarg2;    Revision 1.90  2003/06/24 12:34:15  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): Some bugs corrected for windows. Also, when
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    mle=-1 a template is output in file "or"mypar.txt with the design
      of the covariance matrix to be input.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 static double sqrarg;    mle=-1 a template is output in file "or"mypar.txt with the design
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    of the covariance matrix to be input.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.88  2003/06/23 17:54:56  brouard
 int imx;    * 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.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 int m,nb;    routine fileappend.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.85  2003/06/17 13:12:43  brouard
 double **pmmij, ***probs, ***mobaverage;    * imach.c (Repository): Check when date of death was earlier that
 double dateintmean=0;    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 double *weight;    was wrong (infinity). We still send an "Error" but patch by
 int **s; /* Status */    assuming that the date of death was just one stepm after the
 double *agedc, **covar, idx;    interview.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    memory allocation. But we also truncated to 8 characters (left
 double ftolhess; /* Tolerance for computing hessian */    truncation)
     (Repository): No more line truncation errors.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.84  2003/06/13 21:44:43  brouard
 {    * imach.c (Repository): Replace "freqsummary" at a correct
    char *s;                             /* pointer */    place. It differs from routine "prevalence" which may be called
    int  l1, l2;                         /* length counters */    many times. Probs is memory consuming and must be used with
     parcimony.
    l1 = strlen( path );                 /* length of path */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.83  2003/06/10 13:39:11  lievre
    s = strrchr( path, '\\' );           /* find last / */    *** empty log message ***
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.82  2003/06/05 15:57:20  brouard
 #endif    Add log in  imach.c and  fullversion number is now printed.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  */
       extern char       *getwd( );  /*
      Interpolated Markov Chain
       if ( getwd( dirc ) == NULL ) {  
 #else    Short summary of the programme:
       extern char       *getcwd( );    
     This program computes Healthy Life Expectancies from
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #endif    first survey ("cross") where individuals from different ages are
          return( GLOCK_ERROR_GETCWD );    interviewed on their health status or degree of disability (in the
       }    case of a health survey which is our main interest) -2- at least a
       strcpy( name, path );             /* we've got it */    second wave of interviews ("longitudinal") which measure each change
    } else {                             /* strip direcotry from path */    (if any) in individual health status.  Health expectancies are
       s++;                              /* after this, the filename */    computed from the time spent in each health state according to a
       l2 = strlen( s );                 /* length of filename */    model. More health states you consider, more time is necessary to reach the
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Maximum Likelihood of the parameters involved in the model.  The
       strcpy( name, s );                /* save file name */    simplest model is the multinomial logistic model where pij is the
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    probability to be observed in state j at the second wave
       dirc[l1-l2] = 0;                  /* add zero */    conditional to be observed in state i at the first wave. Therefore
    }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    l1 = strlen( dirc );                 /* length of directory */    'age' is age and 'sex' is a covariate. If you want to have a more
 #ifdef windows    complex model than "constant and age", you should modify the program
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    where the markup *Covariates have to be included here again* invites
 #else    you to do it.  More covariates you add, slower the
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    convergence.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    The advantage of this computer programme, compared to a simple
    s++;    multinomial logistic model, is clear when the delay between waves is not
    strcpy(ext,s);                       /* save extension */    identical for each individual. Also, if a individual missed an
    l1= strlen( name);    intermediate interview, the information is lost, but taken into
    l2= strlen( s)+1;    account using an interpolation or extrapolation.  
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    hPijx is the probability to be observed in state i at age x+h
    return( 0 );                         /* we're done */    conditional to the observed state i at age x. The delay 'h' can be
 }    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 /******************************************/    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 void replace(char *s, char*t)    hPijx.
 {  
   int i;    Also this programme outputs the covariance matrix of the parameters but also
   int lg=20;    of the life expectancies. It also computes the stable prevalence. 
   i=0;    
   lg=strlen(t);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for(i=0; i<= lg; i++) {             Institut national d'études démographiques, Paris.
     (s[i] = t[i]);    This software have been partly granted by Euro-REVES, a concerted action
     if (t[i]== '\\') s[i]='/';    from the European Union.
   }    It is copyrighted identically to a GNU software product, ie programme and
 }    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 int nbocc(char *s, char occ)  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int i,j=0;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   int lg=20;    
   i=0;    **********************************************************************/
   lg=strlen(s);  /*
   for(i=0; i<= lg; i++) {    main
   if  (s[i] == occ ) j++;    read parameterfile
   }    read datafile
   return j;    concatwav
 }    freqsummary
     if (mle >= 1)
 void cutv(char *u,char *v, char*t, char occ)      mlikeli
 {    print results files
   int i,lg,j,p=0;    if mle==1 
   i=0;       computes hessian
   for(j=0; j<=strlen(t)-1; j++) {    read end of parameter file: agemin, agemax, bage, fage, estepm
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;        begin-prev-date,...
   }    open gnuplot file
     open html file
   lg=strlen(t);    stable prevalence
   for(j=0; j<p; j++) {     for age prevalim()
     (u[j] = t[j]);    h Pij x
   }    variance of p varprob
      u[p]='\0';    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
    for(j=0; j<= lg; j++) {    Variance-covariance of DFLE
     if (j>=(p+1))(v[j-p-1] = t[j]);    prevalence()
   }     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 /********************** nrerror ********************/    total life expectancies
     Variance of stable prevalence
 void nrerror(char error_text[])   end
 {  */
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  
 }   
 /*********************** vector *******************/  #include <math.h>
 double *vector(int nl, int nh)  #include <stdio.h>
 {  #include <stdlib.h>
   double *v;  #include <string.h>
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #include <unistd.h>
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  #include <limits.h>
 }  #include <sys/types.h>
   #include <sys/stat.h>
 /************************ free vector ******************/  #include <errno.h>
 void free_vector(double*v, int nl, int nh)  extern int errno;
 {  
   free((FREE_ARG)(v+nl-NR_END));  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define MAXLINE 256
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long 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 */
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define NINTERVMAX 8
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define NCOVMAX 8 /* Maximum number of covariates */
   int **m;  #define MAXN 20000
    #define YEARM 12. /* Number of months per year */
   /* allocate pointers to rows */  #define AGESUP 130
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define AGEBASE 40
   if (!m) nrerror("allocation failure 1 in matrix()");  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m += NR_END;  #ifdef UNIX
   m -= nrl;  #define DIRSEPARATOR '/'
    #define CHARSEPARATOR "/"
    #define ODIRSEPARATOR '\\'
   /* allocate rows and set pointers to them */  #else
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define DIRSEPARATOR '\\'
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define CHARSEPARATOR "\\"
   m[nrl] += NR_END;  #define ODIRSEPARATOR '/'
   m[nrl] -= ncl;  #endif
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /* $Id$ */
    /* $State$ */
   /* return pointer to array of pointers to rows */  
   return m;  char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
 }  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 /****************** free_imatrix *************************/  int nvar;
 void free_imatrix(m,nrl,nrh,ncl,nch)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
       int **m;  int npar=NPARMAX;
       long nch,ncl,nrh,nrl;  int nlstate=2; /* Number of live states */
      /* free an int matrix allocated by imatrix() */  int ndeath=1; /* Number of dead states */
 {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int popbased=0;
   free((FREE_ARG) (m+nrl-NR_END));  
 }  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 /******************* matrix *******************************/  int jmin, jmax; /* min, max spacing between 2 waves */
 double **matrix(long nrl, long nrh, long ncl, long nch)  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;                     to the likelihood and the sum of weights (done by funcone)*/
   double **m;  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   if (!m) nrerror("allocation failure 1 in matrix()");  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   m += NR_END;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   m -= nrl;  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m[nrl] += NR_END;  FILE *ficlog, *ficrespow;
   m[nrl] -= ncl;  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  long ipmx; /* Number of contributions */
   return m;  double sw; /* Sum of weights */
 }  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 /*************************free matrix ************************/  FILE *ficresilk;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *fichtm, *fichtmcov; /* Html File */
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /******************* ma3x *******************************/  char fileresv[FILENAMELENGTH];
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char title[MAXLINE];
   double ***m;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   if (!m) nrerror("allocation failure 1 in matrix()");  char command[FILENAMELENGTH];
   m += NR_END;  int  outcmd=0;
   m -= nrl;  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char filelog[FILENAMELENGTH]; /* Log file */
   m[nrl] += NR_END;  char filerest[FILENAMELENGTH];
   m[nrl] -= ncl;  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m[nrl][ncl] += NR_END;  struct timezone tzp;
   m[nrl][ncl] -= nll;  extern int gettimeofday();
   for (j=ncl+1; j<=nch; j++)  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     m[nrl][j]=m[nrl][j-1]+nlay;  long time_value;
    extern long time();
   for (i=nrl+1; i<=nrh; i++) {  char strcurr[80], strfor[80];
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  char *endptr;
       m[i][j]=m[i][j-1]+nlay;  long lval;
   }  
   return m;  #define NR_END 1
 }  #define FREE_ARG char*
   #define FTOL 1.0e-10
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define NRANSI 
 {  #define ITMAX 200 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define TOL 2.0e-4 
   free((FREE_ARG)(m+nrl-NR_END));  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /***************** f1dim *************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 extern int ncom;  
 extern double *pcom,*xicom;  #define GOLD 1.618034 
 extern double (*nrfunc)(double []);  #define GLIMIT 100.0 
    #define TINY 1.0e-20 
 double f1dim(double x)  
 {  static double maxarg1,maxarg2;
   int j;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double f;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double *xt;    
    #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   xt=vector(1,ncom);  #define rint(a) floor(a+0.5)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  static double sqrarg;
   free_vector(xt,1,ncom);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   return f;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
 /*****************brent *************************/  int imx; 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int stepm=1;
 {  /* Stepm, step in month: minimum step interpolation*/
   int iter;  
   double a,b,d,etemp;  int estepm;
   double fu,fv,fw,fx;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int m,nb;
   double e=0.0;  long *num;
    int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   a=(ax < cx ? ax : cx);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   b=(ax > cx ? ax : cx);  double **pmmij, ***probs;
   x=w=v=bx;  double *ageexmed,*agecens;
   fw=fv=fx=(*f)(x);  double dateintmean=0;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  double *weight;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int **s; /* Status */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  double *agedc, **covar, idx;
     printf(".");fflush(stdout);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 #ifdef DEBUG  double *lsurv, *lpop, *tpop;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 #endif  double ftolhess; /* Tolerance for computing hessian */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /**************** split *************************/
       return fx;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     }  {
     ftemp=fu;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     if (fabs(e) > tol1) {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       r=(x-w)*(fx-fv);    */ 
       q=(x-v)*(fx-fw);    char  *ss;                            /* pointer */
       p=(x-v)*q-(x-w)*r;    int   l1, l2;                         /* length counters */
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    l1 = strlen(path );                   /* length of path */
       q=fabs(q);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       etemp=e;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       e=d;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      strcpy( name, path );               /* we got the fullname name because no directory */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       else {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         d=p/q;      /* get current working directory */
         u=x+d;      /*    extern  char* getcwd ( char *buf , int len);*/
         if (u-a < tol2 || b-u < tol2)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
           d=SIGN(tol1,xm-x);        return( GLOCK_ERROR_GETCWD );
       }      }
     } else {      /* got dirc from getcwd*/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      printf(" DIRC = %s \n",dirc);
     }    } else {                              /* strip direcotry from path */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      ss++;                               /* after this, the filename */
     fu=(*f)(u);      l2 = strlen( ss );                  /* length of filename */
     if (fu <= fx) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       if (u >= x) a=x; else b=x;      strcpy( name, ss );         /* save file name */
       SHFT(v,w,x,u)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         SHFT(fv,fw,fx,fu)      dirc[l1-l2] = 0;                    /* add zero */
         } else {      printf(" DIRC2 = %s \n",dirc);
           if (u < x) a=u; else b=u;    }
           if (fu <= fw || w == x) {    /* We add a separator at the end of dirc if not exists */
             v=w;    l1 = strlen( dirc );                  /* length of directory */
             w=u;    if( dirc[l1-1] != DIRSEPARATOR ){
             fv=fw;      dirc[l1] =  DIRSEPARATOR;
             fw=fu;      dirc[l1+1] = 0; 
           } else if (fu <= fv || v == x || v == w) {      printf(" DIRC3 = %s \n",dirc);
             v=u;    }
             fv=fu;    ss = strrchr( name, '.' );            /* find last / */
           }    if (ss >0){
         }      ss++;
   }      strcpy(ext,ss);                     /* save extension */
   nrerror("Too many iterations in brent");      l1= strlen( name);
   *xmin=x;      l2= strlen(ss)+1;
   return fx;      strncpy( finame, name, l1-l2);
 }      finame[l1-l2]= 0;
     }
 /****************** mnbrak ***********************/  
     return( 0 );                          /* we're done */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  }
             double (*func)(double))  
 {  
   double ulim,u,r,q, dum;  /******************************************/
   double fu;  
    void replace_back_to_slash(char *s, char*t)
   *fa=(*func)(*ax);  {
   *fb=(*func)(*bx);    int i;
   if (*fb > *fa) {    int lg=0;
     SHFT(dum,*ax,*bx,dum)    i=0;
       SHFT(dum,*fb,*fa,dum)    lg=strlen(t);
       }    for(i=0; i<= lg; i++) {
   *cx=(*bx)+GOLD*(*bx-*ax);      (s[i] = t[i]);
   *fc=(*func)(*cx);      if (t[i]== '\\') s[i]='/';
   while (*fb > *fc) {    }
     r=(*bx-*ax)*(*fb-*fc);  }
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int nbocc(char *s, char occ)
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  {
     ulim=(*bx)+GLIMIT*(*cx-*bx);    int i,j=0;
     if ((*bx-u)*(u-*cx) > 0.0) {    int lg=20;
       fu=(*func)(u);    i=0;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    lg=strlen(s);
       fu=(*func)(u);    for(i=0; i<= lg; i++) {
       if (fu < *fc) {    if  (s[i] == occ ) j++;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    }
           SHFT(*fb,*fc,fu,(*func)(u))    return j;
           }  }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  void cutv(char *u,char *v, char*t, char occ)
       fu=(*func)(u);  {
     } else {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       u=(*cx)+GOLD*(*cx-*bx);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       fu=(*func)(u);       gives u="abcedf" and v="ghi2j" */
     }    int i,lg,j,p=0;
     SHFT(*ax,*bx,*cx,u)    i=0;
       SHFT(*fa,*fb,*fc,fu)    for(j=0; j<=strlen(t)-1; j++) {
       }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /*************** linmin ************************/    lg=strlen(t);
     for(j=0; j<p; j++) {
 int ncom;      (u[j] = t[j]);
 double *pcom,*xicom;    }
 double (*nrfunc)(double []);       u[p]='\0';
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))     for(j=0; j<= lg; j++) {
 {      if (j>=(p+1))(v[j-p-1] = t[j]);
   double brent(double ax, double bx, double cx,    }
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /********************** nrerror ********************/
               double *fc, double (*func)(double));  
   int j;  void nrerror(char error_text[])
   double xx,xmin,bx,ax;  {
   double fx,fb,fa;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   ncom=n;    exit(EXIT_FAILURE);
   pcom=vector(1,n);  }
   xicom=vector(1,n);  /*********************** vector *******************/
   nrfunc=func;  double *vector(int nl, int nh)
   for (j=1;j<=n;j++) {  {
     pcom[j]=p[j];    double *v;
     xicom[j]=xi[j];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   }    if (!v) nrerror("allocation failure in vector");
   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 vector ******************/
 #ifdef DEBUG  void free_vector(double*v, int nl, int 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];  /************************ivector *******************************/
   }  int *ivector(long nl,long nh)
   free_vector(xicom,1,n);  {
   free_vector(pcom,1,n);    int *v;
 }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     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 ivector **************************/
   void linmin(double p[], double xi[], int n, double *fret,  void free_ivector(int *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;  /************************lvector *******************************/
   pt=vector(1,n);  long *lvector(long nl,long nh)
   ptt=vector(1,n);  {
   xit=vector(1,n);    long *v;
   xits=vector(1,n);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   *fret=(*func)(p);    if (!v) nrerror("allocation failure in ivector");
   for (j=1;j<=n;j++) pt[j]=p[j];    return v-nl+NR_END;
   for (*iter=1;;++(*iter)) {  }
     fp=(*fret);  
     ibig=0;  /******************free lvector **************************/
     del=0.0;  void free_lvector(long *v, long nl, long nh)
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  {
     for (i=1;i<=n;i++)    free((FREE_ARG)(v+nl-NR_END));
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  /******************* imatrix *******************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       fptt=(*fret);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 #ifdef DEBUG  { 
       printf("fret=%lf \n",*fret);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 #endif    int **m; 
       printf("%d",i);fflush(stdout);    
       linmin(p,xit,n,fret,func);    /* allocate pointers to rows */ 
       if (fabs(fptt-(*fret)) > del) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         del=fabs(fptt-(*fret));    if (!m) nrerror("allocation failure 1 in matrix()"); 
         ibig=i;    m += NR_END; 
       }    m -= nrl; 
 #ifdef DEBUG    
       printf("%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {    /* allocate rows and set pointers to them */ 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         printf(" x(%d)=%.12e",j,xit[j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       }    m[nrl] += NR_END; 
       for(j=1;j<=n;j++)    m[nrl] -= ncl; 
         printf(" p=%.12e",p[j]);    
       printf("\n");    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 #endif    
     }    /* return pointer to array of pointers to rows */ 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    return m; 
 #ifdef DEBUG  } 
       int k[2],l;  
       k[0]=1;  /****************** free_imatrix *************************/
       k[1]=-1;  void free_imatrix(m,nrl,nrh,ncl,nch)
       printf("Max: %.12e",(*func)(p));        int **m;
       for (j=1;j<=n;j++)        long nch,ncl,nrh,nrl; 
         printf(" %.12e",p[j]);       /* free an int matrix allocated by imatrix() */ 
       printf("\n");  { 
       for(l=0;l<=1;l++) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         for (j=1;j<=n;j++) {    free((FREE_ARG) (m+nrl-NR_END)); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  } 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  /******************* matrix *******************************/
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  double **matrix(long nrl, long nrh, long ncl, long nch)
       }  {
 #endif    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
   
       free_vector(xit,1,n);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       free_vector(xits,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
       free_vector(ptt,1,n);    m += NR_END;
       free_vector(pt,1,n);    m -= nrl;
       return;  
     }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for (j=1;j<=n;j++) {    m[nrl] += NR_END;
       ptt[j]=2.0*p[j]-pt[j];    m[nrl] -= ncl;
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     fptt=(*func)(ptt);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     if (fptt < fp) {     */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  }
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /*************************free matrix ************************/
         for (j=1;j<=n;j++) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         }    free((FREE_ARG)(m+nrl-NR_END));
 #ifdef DEBUG  }
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  /******************* ma3x *******************************/
           printf(" %.12e",xit[j]);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         printf("\n");  {
 #endif    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       }    double ***m;
     }  
   }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 }    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /**** Prevalence limit ****************/    m -= nrl;
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    m[nrl] += NR_END;
      matrix by transitions matrix until convergence is reached */    m[nrl] -= ncl;
   
   int i, ii,j,k;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double **out, cov[NCOVMAX], **pmij();    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double **newm;    m[nrl][ncl] += NR_END;
   double agefin, delaymax=50 ; /* Max number of years to converge */    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   for (ii=1;ii<=nlstate+ndeath;ii++)      m[nrl][j]=m[nrl][j-1]+nlay;
     for (j=1;j<=nlstate+ndeath;j++){    
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    for (i=nrl+1; i<=nrh; i++) {
     }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
    cov[1]=1.;        m[i][j]=m[i][j-1]+nlay;
      }
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    return m; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     newm=savm;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     /* Covariates have to be included here again */    */
      cov[2]=agefin;  }
    
       for (k=1; k<=cptcovn;k++) {  /*************************free ma3x ************************/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  {
       }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for (k=1; k<=cptcovprod;k++)    free((FREE_ARG)(m+nrl-NR_END));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /*************** function subdirf ***********/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  char *subdirf(char fileres[])
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     savm=oldm;    strcat(tmpout,"/"); /* Add to the right */
     oldm=newm;    strcat(tmpout,fileres);
     maxmax=0.;    return tmpout;
     for(j=1;j<=nlstate;j++){  }
       min=1.;  
       max=0.;  /*************** function subdirf2 ***********/
       for(i=1; i<=nlstate; i++) {  char *subdirf2(char fileres[], char *preop)
         sumnew=0;  {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    
         prlim[i][j]= newm[i][j]/(1-sumnew);    /* Caution optionfilefiname is hidden */
         max=FMAX(max,prlim[i][j]);    strcpy(tmpout,optionfilefiname);
         min=FMIN(min,prlim[i][j]);    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
       maxmin=max-min;    strcat(tmpout,fileres);
       maxmax=FMAX(maxmax,maxmin);    return tmpout;
     }  }
     if(maxmax < ftolpl){  
       return prlim;  /*************** function subdirf3 ***********/
     }  char *subdirf3(char fileres[], char *preop, char *preop2)
   }  {
 }    
     /* Caution optionfilefiname is hidden */
 /*************** transition probabilities ***************/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    strcat(tmpout,preop);
 {    strcat(tmpout,preop2);
   double s1, s2;    strcat(tmpout,fileres);
   /*double t34;*/    return tmpout;
   int i,j,j1, nc, ii, jj;  }
   
     for(i=1; i<= nlstate; i++){  /***************** f1dim *************************/
     for(j=1; j<i;j++){  extern int ncom; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  extern double *pcom,*xicom;
         /*s2 += param[i][j][nc]*cov[nc];*/  extern double (*nrfunc)(double []); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];   
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  double f1dim(double x) 
       }  { 
       ps[i][j]=s2;    int j; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double f;
     }    double *xt; 
     for(j=i+1; j<=nlstate+ndeath;j++){   
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    xt=vector(1,ncom); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
       ps[i][j]=s2;    return f; 
     }  } 
   }  
     /*ps[3][2]=1;*/  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(i=1; i<= nlstate; i++){  { 
      s1=0;    int iter; 
     for(j=1; j<i; j++)    double a,b,d,etemp;
       s1+=exp(ps[i][j]);    double fu,fv,fw,fx;
     for(j=i+1; j<=nlstate+ndeath; j++)    double ftemp;
       s1+=exp(ps[i][j]);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     ps[i][i]=1./(s1+1.);    double e=0.0; 
     for(j=1; j<i; j++)   
       ps[i][j]= exp(ps[i][j])*ps[i][i];    a=(ax < cx ? ax : cx); 
     for(j=i+1; j<=nlstate+ndeath; j++)    b=(ax > cx ? ax : cx); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    x=w=v=bx; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    fw=fv=fx=(*f)(x); 
   } /* end i */    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       ps[ii][jj]=0;      printf(".");fflush(stdout);
       ps[ii][ii]=1;      fprintf(ficlog,".");fflush(ficlog);
     }  #ifdef DEBUG
   }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
      printf("%lf ",ps[ii][jj]);        *xmin=x; 
    }        return fx; 
     printf("\n ");      } 
     }      ftemp=fu;
     printf("\n ");printf("%lf ",cov[2]);*/      if (fabs(e) > tol1) { 
 /*        r=(x-w)*(fx-fv); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        q=(x-v)*(fx-fw); 
   goto end;*/        p=(x-v)*q-(x-w)*r; 
     return ps;        q=2.0*(q-r); 
 }        if (q > 0.0) p = -p; 
         q=fabs(q); 
 /**************** Product of 2 matrices ******************/        etemp=e; 
         e=d; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   /* 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(...) */          d=p/q; 
   /* in, b, out are matrice of pointers which should have been initialized          u=x+d; 
      before: only the contents of out is modified. The function returns          if (u-a < tol2 || b-u < tol2) 
      a pointer to pointers identical to out */            d=SIGN(tol1,xm-x); 
   long i, j, k;        } 
   for(i=nrl; i<= nrh; i++)      } else { 
     for(k=ncolol; k<=ncoloh; k++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      } 
         out[i][k] +=in[i][j]*b[j][k];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
   return out;      if (fu <= fx) { 
 }        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
 /************* Higher Matrix Product ***************/          } else { 
             if (u < x) a=u; else b=u; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            if (fu <= fw || w == x) { 
 {              v=w; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month              w=u; 
      duration (i.e. until              fv=fw; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.              fw=fu; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step            } else if (fu <= fv || v == x || v == w) { 
      (typically every 2 years instead of every month which is too big).              v=u; 
      Model is determined by parameters x and covariates have to be              fv=fu; 
      included manually here.            } 
           } 
      */    } 
     nrerror("Too many iterations in brent"); 
   int i, j, d, h, k;    *xmin=x; 
   double **out, cov[NCOVMAX];    return fx; 
   double **newm;  } 
   
   /* Hstepm could be zero and should return the unit matrix */  /****************** mnbrak ***********************/
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       oldm[i][j]=(i==j ? 1.0 : 0.0);              double (*func)(double)) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  { 
     }    double ulim,u,r,q, dum;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double fu; 
   for(h=1; h <=nhstepm; h++){   
     for(d=1; d <=hstepm; d++){    *fa=(*func)(*ax); 
       newm=savm;    *fb=(*func)(*bx); 
       /* Covariates have to be included here again */    if (*fb > *fa) { 
       cov[1]=1.;      SHFT(dum,*ax,*bx,dum) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        SHFT(dum,*fb,*fa,dum) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        } 
       for (k=1; k<=cptcovage;k++)    *cx=(*bx)+GOLD*(*bx-*ax); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    *fc=(*func)(*cx); 
       for (k=1; k<=cptcovprod;k++)    while (*fb > *fc) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      if ((*bx-u)*(u-*cx) > 0.0) { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        fu=(*func)(u); 
       savm=oldm;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       oldm=newm;        fu=(*func)(u); 
     }        if (fu < *fc) { 
     for(i=1; i<=nlstate+ndeath; i++)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for(j=1;j<=nlstate+ndeath;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
         po[i][j][h]=newm[i][j];            } 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
          */        u=ulim; 
       }        fu=(*func)(u); 
   } /* end h */      } else { 
   return po;        u=(*cx)+GOLD*(*cx-*bx); 
 }        fu=(*func)(u); 
       } 
       SHFT(*ax,*bx,*cx,u) 
 /*************** log-likelihood *************/        SHFT(*fa,*fb,*fc,fu) 
 double func( double *x)        } 
 {  } 
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*************** linmin ************************/
   double **out;  
   double sw; /* Sum of weights */  int ncom; 
   double lli; /* Individual log likelihood */  double *pcom,*xicom;
   long ipmx;  double (*nrfunc)(double []); 
   /*extern weight */   
   /* We are differentiating ll according to initial status */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  { 
   /*for(i=1;i<imx;i++)    double brent(double ax, double bx, double cx, 
     printf(" %d\n",s[4][i]);                 double (*f)(double), double tol, double *xmin); 
   */    double f1dim(double x); 
   cov[1]=1.;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    int j; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double xx,xmin,bx,ax; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    double fx,fb,fa;
     for(mi=1; mi<= wav[i]-1; mi++){   
       for (ii=1;ii<=nlstate+ndeath;ii++)    ncom=n; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    pcom=vector(1,n); 
       for(d=0; d<dh[mi][i]; d++){    xicom=vector(1,n); 
         newm=savm;    nrfunc=func; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    for (j=1;j<=n;j++) { 
         for (kk=1; kk<=cptcovage;kk++) {      pcom[j]=p[j]; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      xicom[j]=xi[j]; 
         }    } 
            ax=0.0; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    xx=1.0; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         savm=oldm;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         oldm=newm;  #ifdef DEBUG
            printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
            fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       } /* end mult */  #endif
          for (j=1;j<=n;j++) { 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      xi[j] *= xmin; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      p[j] += xi[j]; 
       ipmx +=1;    } 
       sw += weight[i];    free_vector(xicom,1,n); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    free_vector(pcom,1,n); 
     } /* end of wave */  } 
   } /* end of individual */  
   char *asc_diff_time(long time_sec, char ascdiff[])
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    long sec_left, days, hours, minutes;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    days = (time_sec) / (60*60*24);
   return -l;    sec_left = (time_sec) % (60*60*24);
 }    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
 /*********** Maximum Likelihood Estimation ***************/    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    return ascdiff;
 {  }
   int i,j, iter;  
   double **xi,*delti;  /*************** powell ************************/
   double fret;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   xi=matrix(1,npar,1,npar);              double (*func)(double [])) 
   for (i=1;i<=npar;i++)  { 
     for (j=1;j<=npar;j++)    void linmin(double p[], double xi[], int n, double *fret, 
       xi[i][j]=(i==j ? 1.0 : 0.0);                double (*func)(double [])); 
   printf("Powell\n");    int i,ibig,j; 
   powell(p,xi,npar,ftol,&iter,&fret,func);    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double *xits;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    int niterf, itmp;
   
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
 /**** Computes Hessian and covariance matrix ***/    xit=vector(1,n); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    xits=vector(1,n); 
 {    *fret=(*func)(p); 
   double  **a,**y,*x,pd;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **hess;    for (*iter=1;;++(*iter)) { 
   int i, j,jk;      fp=(*fret); 
   int *indx;      ibig=0; 
       del=0.0; 
   double hessii(double p[], double delta, int theta, double delti[]);      last_time=curr_time;
   double hessij(double p[], double delti[], int i, int j);      (void) gettimeofday(&curr_time,&tzp);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      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);
   void ludcmp(double **a, int npar, int *indx, double *d) ;      /*    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);
   hess=matrix(1,npar,1,npar);      */
      for (i=1;i<=n;i++) {
   printf("\nCalculation of the hessian matrix. Wait...\n");        printf(" %d %.12f",i, p[i]);
   for (i=1;i<=npar;i++){        fprintf(ficlog," %d %.12lf",i, p[i]);
     printf("%d",i);fflush(stdout);        fprintf(ficrespow," %.12lf", p[i]);
     hess[i][i]=hessii(p,ftolhess,i,delti);      }
     /*printf(" %f ",p[i]);*/      printf("\n");
     /*printf(" %lf ",hess[i][i]);*/      fprintf(ficlog,"\n");
   }      fprintf(ficrespow,"\n");fflush(ficrespow);
        if(*iter <=3){
   for (i=1;i<=npar;i++) {        tm = *localtime(&curr_time.tv_sec);
     for (j=1;j<=npar;j++)  {        strcpy(strcurr,asctime(&tm));
       if (j>i) {  /*       asctime_r(&tm,strcurr); */
         printf(".%d%d",i,j);fflush(stdout);        forecast_time=curr_time; 
         hess[i][j]=hessij(p,delti,i,j);        itmp = strlen(strcurr);
         hess[j][i]=hess[i][j];            if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         /*printf(" %lf ",hess[i][j]);*/          strcurr[itmp-1]='\0';
       }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   }        for(niterf=10;niterf<=30;niterf+=10){
   printf("\n");          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /*      asctime_r(&tmf,strfor); */
            strcpy(strfor,asctime(&tmf));
   a=matrix(1,npar,1,npar);          itmp = strlen(strfor);
   y=matrix(1,npar,1,npar);          if(strfor[itmp-1]=='\n')
   x=vector(1,npar);          strfor[itmp-1]='\0';
   indx=ivector(1,npar);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   for (i=1;i<=npar;i++)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);      }
       for (i=1;i<=n;i++) { 
   for (j=1;j<=npar;j++) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     for (i=1;i<=npar;i++) x[i]=0;        fptt=(*fret); 
     x[j]=1;  #ifdef DEBUG
     lubksb(a,npar,indx,x);        printf("fret=%lf \n",*fret);
     for (i=1;i<=npar;i++){        fprintf(ficlog,"fret=%lf \n",*fret);
       matcov[i][j]=x[i];  #endif
     }        printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
   printf("\n#Hessian matrix#\n");        if (fabs(fptt-(*fret)) > del) { 
   for (i=1;i<=npar;i++) {          del=fabs(fptt-(*fret)); 
     for (j=1;j<=npar;j++) {          ibig=i; 
       printf("%.3e ",hess[i][j]);        } 
     }  #ifdef DEBUG
     printf("\n");        printf("%d %.12e",i,(*fret));
   }        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   /* Recompute Inverse */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for (i=1;i<=npar;i++)          printf(" x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   ludcmp(a,npar,indx,&pd);        }
         for(j=1;j<=n;j++) {
   /*  printf("\n#Hessian matrix recomputed#\n");          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.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);  #endif
     for (i=1;i<=npar;i++){      } 
       y[i][j]=x[i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       printf("%.3e ",y[i][j]);  #ifdef DEBUG
     }        int k[2],l;
     printf("\n");        k[0]=1;
   }        k[1]=-1;
   */        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   free_matrix(a,1,npar,1,npar);        for (j=1;j<=n;j++) {
   free_matrix(y,1,npar,1,npar);          printf(" %.12e",p[j]);
   free_vector(x,1,npar);          fprintf(ficlog," %.12e",p[j]);
   free_ivector(indx,1,npar);        }
   free_matrix(hess,1,npar,1,npar);        printf("\n");
         fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 }          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 /*************** hessian matrix ****************/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 double hessii( double x[], double delta, int theta, double delti[])            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {          }
   int i;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int l=1, lmax=20;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double k1,k2;        }
   double p2[NPARMAX+1];  #endif
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;        free_vector(xit,1,n); 
   int k=0,kmax=10;        free_vector(xits,1,n); 
   double l1;        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   fx=func(x);        return; 
   for (i=1;i<=npar;i++) p2[i]=x[i];      } 
   for(l=0 ; l <=lmax; l++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     l1=pow(10,l);      for (j=1;j<=n;j++) { 
     delts=delt;        ptt[j]=2.0*p[j]-pt[j]; 
     for(k=1 ; k <kmax; k=k+1){        xit[j]=p[j]-pt[j]; 
       delt = delta*(l1*k);        pt[j]=p[j]; 
       p2[theta]=x[theta] +delt;      } 
       k1=func(p2)-fx;      fptt=(*func)(ptt); 
       p2[theta]=x[theta]-delt;      if (fptt < fp) { 
       k2=func(p2)-fx;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        if (t < 0.0) { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          linmin(p,xit,n,fret,func); 
                for (j=1;j<=n;j++) { 
 #ifdef DEBUG            xi[j][ibig]=xi[j][n]; 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);            xi[j][n]=xit[j]; 
 #endif          }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  #ifdef DEBUG
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         k=kmax;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       }          for(j=1;j<=n;j++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            printf(" %.12e",xit[j]);
         k=kmax; l=lmax*10.;            fprintf(ficlog," %.12e",xit[j]);
       }          }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          printf("\n");
         delts=delt;          fprintf(ficlog,"\n");
       }  #endif
     }        }
   }      } 
   delti[theta]=delts;    } 
   return res;  } 
    
 }  /**** Prevalence limit (stable prevalence)  ****************/
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 {  {
   int i;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   int l=1, l1, lmax=20;       matrix by transitions matrix until convergence is reached */
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    int i, ii,j,k;
   int k;    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
   fx=func(x);    double **out, cov[NCOVMAX], **pmij();
   for (k=1; k<=2; k++) {    double **newm;
     for (i=1;i<=npar;i++) p2[i]=x[i];    double agefin, delaymax=50 ; /* Max number of years to converge */
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for (ii=1;ii<=nlstate+ndeath;ii++)
     k1=func(p2)-fx;      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;     cov[1]=1.;
     
     p2[thetai]=x[thetai]-delti[thetai]/k;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     k3=func(p2)-fx;      newm=savm;
        /* Covariates have to be included here again */
     p2[thetai]=x[thetai]-delti[thetai]/k;       cov[2]=agefin;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    
     k4=func(p2)-fx;        for (k=1; k<=cptcovn;k++) {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 #ifdef DEBUG          /*      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]]);*/
     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);        }
 #endif        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }        for (k=1; k<=cptcovprod;k++)
   return res;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 }  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 /************** Inverse of matrix **************/        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 void ludcmp(double **a, int n, int *indx, double *d)        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   int i,imax,j,k;  
   double big,dum,sum,temp;      savm=oldm;
   double *vv;      oldm=newm;
        maxmax=0.;
   vv=vector(1,n);      for(j=1;j<=nlstate;j++){
   *d=1.0;        min=1.;
   for (i=1;i<=n;i++) {        max=0.;
     big=0.0;        for(i=1; i<=nlstate; i++) {
     for (j=1;j<=n;j++)          sumnew=0;
       if ((temp=fabs(a[i][j])) > big) big=temp;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          prlim[i][j]= newm[i][j]/(1-sumnew);
     vv[i]=1.0/big;          max=FMAX(max,prlim[i][j]);
   }          min=FMIN(min,prlim[i][j]);
   for (j=1;j<=n;j++) {        }
     for (i=1;i<j;i++) {        maxmin=max-min;
       sum=a[i][j];        maxmax=FMAX(maxmax,maxmin);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      }
       a[i][j]=sum;      if(maxmax < ftolpl){
     }        return prlim;
     big=0.0;      }
     for (i=j;i<=n;i++) {    }
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  /*************** transition probabilities ***************/ 
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         big=dum;  {
         imax=i;    double s1, s2;
       }    /*double t34;*/
     }    int i,j,j1, nc, ii, jj;
     if (j != imax) {  
       for (k=1;k<=n;k++) {      for(i=1; i<= nlstate; i++){
         dum=a[imax][k];        for(j=1; j<i;j++){
         a[imax][k]=a[j][k];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         a[j][k]=dum;            /*s2 += param[i][j][nc]*cov[nc];*/
       }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       *d = -(*d);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       vv[imax]=vv[j];          }
     }          ps[i][j]=s2;
     indx[j]=imax;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {        for(j=i+1; j<=nlstate+ndeath;j++){
       dum=1.0/(a[j][j]);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   }          }
   free_vector(vv,1,n);  /* Doesn't work */          ps[i][j]=s2;
 ;        }
 }      }
       /*ps[3][2]=1;*/
 void lubksb(double **a, int n, int *indx, double b[])      
 {      for(i=1; i<= nlstate; i++){
   int i,ii=0,ip,j;        s1=0;
   double sum;        for(j=1; j<i; j++)
            s1+=exp(ps[i][j]);
   for (i=1;i<=n;i++) {        for(j=i+1; j<=nlstate+ndeath; j++)
     ip=indx[i];          s1+=exp(ps[i][j]);
     sum=b[ip];        ps[i][i]=1./(s1+1.);
     b[ip]=b[i];        for(j=1; j<i; j++)
     if (ii)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for(j=i+1; j<=nlstate+ndeath; j++)
     else if (sum) ii=i;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     b[i]=sum;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   }      } /* end i */
   for (i=n;i>=1;i--) {      
     sum=b[i];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for(jj=1; jj<= nlstate+ndeath; jj++){
     b[i]=sum/a[i][i];          ps[ii][jj]=0;
   }          ps[ii][ii]=1;
 }        }
       }
 /************ Frequencies ********************/      
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  
 {  /* Some frequencies */  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
    /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  /*         printf("ddd %lf ",ps[ii][jj]); */
   double ***freq; /* Frequencies */  /*       } */
   double *pp;  /*       printf("\n "); */
   double pos, k2, dateintsum=0,k2cpt=0;  /*        } */
   FILE *ficresp;  /*        printf("\n ");printf("%lf ",cov[2]); */
   char fileresp[FILENAMELENGTH];         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   pp=vector(1,nlstate);        goto end;*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      return ps;
   strcpy(fileresp,"p");  }
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /**************** Product of 2 matrices ******************/
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   }  {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   j1=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
   j=cptcoveff;       before: only the contents of out is modified. The function returns
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       a pointer to pointers identical to out */
      long i, j, k;
   for(k1=1; k1<=j;k1++){    for(i=nrl; i<= nrh; i++)
     for(i1=1; i1<=ncodemax[k1];i1++){      for(k=ncolol; k<=ncoloh; k++)
       j1++;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          out[i][k] +=in[i][j]*b[j][k];
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)      return out;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    }
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  
        /************* Higher Matrix Product ***************/
       dateintsum=0;  
       k2cpt=0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       for (i=1; i<=imx; i++) {  {
         bool=1;    /* Computes the transition matrix starting at age 'age' over 
         if  (cptcovn>0) {       'nhstepm*hstepm*stepm' months (i.e. until
           for (z1=1; z1<=cptcoveff; z1++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       nhstepm*hstepm matrices. 
               bool=0;       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 
         if (bool==1) {       for the memory).
           for(m=firstpass; m<=lastpass; m++){       Model is determined by parameters x and covariates have to be 
             k2=anint[m][i]+(mint[m][i]/12.);       included manually here. 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;       */
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    int i, j, d, h, k;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double **out, cov[NCOVMAX];
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double **newm;
               }  
                  /* Hstepm could be zero and should return the unit matrix */
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    for (i=1;i<=nlstate+ndeath;i++)
                 dateintsum=dateintsum+k2;      for (j=1;j<=nlstate+ndeath;j++){
                 k2cpt++;        oldm[i][j]=(i==j ? 1.0 : 0.0);
               }        po[i][j][0]=(i==j ? 1.0 : 0.0);
             }      }
           }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         }    for(h=1; h <=nhstepm; h++){
       }      for(d=1; d <=hstepm; d++){
                newm=savm;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /* Covariates have to be included here again */
         cov[1]=1.;
       if  (cptcovn>0) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         fprintf(ficresp, "\n#********** Variable ");        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (k=1; k<=cptcovage;k++)
         fprintf(ficresp, "**********\n#");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }        for (k=1; k<=cptcovprod;k++)
       for(i=1; i<=nlstate;i++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");  
              /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for(i=(int)agemin; i <= (int)agemax+3; i++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         if(i==(int)agemax+3)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           printf("Total");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         else        savm=oldm;
           printf("Age %d", i);        oldm=newm;
         for(jk=1; jk <=nlstate ; jk++){      }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for(i=1; i<=nlstate+ndeath; i++)
             pp[jk] += freq[jk][m][i];        for(j=1;j<=nlstate+ndeath;j++) {
         }          po[i][j][h]=newm[i][j];
         for(jk=1; jk <=nlstate ; jk++){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
           for(m=-1, pos=0; m <=0 ; m++)           */
             pos += freq[jk][m][i];        }
           if(pp[jk]>=1.e-10)    } /* end h */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    return po;
           else  }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
         }  
   /*************** log-likelihood *************/
         for(jk=1; jk <=nlstate ; jk++){  double func( double *x)
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  {
             pp[jk] += freq[jk][m][i];    int i, ii, j, k, mi, d, kk;
         }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double sw; /* Sum of weights */
           pos += pp[jk];    double lli; /* Individual log likelihood */
         for(jk=1; jk <=nlstate ; jk++){    int s1, s2;
           if(pos>=1.e-5)    double bbh, survp;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    long ipmx;
           else    /*extern weight */
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /* We are differentiating ll according to initial status */
           if( i <= (int) agemax){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             if(pos>=1.e-5){    /*for(i=1;i<imx;i++) 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      printf(" %d\n",s[4][i]);
               probs[i][jk][j1]= pp[jk]/pos;    */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    cov[1]=1.;
             }  
             else    for(k=1; k<=nlstate; k++) ll[k]=0.;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  
           }    if(mle==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(jk=-1; jk <=nlstate+ndeath; jk++)        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=-1; m <=nlstate+ndeath; m++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            for (j=1;j<=nlstate+ndeath;j++){
         if(i <= (int) agemax)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficresp,"\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf("\n");            }
       }          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   dateintmean=dateintsum/k2cpt;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fclose(ficresp);            }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(pp,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   /* End of Freq */            oldm=newm;
 }          } /* end mult */
         
 /************ Prevalence ********************/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 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)          /* But now since version 0.9 we anticipate for bias at large stepm.
 {  /* Some frequencies */           * 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 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double ***freq; /* Frequencies */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double *pp;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double pos, k2;           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   pp=vector(1,nlstate);           * -stepm/2 to stepm/2 .
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * 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. 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           */
   j1=0;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   j=cptcoveff;          bbh=(double)bh[mi][i]/(double)stepm; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          /* bias bh is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
  for(k1=1; k1<=j;k1++){           */
     for(i1=1; i1<=ncodemax[k1];i1++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       j1++;          if( s2 > nlstate){ 
              /* i.e. if s2 is a death state and if the date of death is known 
       for (i=-1; i<=nlstate+ndeath; i++)                 then the contribution to the likelihood is the probability to 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                 die between last step unit time and current  step unit time, 
           for(m=agemin; m <= agemax+3; m++)               which is also equal to probability to die before dh 
             freq[i][jk][m]=0;               minus probability to die before dh-stepm . 
                     In version up to 0.92 likelihood was computed
       for (i=1; i<=imx; i++) {          as if date of death was unknown. Death was treated as any other
         bool=1;          health state: the date of the interview describes the actual state
         if  (cptcovn>0) {          and not the date of a change in health state. The former idea was
           for (z1=1; z1<=cptcoveff; z1++)          to consider that at each interview the state was recorded
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          (healthy, disable or death) and IMaCh was corrected; but when we
               bool=0;          introduced the exact date of death then we should have modified
         }          the contribution of an exact death to the likelihood. This new
         if (bool==1) {          contribution is smaller and very dependent of the step unit
           for(m=firstpass; m<=lastpass; m++){          stepm. It is no more the probability to die between last interview
             k2=anint[m][i]+(mint[m][i]/12.);          and month of death but the probability to survive from last
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          interview up to one month before death multiplied by the
               if(agev[m][i]==0) agev[m][i]=agemax+1;          probability to die within a month. Thanks to Chris
               if(agev[m][i]==1) agev[m][i]=agemax+2;          Jackson for correcting this bug.  Former versions increased
               if (m<lastpass)          mortality artificially. The bad side is that we add another loop
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          which slows down the processing. The difference can be up to 10%
               else          lower mortality.
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            */
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            lli=log(out[s1][s2] - savm[s1][s2]);
             }  
           }  
         }          } else if  (s2==-2) {
       }            for (j=1,survp=0. ; j<=nlstate; j++) 
         for(i=(int)agemin; i <= (int)agemax+3; i++){              survp += out[s1][j];
           for(jk=1; jk <=nlstate ; jk++){            lli= survp;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          }
               pp[jk] += freq[jk][m][i];          
           }          else if  (s2==-4) {
           for(jk=1; jk <=nlstate ; jk++){            for (j=3,survp=0. ; j<=nlstate; j++) 
             for(m=-1, pos=0; m <=0 ; m++)              survp += out[s1][j];
             pos += freq[jk][m][i];            lli= survp;
         }          }
                  
          for(jk=1; jk <=nlstate ; jk++){          else if  (s2==-5) {
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            for (j=1,survp=0. ; j<=2; j++) 
              pp[jk] += freq[jk][m][i];              survp += out[s1][j];
          }            lli= survp;
                    }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
   
          for(jk=1; jk <=nlstate ; jk++){                    else{
            if( i <= (int) agemax){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
              if(pos>=1.e-5){            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                probs[i][jk][j1]= pp[jk]/pos;          } 
              }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            }          /*if(lli ==000.0)*/
          }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                    ipmx +=1;
         }          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
       } /* end of individual */
      }  else if(mle==2){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_vector(pp,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
 }  /* End of Freq */          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 /************* Waves Concatenation ***************/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            }
 {          for(d=0; d<=dh[mi][i]; d++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            newm=savm;
      Death is a valid wave (if date is known).            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            for (kk=1; kk<=cptcovage;kk++) {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      and mw[mi+1][i]. dh depends on stepm.            }
      */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i, mi, m;            savm=oldm;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            oldm=newm;
      double sum=0., jmean=0.;*/          } /* end mult */
         
   int j, k=0,jk, ju, jl;          s1=s[mw[mi][i]][i];
   double sum=0.;          s2=s[mw[mi+1][i]][i];
   jmin=1e+5;          bbh=(double)bh[mi][i]/(double)stepm; 
   jmax=-1;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   jmean=0.;          ipmx +=1;
   for(i=1; i<=imx; i++){          sw += weight[i];
     mi=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     m=firstpass;        } /* end of wave */
     while(s[m][i] <= nlstate){      } /* end of individual */
       if(s[m][i]>=1)    }  else if(mle==3){  /* exponential inter-extrapolation */
         mw[++mi][i]=m;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if(m >=lastpass)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         break;        for(mi=1; mi<= wav[i]-1; mi++){
       else          for (ii=1;ii<=nlstate+ndeath;ii++)
         m++;            for (j=1;j<=nlstate+ndeath;j++){
     }/* end while */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (s[m][i] > nlstate){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       mi++;     /* Death is another wave */            }
       /* if(mi==0)  never been interviewed correctly before death */          for(d=0; d<dh[mi][i]; d++){
          /* Only death is a correct wave */            newm=savm;
       mw[mi][i]=m;            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];
     wav[i]=mi;            }
     if(mi==0)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
             oldm=newm;
   for(i=1; i<=imx; i++){          } /* end mult */
     for(mi=1; mi<wav[i];mi++){        
       if (stepm <=0)          s1=s[mw[mi][i]][i];
         dh[mi][i]=1;          s2=s[mw[mi+1][i]][i];
       else{          bbh=(double)bh[mi][i]/(double)stepm; 
         if (s[mw[mi+1][i]][i] > nlstate) {          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           if (agedc[i] < 2*AGESUP) {          ipmx +=1;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          sw += weight[i];
           if(j==0) j=1;  /* Survives at least one month after exam */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           k=k+1;        } /* end of wave */
           if (j >= jmax) jmax=j;      } /* end of individual */
           if (j <= jmin) jmin=j;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           sum=sum+j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           /*if (j<0) printf("j=%d num=%d \n",j,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++)
         else{            for (j=1;j<=nlstate+ndeath;j++){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (j >= jmax) jmax=j;            }
           else if (j <= jmin)jmin=j;          for(d=0; d<dh[mi][i]; d++){
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            newm=savm;
           sum=sum+j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
         jk= j/stepm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         jl= j -jk*stepm;            }
         ju= j -(jk+1)*stepm;          
         if(jl <= -ju)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           dh[mi][i]=jk;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         else            savm=oldm;
           dh[mi][i]=jk+1;            oldm=newm;
         if(dh[mi][i]==0)          } /* end mult */
           dh[mi][i]=1; /* At least one step */        
       }          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
   }          if( s2 > nlstate){ 
   jmean=sum/k;            lli=log(out[s1][s2] - savm[s1][s2]);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          }else{
  }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 /*********** Tricode ****************************/          }
 void tricode(int *Tvar, int **nbcode, int imx)          ipmx +=1;
 {          sw += weight[i];
   int Ndum[20],ij=1, k, j, i;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int cptcode=0;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   cptcoveff=0;        } /* end of wave */
        } /* end of individual */
   for (k=0; k<19; k++) Ndum[k]=0;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   for (k=1; k<=7; k++) ncodemax[k]=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1; i<=imx; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       ij=(int)(covar[Tvar[j]][i]);            for (j=1;j<=nlstate+ndeath;j++){
       Ndum[ij]++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (ij > cptcode) cptcode=ij;            }
     }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for (i=0; i<=cptcode; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(Ndum[i]!=0) ncodemax[j]++;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     ij=1;            }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=1; i<=ncodemax[j]; i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=0; k<=19; k++) {            savm=oldm;
         if (Ndum[k] != 0) {            oldm=newm;
           nbcode[Tvar[j]][ij]=k;          } /* end mult */
                  
           ij++;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         if (ij > ncodemax[j]) break;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }            ipmx +=1;
     }          sw += weight[i];
   }            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
  for (k=0; k<19; k++) Ndum[k]=0;        } /* end of wave */
       } /* end of individual */
  for (i=1; i<=ncovmodel-2; i++) {    } /* End of if */
       ij=Tvar[i];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       Ndum[ij]++;    /* 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 */
     return -l;
  ij=1;  }
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){  /*************** log-likelihood *************/
      Tvaraff[ij]=i;  double funcone( double *x)
      ij++;  {
    }    /* Same as likeli but slower because of a lot of printf and if */
  }    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
     cptcoveff=ij-1;    double **out;
 }    double lli; /* Individual log likelihood */
     double llt;
 /*********** Health Expectancies ****************/    int s1, s2;
     double bbh, survp;
 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 )    /*extern weight */
     /* We are differentiating ll according to initial status */
 {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /* Health expectancies */    /*for(i=1;i<imx;i++) 
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      printf(" %d\n",s[4][i]);
   double age, agelim, hf;    */
   double ***p3mat,***varhe;    cov[1]=1.;
   double **dnewm,**doldm;  
   double *xp;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double **gp, **gm;  
   double ***gradg, ***trgradg;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int theta;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        for (ii=1;ii<=nlstate+ndeath;ii++)
   xp=vector(1,npar);          for (j=1;j<=nlstate+ndeath;j++){
   dnewm=matrix(1,nlstate*2,1,npar);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate*2,1,nlstate*2);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
   fprintf(ficreseij,"# Health expectancies\n");        for(d=0; d<dh[mi][i]; d++){
   fprintf(ficreseij,"# Age");          newm=savm;
   for(i=1; i<=nlstate;i++)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(j=1; j<=nlstate;j++)          for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficreseij," %1d-%1d (SE)",i,j);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficreseij,"\n");          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if(estepm < stepm){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf ("Problem %d lower than %d\n",estepm, stepm);          savm=oldm;
   }          oldm=newm;
   else  hstepm=estepm;          } /* end mult */
   /* We compute the life expectancy from trapezoids spaced every estepm months        
    * This is mainly to measure the difference between two models: for example        s1=s[mw[mi][i]][i];
    * if stepm=24 months pijx are given only every 2 years and by summing them        s2=s[mw[mi+1][i]][i];
    * we are calculating an estimate of the Life Expectancy assuming a linear        bbh=(double)bh[mi][i]/(double)stepm; 
    * progression inbetween and thus overestimating or underestimating according        /* bias is positive if real duration
    * to the curvature of the survival function. If, for the same date, we         * is higher than the multiple of stepm and negative otherwise.
    * estimate the model with stepm=1 month, we can keep estepm to 24 months         */
    * to compare the new estimate of Life expectancy with the same linear        if( s2 > nlstate && (mle <5) ){  /* Jackson */
    * hypothesis. A more precise result, taking into account a more precise          lli=log(out[s1][s2] - savm[s1][s2]);
    * curvature will be obtained if estepm is as small as stepm. */        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /* For example we decided to compute the life expectancy with the smallest unit */        } else if(mle==2){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is 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 */
      nhstepm is the number of hstepm from age to agelim        } else if(mle==3){  /* exponential inter-extrapolation */
      nstepm is the number of stepm from age to agelin.          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 */
      Look at hpijx to understand the reason of that which relies in memory size        } else if (mle==4){  /* mle=4 no inter-extrapolation */
      and note for a fixed period like estepm months */          lli=log(out[s1][s2]); /* Original formula */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
      survival function given by stepm (the optimization length). Unfortunately it          lli=log(out[s1][s2]); /* Original formula */
      means that if the survival funtion is printed only each two years of age and if        } /* End of if */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        ipmx +=1;
      results. So we changed our mind and took the option of the best precision.        sw += weight[i];
   */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
   agelim=AGESUP;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */   %10.6f %10.6f %10.6f ", \
     /* nhstepm age range expressed in number of stepm */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     nstepm=(int) rint((agelim-age)*YEARM/stepm);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     /* if (stepm >= YEARM) hstepm=1;*/            llt +=ll[k]*gipmx/gsw;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          fprintf(ficresilk," %10.6f\n", -llt);
     gp=matrix(0,nhstepm,1,nlstate*2);        }
     gm=matrix(0,nhstepm,1,nlstate*2);      } /* end of wave */
     } /* end of individual */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      gsw=sw;
     }
     /* Computing Variances of health expectancies */    return -l;
   }
      for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*************** function likelione ***********/
       }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {
      /* This routine should help understanding what is done with 
       cptj=0;       the selection of individuals/waves and
       for(j=1; j<= nlstate; j++){       to check the exact contribution to the likelihood.
         for(i=1; i<=nlstate; i++){       Plotting could be done.
           cptj=cptj+1;     */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    int k;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    if(*globpri !=0){ /* Just counts and sums, no printings */
         }      strcpy(fileresilk,"ilk"); 
       }      strcat(fileresilk,fileres);
            if((ficresilk=fopen(fileresilk,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", fileresilk);
       for(i=1; i<=npar; i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      }
       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, gm[h][cptj]=0.; h<=nhstepm-1; h++){    }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
       }      fclose(ficresilk);
            fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
          fflush(fichtm); 
     } 
       for(j=1; j<= nlstate*2; j++)    return;
         for(h=0; h<=nhstepm-1; h++){  }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }  
   /*********** Maximum Likelihood Estimation ***************/
      }  
      void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 /* End theta */  {
     int i,j, iter;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    double **xi;
     double fret;
      for(h=0; h<=nhstepm-1; h++)    double fretone; /* Only one call to likelihood */
       for(j=1; j<=nlstate*2;j++)    /*  char filerespow[FILENAMELENGTH];*/
         for(theta=1; theta <=npar; theta++)    xi=matrix(1,npar,1,npar);
         trgradg[h][j][theta]=gradg[h][theta][j];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
      for(i=1;i<=nlstate*2;i++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       for(j=1;j<=nlstate*2;j++)    strcpy(filerespow,"pow"); 
         varhe[i][j][(int)age] =0.;    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(h=0;h<=nhstepm-1;h++){      printf("Problem with resultfile: %s\n", filerespow);
       for(k=0;k<=nhstepm-1;k++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         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]);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         for(i=1;i<=nlstate*2;i++)    for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate*2;j++)      for(j=1;j<=nlstate+ndeath;j++)
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       }    fprintf(ficrespow,"\n");
     }  
     powell(p,xi,npar,ftol,&iter,&fret,func);
        
     /* Computing expectancies */    free_matrix(xi,1,npar,1,npar);
     for(i=1; i<=nlstate;i++)    fclose(ficrespow);
       for(j=1; j<=nlstate;j++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
            
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/  }
   
         }  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     fprintf(ficreseij,"%3.0f",age );  {
     cptj=0;    double  **a,**y,*x,pd;
     for(i=1; i<=nlstate;i++)    double **hess;
       for(j=1; j<=nlstate;j++){    int i, j,jk;
         cptj++;    int *indx;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  
       }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fprintf(ficreseij,"\n");    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
        void lubksb(double **a, int npar, int *indx, double b[]) ;
     free_matrix(gm,0,nhstepm,1,nlstate*2);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     free_matrix(gp,0,nhstepm,1,nlstate*2);    double gompertz(double p[]);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    hess=matrix(1,npar,1,npar);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\nCalculation of the hessian matrix. Wait...\n");
   }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   free_vector(xp,1,npar);    for (i=1;i<=npar;i++){
   free_matrix(dnewm,1,nlstate*2,1,npar);      printf("%d",i);fflush(stdout);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      fprintf(ficlog,"%d",i);fflush(ficlog);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);     
 }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
 /************ Variance ******************/      /*  printf(" %f ",p[i]);
 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)          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
 {    }
   /* Variance of health expectancies */    
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=1;i<=npar;i++) {
   double **newm;      for (j=1;j<=npar;j++)  {
   double **dnewm,**doldm;        if (j>i) { 
   int i, j, nhstepm, hstepm, h, nstepm ;          printf(".%d%d",i,j);fflush(stdout);
   int k, cptcode;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double *xp;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   double **gp, **gm;          
   double ***gradg, ***trgradg;          hess[j][i]=hess[i][j];    
   double ***p3mat;          /*printf(" %lf ",hess[i][j]);*/
   double age,agelim, hf;        }
   int theta;      }
     }
    fprintf(ficresvij,"# Covariances of life expectancies\n");    printf("\n");
   fprintf(ficresvij,"# Age");    fprintf(ficlog,"\n");
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficresvij,"\n");    
     a=matrix(1,npar,1,npar);
   xp=vector(1,npar);    y=matrix(1,npar,1,npar);
   dnewm=matrix(1,nlstate,1,npar);    x=vector(1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    indx=ivector(1,npar);
      for (i=1;i<=npar;i++)
   if(estepm < stepm){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     printf ("Problem %d lower than %d\n",estepm, stepm);    ludcmp(a,npar,indx,&pd);
   }  
   else  hstepm=estepm;      for (j=1;j<=npar;j++) {
   /* For example we decided to compute the life expectancy with the smallest unit */      for (i=1;i<=npar;i++) x[i]=0;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      x[j]=1;
      nhstepm is the number of hstepm from age to agelim      lubksb(a,npar,indx,x);
      nstepm is the number of stepm from age to agelin.      for (i=1;i<=npar;i++){ 
      Look at hpijx to understand the reason of that which relies in memory size        matcov[i][j]=x[i];
      and note for a fixed period like k years */      }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    }
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    printf("\n#Hessian matrix#\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    fprintf(ficlog,"\n#Hessian matrix#\n");
      results. So we changed our mind and took the option of the best precision.    for (i=1;i<=npar;i++) { 
   */      for (j=1;j<=npar;j++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        printf("%.3e ",hess[i][j]);
   agelim = AGESUP;        fprintf(ficlog,"%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("\n");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      fprintf(ficlog,"\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);    /* Recompute Inverse */
     gm=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(theta=1; theta <=npar; theta++){    ludcmp(a,npar,indx,&pd);
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*  printf("\n#Hessian matrix recomputed#\n");
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (j=1;j<=npar;j++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       if (popbased==1) {      lubksb(a,npar,indx,x);
         for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
           prlim[i][i]=probs[(int)age][i][ij];        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
          fprintf(ficlog,"%.3e ",y[i][j]);
       for(j=1; j<= nlstate; j++){      }
         for(h=0; h<=nhstepm; h++){      printf("\n");
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      fprintf(ficlog,"\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }    */
       }  
        free_matrix(a,1,npar,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    free_matrix(y,1,npar,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    free_vector(x,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      free_ivector(indx,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    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 ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       for(j=1; j<= nlstate; j++){  {
         for(h=0; h<=nhstepm; h++){    int i;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    int l=1, lmax=20;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double k1,k2;
         }    double p2[NPARMAX+1];
       }    double res;
     double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for(j=1; j<= nlstate; j++)    double fx;
         for(h=0; h<=nhstepm; h++){    int k=0,kmax=10;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double l1;
         }  
     } /* End theta */    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
     for(h=0; h<=nhstepm; h++)      delts=delt;
       for(j=1; j<=nlstate;j++)      for(k=1 ; k <kmax; k=k+1){
         for(theta=1; theta <=npar; theta++)        delt = delta*(l1*k);
           trgradg[h][j][theta]=gradg[h][theta][j];        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        p2[theta]=x[theta]-delt;
     for(i=1;i<=nlstate;i++)        k2=func(p2)-fx;
       for(j=1;j<=nlstate;j++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
         vareij[i][j][(int)age] =0.;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
     for(h=0;h<=nhstepm;h++){  #ifdef DEBUG
       for(k=0;k<=nhstepm;k++){        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);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        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);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  #endif
         for(i=1;i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           for(j=1;j<=nlstate;j++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          k=kmax;
       }        }
     }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
     fprintf(ficresvij,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(j=1; j<=nlstate;j++){          delts=delt;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        }
       }      }
     fprintf(ficresvij,"\n");    }
     free_matrix(gp,0,nhstepm,1,nlstate);    delti[theta]=delts;
     free_matrix(gm,0,nhstepm,1,nlstate);    return res; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
    {
   free_vector(xp,1,npar);    int i;
   free_matrix(doldm,1,nlstate,1,npar);    int l=1, l1, lmax=20;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
 }    int k;
   
 /************ Variance of prevlim ******************/    fx=func(x);
 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)    for (k=1; k<=2; k++) {
 {      for (i=1;i<=npar;i++) p2[i]=x[i];
   /* Variance of prevalence limit */      p2[thetai]=x[thetai]+delti[thetai]/k;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **newm;      k1=func(p2)-fx;
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int k, cptcode;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double *xp;      k2=func(p2)-fx;
   double *gp, *gm;    
   double **gradg, **trgradg;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double age,agelim;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int theta;      k3=func(p2)-fx;
        
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
   fprintf(ficresvpl,"# Age");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(i=1; i<=nlstate;i++)      k4=func(p2)-fx;
       fprintf(ficresvpl," %1d-%1d",i,i);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   fprintf(ficresvpl,"\n");  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   xp=vector(1,npar);      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);
   dnewm=matrix(1,nlstate,1,npar);  #endif
   doldm=matrix(1,nlstate,1,nlstate);    }
      return res;
   hstepm=1*YEARM; /* Every year of age */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  /************** Inverse of matrix **************/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  void ludcmp(double **a, int n, int *indx, double *d) 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  { 
     if (stepm >= YEARM) hstepm=1;    int i,imax,j,k; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double big,dum,sum,temp; 
     gradg=matrix(1,npar,1,nlstate);    double *vv; 
     gp=vector(1,nlstate);   
     gm=vector(1,nlstate);    vv=vector(1,n); 
     *d=1.0; 
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=n;i++) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */      big=0.0; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (j=1;j<=n;j++) 
       }        if ((temp=fabs(a[i][j])) > big) big=temp; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for(i=1;i<=nlstate;i++)      vv[i]=1.0/big; 
         gp[i] = prlim[i][i];    } 
        for (j=1;j<=n;j++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=1;i<j;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        sum=a[i][j]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
         gm[i] = prlim[i][i];      } 
       big=0.0; 
       for(i=1;i<=nlstate;i++)      for (i=j;i<=n;i++) { 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        sum=a[i][j]; 
     } /* End theta */        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
     trgradg =matrix(1,nlstate,1,npar);        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(j=1; j<=nlstate;j++)          big=dum; 
       for(theta=1; theta <=npar; theta++)          imax=i; 
         trgradg[j][theta]=gradg[theta][j];        } 
       } 
     for(i=1;i<=nlstate;i++)      if (j != imax) { 
       varpl[i][(int)age] =0.;        for (k=1;k<=n;k++) { 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          dum=a[imax][k]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          a[imax][k]=a[j][k]; 
     for(i=1;i<=nlstate;i++)          a[j][k]=dum; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        } 
         *d = -(*d); 
     fprintf(ficresvpl,"%.0f ",age );        vv[imax]=vv[j]; 
     for(i=1; i<=nlstate;i++)      } 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      indx[j]=imax; 
     fprintf(ficresvpl,"\n");      if (a[j][j] == 0.0) a[j][j]=TINY; 
     free_vector(gp,1,nlstate);      if (j != n) { 
     free_vector(gm,1,nlstate);        dum=1.0/(a[j][j]); 
     free_matrix(gradg,1,npar,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_matrix(trgradg,1,nlstate,1,npar);      } 
   } /* End age */    } 
     free_vector(vv,1,n);  /* Doesn't work */
   free_vector(xp,1,npar);  ;
   free_matrix(doldm,1,nlstate,1,npar);  } 
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   void lubksb(double **a, int n, int *indx, double b[]) 
 }  { 
     int i,ii=0,ip,j; 
 /************ Variance of one-step probabilities  ******************/    double sum; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)   
 {    for (i=1;i<=n;i++) { 
   int i, j, i1, k1, j1, z1;      ip=indx[i]; 
   int k=0, cptcode;      sum=b[ip]; 
   double **dnewm,**doldm;      b[ip]=b[i]; 
   double *xp;      if (ii) 
   double *gp, *gm;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double **gradg, **trgradg;      else if (sum) ii=i; 
   double age,agelim, cov[NCOVMAX];      b[i]=sum; 
   int theta;    } 
   char fileresprob[FILENAMELENGTH];    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   strcpy(fileresprob,"prob");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   strcat(fileresprob,fileres);      b[i]=sum/a[i][i]; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    } 
     printf("Problem with resultfile: %s\n", fileresprob);  } 
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  /************ Frequencies ********************/
    void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");  {  /* Some frequencies */
   fprintf(ficresprob,"# Age");    
   for(i=1; i<=nlstate;i++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     for(j=1; j<=(nlstate+ndeath);j++)    int first;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    double ***freq; /* Frequencies */
     double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   fprintf(ficresprob,"\n");    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
     
   xp=vector(1,npar);    pp=vector(1,nlstate);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   cov[1]=1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   j=cptcoveff;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   j1=0;      exit(0);
   for(k1=1; k1<=1;k1++){    }
     for(i1=1; i1<=ncodemax[k1];i1++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1++;    j1=0;
     
     if  (cptcovn>0) {    j=cptcoveff;
       fprintf(ficresprob, "\n#********** Variable ");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficresprob, "**********\n#");    first=1;
     }  
        for(k1=1; k1<=j;k1++){
       for (age=bage; age<=fage; age ++){      for(i1=1; i1<=ncodemax[k1];i1++){
         cov[2]=age;        j1++;
         for (k=1; k<=cptcovn;k++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          scanf("%d", i);*/
                  for (i=-5; i<=nlstate+ndeath; i++)  
         }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            for(m=iagemin; m <= iagemax+3; m++)
         for (k=1; k<=cptcovprod;k++)              freq[i][jk][m]=0;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
              for (i=1; i<=nlstate; i++)  
         gradg=matrix(1,npar,1,9);        for(m=iagemin; m <= iagemax+3; m++)
         trgradg=matrix(1,9,1,npar);          prop[i][m]=0;
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        dateintsum=0;
            k2cpt=0;
         for(theta=1; theta <=npar; theta++){        for (i=1; i<=imx; i++) {
           for(i=1; i<=npar; i++)          bool=1;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          if  (cptcovn>0) {
                      for (z1=1; z1<=cptcoveff; z1++) 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                          bool=0;
           k=0;          }
           for(i=1; i<= (nlstate+ndeath); i++){          if (bool==1){
             for(j=1; j<=(nlstate+ndeath);j++){            for(m=firstpass; m<=lastpass; m++){
               k=k+1;              k2=anint[m][i]+(mint[m][i]/12.);
               gp[k]=pmmij[i][j];              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                          if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
           for(i=1; i<=npar; i++)                if (m<lastpass) {
             xp[i] = x[i] - (i==theta ?delti[theta]:0);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                      freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                }
           k=0;                
           for(i=1; i<=(nlstate+ndeath); i++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
             for(j=1; j<=(nlstate+ndeath);j++){                  dateintsum=dateintsum+k2;
               k=k+1;                  k2cpt++;
               gm[k]=pmmij[i][j];                }
             }                /*}*/
           }            }
                }
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];           
         }        /*      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(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        if  (cptcovn>0) {
           for(theta=1; theta <=npar; theta++)          fprintf(ficresp, "\n#********** Variable "); 
             trgradg[j][theta]=gradg[theta][j];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresp, "**********\n#");
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        }
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        for(i=1; i<=nlstate;i++) 
                  fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         pmij(pmmij,cov,ncovmodel,x,nlstate);        fprintf(ficresp, "\n");
                
         k=0;        for(i=iagemin; i <= iagemax+3; i++){
         for(i=1; i<=(nlstate+ndeath); i++){          if(i==iagemax+3){
           for(j=1; j<=(nlstate+ndeath);j++){            fprintf(ficlog,"Total");
             k=k+1;          }else{
             gm[k]=pmmij[i][j];            if(first==1){
           }              first=0;
         }              printf("See log file for details...\n");
                  }
      /*printf("\n%d ",(int)age);            fprintf(ficlog,"Age %d", i);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          for(jk=1; jk <=nlstate ; jk++){
      }*/            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
         fprintf(ficresprob,"\n%d ",(int)age);          }
           for(jk=1; jk <=nlstate ; jk++){
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)            for(m=-1, pos=0; m <=0 ; m++)
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
       }              if(first==1){
     }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            }else{
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   free_vector(xp,1,npar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fclose(ficresprob);            }
            }
 }  
           for(jk=1; jk <=nlstate ; jk++){
 /******************* Printing html file ***********/            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              pp[jk] += freq[jk][m][i];
  int lastpass, int stepm, int weightopt, char model[],\          }       
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\            pos += pp[jk];
  char version[], int popforecast, int estepm ){            posprop += prop[jk][i];
   int jj1, k1, i1, cpt;          }
   FILE *fichtm;          for(jk=1; jk <=nlstate ; jk++){
   /*char optionfilehtm[FILENAMELENGTH];*/            if(pos>=1.e-5){
               if(first==1)
   strcpy(optionfilehtm,optionfile);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   strcat(optionfilehtm,".htm");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            }else{
     printf("Problem with %s \n",optionfilehtm), exit(0);              if(first==1)
   }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  fprintf(fichtm,"<body> <font size=\"2\">%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            if( i <= iagemax){
 \n              if(pos>=1.e-5){
 Total number of observations=%d <br>\n                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                /*probs[i][jk][j1]= pp[jk]/pos;*/
 <hr  size=\"2\" color=\"#EC5E5E\">                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
  <ul><li>Outputs files<br>\n              }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n              else
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
  - 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          
  - 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);          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
  fprintf(fichtm,"\n              if(freq[jk][m][i] !=0 ) {
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n              if(first==1)
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  - 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);          if(i <= iagemax)
             fprintf(ficresp,"\n");
  if(popforecast==1) fprintf(fichtm,"\n          if(first==1)
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n            printf("Others in log...\n");
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          fprintf(ficlog,"\n");
         <br>",fileres,fileres,fileres,fileres);        }
  else      }
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    }
 fprintf(fichtm," <li>Graphs</li><p>");    dateintmean=dateintsum/k2cpt; 
    
  m=cptcoveff;    fclose(ficresp);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
  jj1=0;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  for(k1=1; k1<=m;k1++){    /* End of Freq */
    for(i1=1; i1<=ncodemax[k1];i1++){  }
        jj1++;  
        if (cptcovn > 0) {  /************ Prevalence ********************/
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
          for (cpt=1; cpt<=cptcoveff;cpt++)  {  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       in each health status at the date of interview (if between dateprev1 and dateprev2).
        }       We still use firstpass and lastpass as another selection.
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       
        for(cpt=1; cpt<nlstate;cpt++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    double ***freq; /* Frequencies */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double *pp, **prop;
        }    double pos,posprop; 
     for(cpt=1; cpt<=nlstate;cpt++) {    double  y2; /* in fractional years */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    int iagemin, iagemax;
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      iagemin= (int) agemin;
      }    iagemax= (int) agemax;
      for(cpt=1; cpt<=nlstate;cpt++) {    /*pp=vector(1,nlstate);*/
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    prop=matrix(1,nlstate,iagemin,iagemax+3); 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      }    j1=0;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.gif<br>    j=cptcoveff;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 fprintf(fichtm,"\n</body>");    
    }    for(k1=1; k1<=j;k1++){
    }      for(i1=1; i1<=ncodemax[k1];i1++){
 fclose(fichtm);        j1++;
 }        
         for (i=1; i<=nlstate; i++)  
 /******************* Gnuplot file **************/          for(m=iagemin; m <= iagemax+3; m++)
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){            prop[i][m]=0.0;
        
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   strcpy(optionfilegnuplot,optionfilefiname);          if  (cptcovn>0) {
   strcat(optionfilegnuplot,".gp.txt");            for (z1=1; z1<=cptcoveff; z1++) 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     printf("Problem with file %s",optionfilegnuplot);                bool=0;
   }          } 
           if (bool==1) { 
 #ifdef windows            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     fprintf(ficgp,"cd \"%s\" \n",pathc);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 #endif              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 m=pow(2,cptcoveff);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
  /* 1eme*/                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   for (cpt=1; cpt<= nlstate ; cpt ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
    for (k1=1; k1<= m ; k1 ++) {                  /*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]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
      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);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
 for (i=1; i<= nlstate ; i ++) {              }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            } /* end selection of waves */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }        }
     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=iagemin; i <= iagemax+3; i++){  
     for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            posprop += prop[jk][i]; 
 }          } 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {          for(jk=1; jk <=nlstate ; jk++){     
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            if( i <=  iagemax){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(posprop>=1.e-5){ 
 }                  probs[i][jk][j1]= prop[jk][i]/posprop;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));              } 
             } 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }/* end jk */ 
    }        }/* end i */ 
   }      } /* end i1 */
   /*2 eme*/    } /* end k1 */
     
   for (k1=1; k1<= m ; k1 ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    /*free_vector(pp,1,nlstate);*/
        free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for (i=1; i<= nlstate+1 ; i ++) {  }  /* End of prevalence */
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  /************* Waves Concatenation ***************/
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) 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)
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {
 }      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       Death is a valid wave (if date is known).
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for (j=1; j<= nlstate+1 ; j ++) {       and mw[mi+1][i]. dh depends on stepm.
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       */
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      int i, mi, m;
       fprintf(ficgp,"\" t\"\" w l 0,");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);       double sum=0., jmean=0.;*/
       for (j=1; j<= nlstate+1 ; j ++) {    int first;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int j, k=0,jk, ju, jl;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double sum=0.;
 }      first=0;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    jmin=1e+5;
       else fprintf(ficgp,"\" t\"\" w l 0,");    jmax=-1;
     }    jmean=0.;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    for(i=1; i<=imx; i++){
   }      mi=0;
        m=firstpass;
   /*3eme*/      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   for (k1=1; k1<= m ; k1 ++) {          mw[++mi][i]=m;
     for (cpt=1; cpt<= nlstate ; cpt ++) {        if(m >=lastpass)
       k=2+nlstate*(2*cpt-2);          break;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        else
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          m++;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      }/* end while */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      if (s[m][i] > nlstate){
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        mi++;     /* Death is another wave */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        /* if(mi==0)  never been interviewed correctly before death */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);           /* Only death is a correct wave */
         mw[mi][i]=m;
 */      }
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);      wav[i]=mi;
       if(mi==0){
       }        nbwarn++;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        if(first==0){
     }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     }          first=1;
          }
   /* CV preval stat */        if(first==1){
     for (k1=1; k1<= m ; k1 ++) {          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     for (cpt=1; cpt<nlstate ; cpt ++) {        }
       k=3;      } /* end mi==0 */
       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);    } /* End individuals */
   
       for (i=1; i< nlstate ; i ++)    for(i=1; i<=imx; i++){
         fprintf(ficgp,"+$%d",k+i+1);      for(mi=1; mi<wav[i];mi++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        if (stepm <=0)
                dh[mi][i]=1;
       l=3+(nlstate+ndeath)*cpt;        else{
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for (i=1; i< nlstate ; i ++) {            if (agedc[i] < 2*AGESUP) {
         l=3+(nlstate+ndeath)*cpt;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         fprintf(ficgp,"+$%d",l+i+1);              if(j==0) j=1;  /* Survives at least one month after exam */
       }              else if(j<0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  nberr++;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }                j=1; /* Temporary Dangerous patch */
   }                  printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                  fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   /* proba elementaires */                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
    for(i=1,jk=1; i <=nlstate; i++){              }
     for(k=1; k <=(nlstate+ndeath); k++){              k=k+1;
       if (k != i) {              if (j >= jmax){
         for(j=1; j <=ncovmodel; j++){                jmax=j;
                        ijmax=i;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              }
           jk++;              if (j <= jmin){
           fprintf(ficgp,"\n");                jmin=j;
         }                ijmin=i;
       }              }
     }              sum=sum+j;
     }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(jk=1; jk <=m; jk++) {            }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          }
    i=1;          else{
    for(k2=1; k2<=nlstate; k2++) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
      k3=i;  /*        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]); */
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){            k=k+1;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            if (j >= jmax) {
 ij=1;              jmax=j;
         for(j=3; j <=ncovmodel; j++) {              ijmax=i;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            else if (j <= jmin){
             ij++;              jmin=j;
           }              ijmin=i;
           else            }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         }            /*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,")/(1");            if(j<0){
                      nberr++;
         for(k1=1; k1 <=nlstate; k1++){                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(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              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]);
 ij=1;            }
           for(j=3; j <=ncovmodel; j++){            sum=sum+j;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          jk= j/stepm;
             ij++;          jl= j -jk*stepm;
           }          ju= j -(jk+1)*stepm;
           else          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            if(jl==0){
           }              dh[mi][i]=jk;
           fprintf(ficgp,")");              bh[mi][i]=0;
         }            }else{ /* We want a negative bias in order to only have interpolation ie
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                    * at the price of an extra matrix product in likelihood */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              dh[mi][i]=jk+1;
         i=i+ncovmodel;              bh[mi][i]=ju;
        }            }
      }          }else{
    }            if(jl <= -ju){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              dh[mi][i]=jk;
    }              bh[mi][i]=jl;       /* bias is positive if real duration
                                       * is higher than the multiple of stepm and negative otherwise.
   fclose(ficgp);                                   */
 }  /* end gnuplot */            }
             else{
               dh[mi][i]=jk+1;
 /*************** Moving average **************/              bh[mi][i]=ju;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){            }
             if(dh[mi][i]==0){
   int i, cpt, cptcod;              dh[mi][i]=1; /* At least one step */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)              bh[mi][i]=ju; /* At least one step */
       for (i=1; i<=nlstate;i++)              /*  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);*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            }
           mobaverage[(int)agedeb][i][cptcod]=0.;          } /* end if mle */
            }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      } /* end wave */
       for (i=1; i<=nlstate;i++){    }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    jmean=sum/k;
           for (cpt=0;cpt<=4;cpt++){    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);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
           }   }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }  /*********** Tricode ****************************/
       }  void tricode(int *Tvar, int **nbcode, int imx)
     }  {
        
 }    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
     cptcoveff=0; 
 /************** Forecasting ******************/   
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    for (k=0; k<maxncov; k++) Ndum[k]=0;
      for (k=1; k<=7; k++) ncodemax[k]=0;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   double *popeffectif,*popcount;                                 modality*/ 
   double ***p3mat;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   char fileresf[FILENAMELENGTH];        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  agelim=AGESUP;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      }
    
        for (i=0; i<=cptcode; i++) {
   strcpy(fileresf,"f");        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 */
   strcat(fileresf,fileres);      }
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);      ij=1; 
   }      for (i=1; i<=ncodemax[j]; i++) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            nbcode[Tvar[j]][ij]=k; 
             /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   if (mobilav==1) {            
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            ij++;
     movingaverage(agedeb, fage, ageminpar, mobaverage);          }
   }          if (ij > ncodemax[j]) break; 
         }  
   stepsize=(int) (stepm+YEARM-1)/YEARM;      } 
   if (stepm<=12) stepsize=1;    }  
    
   agelim=AGESUP;   for (k=0; k< maxncov; k++) Ndum[k]=0;
    
   hstepm=1;   for (i=1; i<=ncovmodel-2; i++) { 
   hstepm=hstepm/stepm;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   yp1=modf(dateintmean,&yp);     ij=Tvar[i];
   anprojmean=yp;     Ndum[ij]++;
   yp2=modf((yp1*12),&yp);   }
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);   ij=1;
   jprojmean=yp;   for (i=1; i<= maxncov; i++) {
   if(jprojmean==0) jprojmean=1;     if((Ndum[i]!=0) && (i<=ncovcol)){
   if(mprojmean==0) jprojmean=1;       Tvaraff[ij]=i; /*For printing */
         ij++;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);     }
     }
   for(cptcov=1;cptcov<=i2;cptcov++){   
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   cptcoveff=ij-1; /*Number of simple covariates*/
       k=k+1;  }
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {  /*********** Health Expectancies ****************/
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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,char strstart[] )
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");  {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    /* Health expectancies */
          int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
          double age, agelim, hf;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    double ***p3mat,***varhe;
         fprintf(ficresf,"\n");    double **dnewm,**doldm;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double *xp;
     double **gp, **gm;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double ***gradg, ***trgradg;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int theta;
           nhstepm = nhstepm/hstepm;  
              varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    xp=vector(1,npar);
           oldm=oldms;savm=savms;    dnewm=matrix(1,nlstate*nlstate,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
            
           for (h=0; h<=nhstepm; h++){    fprintf(ficreseij,"# Local time at start: %s", strstart);
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficreseij,"# Health expectancies\n");
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    fprintf(ficreseij,"# Age");
             }    for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {      for(j=1; j<=nlstate;j++)
               kk1=0.;kk2=0;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
               for(i=1; i<=nlstate;i++) {                  fprintf(ficreseij,"\n");
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    if(estepm < stepm){
                 else {      printf ("Problem %d lower than %d\n",estepm, stepm);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    }
                 }    else  hstepm=estepm;   
                    /* We compute the life expectancy from trapezoids spaced every estepm months
               }     * This is mainly to measure the difference between two models: for example
               if (h==(int)(calagedate+12*cpt)){     * if stepm=24 months pijx are given only every 2 years and by summing them
                 fprintf(ficresf," %.3f", kk1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
                             * progression in between and thus overestimating or underestimating according
               }     * to the curvature of the survival function. If, for the same date, we 
             }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           }     * to compare the new estimate of Life expectancy with the same linear 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * hypothesis. A more precise result, taking into account a more precise
         }     * curvature will be obtained if estepm is as small as stepm. */
       }  
     }    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* 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 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   fclose(ficresf);       and note for a fixed period like estepm months */
 }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 /************** Forecasting ******************/       survival function given by stepm (the optimization length). Unfortunately it
 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){       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 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;       results. So we changed our mind and took the option of the best precision.
   int *popage;    */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;    agelim=AGESUP;
   char filerespop[FILENAMELENGTH];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   agelim=AGESUP;      /* if (stepm >= YEARM) hstepm=1;*/
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
        gp=matrix(0,nhstepm,1,nlstate*nlstate);
        gm=matrix(0,nhstepm,1,nlstate*nlstate);
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   if((ficrespop=fopen(filerespop,"w"))==NULL) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     printf("Problem with forecast resultfile: %s\n", filerespop);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   }   
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       /* Computing  Variances of health expectancies */
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       for(theta=1; theta <=npar; theta++){
     movingaverage(agedeb, fage, ageminpar, mobaverage);        for(i=1; i<=npar; i++){ 
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (stepm<=12) stepsize=1;    
          cptj=0;
   agelim=AGESUP;        for(j=1; j<= nlstate; j++){
            for(i=1; i<=nlstate; i++){
   hstepm=1;            cptj=cptj+1;
   hstepm=hstepm/stepm;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if (popforecast==1) {            }
     if((ficpop=fopen(popfile,"r"))==NULL) {          }
       printf("Problem with population file : %s\n",popfile);exit(0);        }
     }       
     popage=ivector(0,AGESUP);       
     popeffectif=vector(0,AGESUP);        for(i=1; i<=npar; i++) 
     popcount=vector(0,AGESUP);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     i=1;          
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        cptj=0;
            for(j=1; j<= nlstate; j++){
     imx=i;          for(i=1;i<=nlstate;i++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            cptj=cptj+1;
   }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
   for(cptcov=1;cptcov<=i2;cptcov++){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            }
       k=k+1;          }
       fprintf(ficrespop,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {        for(j=1; j<= nlstate*nlstate; j++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(h=0; h<=nhstepm-1; h++){
       }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       fprintf(ficrespop,"******\n");          }
       fprintf(ficrespop,"# Age");       } 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);     
       if (popforecast==1)  fprintf(ficrespop," [Population]");  /* End theta */
        
       for (cpt=0; cpt<=0;cpt++) {       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
               for(h=0; h<=nhstepm-1; h++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(j=1; j<=nlstate*nlstate;j++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for(theta=1; theta <=npar; theta++)
           nhstepm = nhstepm/hstepm;            trgradg[h][j][theta]=gradg[h][theta][j];
                 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;       for(i=1;i<=nlstate*nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=1;j<=nlstate*nlstate;j++)
                  varhe[i][j][(int)age] =0.;
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {       printf("%d|",(int)age);fflush(stdout);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             }       for(h=0;h<=nhstepm-1;h++){
             for(j=1; j<=nlstate+ndeath;j++) {        for(k=0;k<=nhstepm-1;k++){
               kk1=0.;kk2=0;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
               for(i=1; i<=nlstate;i++) {                        matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                 if (mobilav==1)          for(i=1;i<=nlstate*nlstate;i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            for(j=1;j<=nlstate*nlstate;j++)
                 else {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }
                 }      }
               }      /* Computing expectancies */
               if (h==(int)(calagedate+12*cpt)){      for(i=1; i<=nlstate;i++)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        for(j=1; j<=nlstate;j++)
                   /*fprintf(ficrespop," %.3f", kk1);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               }            
             }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
             for(i=1; i<=nlstate;i++){  
               kk1=0.;          }
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      fprintf(ficreseij,"%3.0f",age );
                 }      cptj=0;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      for(i=1; i<=nlstate;i++)
             }        for(j=1; j<=nlstate;j++){
           cptj++;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        }
           }      fprintf(ficreseij,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     
         }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        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);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      printf("\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficlog,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    free_vector(xp,1,npar);
              free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           oldm=oldms;savm=savms;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    }
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  /************ Variance ******************/
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
             }  {
             for(j=1; j<=nlstate+ndeath;j++) {    /* Variance of health expectancies */
               kk1=0.;kk2=0;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
               for(i=1; i<=nlstate;i++) {                  /* double **newm;*/
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        double **dnewm,**doldm;
               }    double **dnewmp,**doldmp;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    int i, j, nhstepm, hstepm, h, nstepm ;
             }    int k, cptcode;
           }    double *xp;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **gp, **gm;  /* for var eij */
         }    double ***gradg, ***trgradg; /*for var eij */
       }    double **gradgp, **trgradgp; /* for var p point j */
    }    double *gpp, *gmp; /* for var p point j */
   }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      double ***p3mat;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double age,agelim, hf;
     double ***mobaverage;
   if (popforecast==1) {    int theta;
     free_ivector(popage,0,AGESUP);    char digit[4];
     free_vector(popeffectif,0,AGESUP);    char digitp[25];
     free_vector(popcount,0,AGESUP);  
   }    char fileresprobmorprev[FILENAMELENGTH];
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if(popbased==1){
   fclose(ficrespop);      if(mobilav!=0)
 }        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
 /***********************************************/    }
 /**************** Main Program *****************/    else 
 /***********************************************/      strcpy(digitp,"-stablbased-");
   
 int main(int argc, char *argv[])    if (mobilav!=0) {
 {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   double agedeb, agefin,hf;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      }
     }
   double fret;  
   double **xi,tmp,delta;    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   double dum; /* Dummy variable */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   double ***p3mat;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   int *indx;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   char line[MAXLINE], linepar[MAXLINE];    strcat(fileresprobmorprev,fileres);
   char title[MAXLINE];    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   char filerest[FILENAMELENGTH];    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   char fileregp[FILENAMELENGTH];    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   char popfile[FILENAMELENGTH];    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   int firstobs=1, lastobs=10;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   int sdeb, sfin; /* Status at beginning and end */      fprintf(ficresprobmorprev," p.%-d SE",j);
   int c,  h , cpt,l;      for(i=1; i<=nlstate;i++)
   int ju,jl, mi;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    }  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    fprintf(ficresprobmorprev,"\n");
   int mobilav=0,popforecast=0;    fprintf(ficgp,"\n# Routine varevsij");
   int hstepm, nhstepm;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    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");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   double bage, fage, age, agelim, agebase;  /*   } */
   double ftolpl=FTOL;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double **prlim;   fprintf(ficresvij, "#Local time at start: %s", strstart);
   double *severity;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   double ***param; /* Matrix of parameters */    fprintf(ficresvij,"# Age");
   double  *p;    for(i=1; i<=nlstate;i++)
   double **matcov; /* Matrix of covariance */      for(j=1; j<=nlstate;j++)
   double ***delti3; /* Scale */        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   double *delti; /* Scale */    fprintf(ficresvij,"\n");
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */    xp=vector(1,npar);
   double *epj, vepp;    dnewm=matrix(1,nlstate,1,npar);
   double kk1, kk2;    doldm=matrix(1,nlstate,1,nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   char z[1]="c", occ;    
 #include <sys/time.h>    if(estepm < stepm){
 #include <time.h>      printf ("Problem %d lower than %d\n",estepm, stepm);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    }
      else  hstepm=estepm;   
   /* long total_usecs;    /* For example we decided to compute the life expectancy with the smallest unit */
   struct timeval start_time, end_time;    /* 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 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */       nstepm is the number of stepm from age to agelin. 
   getcwd(pathcd, size);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   printf("\n%s",version);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if(argc <=1){       survival function given by stepm (the optimization length). Unfortunately it
     printf("\nEnter the parameter file name: ");       means that if the survival funtion is printed every two years of age and if
     scanf("%s",pathtot);       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.
   else{    */
     strcpy(pathtot,argv[1]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }    agelim = AGESUP;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /*cygwin_split_path(pathtot,path,optionfile);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /* cutv(path,optionfile,pathtot,'\\');*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      gp=matrix(0,nhstepm,1,nlstate);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      gm=matrix(0,nhstepm,1,nlstate);
   chdir(path);  
   replace(pathc,path);  
       for(theta=1; theta <=npar; theta++){
 /*-------- arguments in the command line --------*/        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcpy(fileres,"r");        }
   strcat(fileres, optionfilefiname);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcat(fileres,".txt");    /* Other files have txt extension */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   /*---------arguments file --------*/        if (popbased==1) {
           if(mobilav ==0){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            for(i=1; i<=nlstate;i++)
     printf("Problem with optionfile %s\n",optionfile);              prlim[i][i]=probs[(int)age][i][ij];
     goto end;          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   strcpy(filereso,"o");          }
   strcat(filereso,fileres);        }
   if((ficparo=fopen(filereso,"w"))==NULL) {    
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        for(j=1; j<= nlstate; j++){
   }          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        /* This for computing probability of death (h=1 means
     puts(line);           computed over hstepm matrices product = hstepm*stepm months) 
     fputs(line,ficparo);           as a weighted average of prlim.
   }        */
   ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
   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);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   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);        /* end probability of death */
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     fgets(line, MAXLINE, ficpar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     puts(line);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }   
   ungetc(c,ficpar);        if (popbased==1) {
            if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
   covar=matrix(0,NCOVMAX,1,n);              prlim[i][i]=probs[(int)age][i][ij];
   cptcovn=0;          }else{ /* mobilav */ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   ncovmodel=2+cptcovn;          }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        }
    
   /* Read guess parameters */        for(j=1; j<= nlstate; j++){
   /* Reads comments: lines beginning with '#' */          for(h=0; h<=nhstepm; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     ungetc(c,ficpar);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     fgets(line, MAXLINE, ficpar);          }
     puts(line);        }
     fputs(line,ficparo);        /* This for computing probability of death (h=1 means
   }           computed over hstepm matrices product = hstepm*stepm months) 
   ungetc(c,ficpar);           as a weighted average of prlim.
          */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(i=1; i <=nlstate; i++)          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     for(j=1; j <=nlstate+ndeath-1; j++){           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }    
       fprintf(ficparo,"%1d%1d",i1,j1);        /* end probability of death */
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){        for(j=1; j<= nlstate; j++) /* vareij */
         fscanf(ficpar," %lf",&param[i][j][k]);          for(h=0; h<=nhstepm; h++){
         printf(" %lf",param[i][j][k]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         fprintf(ficparo," %lf",param[i][j][k]);          }
       }  
       fscanf(ficpar,"\n");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       printf("\n");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       fprintf(ficparo,"\n");        }
     }  
        } /* End theta */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   p=param[1][1];  
        for(h=0; h<=nhstepm; h++) /* veij */
   /* Reads comments: lines beginning with '#' */        for(j=1; j<=nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){          for(theta=1; theta <=npar; theta++)
     ungetc(c,ficpar);            trgradg[h][j][theta]=gradg[h][theta][j];
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     fputs(line,ficparo);        for(theta=1; theta <=npar; theta++)
   }          trgradgp[j][theta]=gradgp[theta][j];
   ungetc(c,ficpar);    
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      for(i=1;i<=nlstate;i++)
   for(i=1; i <=nlstate; i++){        for(j=1;j<=nlstate;j++)
     for(j=1; j <=nlstate+ndeath-1; j++){          vareij[i][j][(int)age] =0.;
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);      for(h=0;h<=nhstepm;h++){
       fprintf(ficparo,"%1d%1d",i1,j1);        for(k=0;k<=nhstepm;k++){
       for(k=1; k<=ncovmodel;k++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         printf(" %le",delti3[i][j][k]);          for(i=1;i<=nlstate;i++)
         fprintf(ficparo," %le",delti3[i][j][k]);            for(j=1;j<=nlstate;j++)
       }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fscanf(ficpar,"\n");        }
       printf("\n");      }
       fprintf(ficparo,"\n");    
     }      /* pptj */
   }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   delti=delti3[1][1];      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
   /* Reads comments: lines beginning with '#' */        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){          varppt[j][i]=doldmp[j][i];
     ungetc(c,ficpar);      /* end ppptj */
     fgets(line, MAXLINE, ficpar);      /*  x centered again */
     puts(line);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     fputs(line,ficparo);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   }   
   ungetc(c,ficpar);      if (popbased==1) {
          if(mobilav ==0){
   matcov=matrix(1,npar,1,npar);          for(i=1; i<=nlstate;i++)
   for(i=1; i <=npar; i++){            prlim[i][i]=probs[(int)age][i][ij];
     fscanf(ficpar,"%s",&str);        }else{ /* mobilav */ 
     printf("%s",str);          for(i=1; i<=nlstate;i++)
     fprintf(ficparo,"%s",str);            prlim[i][i]=mobaverage[(int)age][i][ij];
     for(j=1; j <=i; j++){        }
       fscanf(ficpar," %le",&matcov[i][j]);      }
       printf(" %.5le",matcov[i][j]);               
       fprintf(ficparo," %.5le",matcov[i][j]);      /* This for computing probability of death (h=1 means
     }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     fscanf(ficpar,"\n");         as a weighted average of prlim.
     printf("\n");      */
     fprintf(ficparo,"\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   for(i=1; i <=npar; i++)          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     for(j=i+1;j<=npar;j++)      }    
       matcov[i][j]=matcov[j][i];      /* end probability of death */
      
   printf("\n");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     /*-------- Rewriting paramater file ----------*/        for(i=1; i<=nlstate;i++){
      strcpy(rfileres,"r");    /* "Rparameterfile */          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        }
      strcat(rfileres,".");    /* */      } 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      fprintf(ficresprobmorprev,"\n");
     if((ficres =fopen(rfileres,"w"))==NULL) {  
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      fprintf(ficresvij,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
     fprintf(ficres,"#%s\n",version);        for(j=1; j<=nlstate;j++){
              fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     /*-------- data file ----------*/        }
     if((fic=fopen(datafile,"r"))==NULL)    {      fprintf(ficresvij,"\n");
       printf("Problem with datafile: %s\n", datafile);goto end;      free_matrix(gp,0,nhstepm,1,nlstate);
     }      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     n= lastobs;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     severity = vector(1,maxwav);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     outcome=imatrix(1,maxwav+1,1,n);    } /* End age */
     num=ivector(1,n);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     moisnais=vector(1,n);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     annais=vector(1,n);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     moisdc=vector(1,n);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     andc=vector(1,n);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     agedc=vector(1,n);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     cod=ivector(1,n);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     weight=vector(1,n);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     mint=matrix(1,maxwav,1,n);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     anint=matrix(1,maxwav,1,n);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     s=imatrix(1,maxwav+1,1,n);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     adl=imatrix(1,maxwav+1,1,n);        fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     tab=ivector(1,NCOVMAX);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     ncodemax=ivector(1,8);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
     i=1;  */
     while (fgets(line, MAXLINE, fic) != NULL)    {  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       if ((i >= firstobs) && (i <=lastobs)) {    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
          
         for (j=maxwav;j>=1;j--){    free_vector(xp,1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    free_matrix(doldm,1,nlstate,1,nlstate);
           strcpy(line,stra);    free_matrix(dnewm,1,nlstate,1,npar);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(ficresprobmorprev);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fflush(ficgp);
     fflush(fichtm); 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  }  /* end varevsij */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
   /************ Variance of prevlim ******************/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
         for (j=ncovcol;j>=1;j--){  {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* Variance of prevalence limit */
         }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         num[i]=atol(stra);    double **newm;
            double **dnewm,**doldm;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    int i, j, nhstepm, hstepm;
           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;}*/    int k, cptcode;
     double *xp;
         i=i+1;    double *gp, *gm;
       }    double **gradg, **trgradg;
     }    double age,agelim;
     /* printf("ii=%d", ij);    int theta;
        scanf("%d",i);*/    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
   imx=i-1; /* Number of individuals */    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
   /* for (i=1; i<=imx; i++){    for(i=1; i<=nlstate;i++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        fprintf(ficresvpl," %1d-%1d",i,i);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    fprintf(ficresvpl,"\n");
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }*/    xp=vector(1,npar);
    /*  for (i=1; i<=imx; i++){    dnewm=matrix(1,nlstate,1,npar);
      if (s[4][i]==9)  s[4][i]=-1;    doldm=matrix(1,nlstate,1,nlstate);
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/    
      hstepm=1*YEARM; /* Every year of age */
      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   /* Calculation of the number of parameter from char model*/    agelim = AGESUP;
   Tvar=ivector(1,15);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   Tprod=ivector(1,15);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   Tvaraff=ivector(1,15);      if (stepm >= YEARM) hstepm=1;
   Tvard=imatrix(1,15,1,2);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   Tage=ivector(1,15);            gradg=matrix(1,npar,1,nlstate);
          gp=vector(1,nlstate);
   if (strlen(model) >1){      gm=vector(1,nlstate);
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');      for(theta=1; theta <=npar; theta++){
     j1=nbocc(model,'*');        for(i=1; i<=npar; i++){ /* Computes gradient */
     cptcovn=j+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     cptcovprod=j1;        }
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     strcpy(modelsav,model);        for(i=1;i<=nlstate;i++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          gp[i] = prlim[i][i];
       printf("Error. Non available option model=%s ",model);      
       goto end;        for(i=1; i<=npar; i++) /* Computes gradient */
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for(i=(j+1); i>=1;i--){        for(i=1;i<=nlstate;i++)
       cutv(stra,strb,modelsav,'+');          gm[i] = prlim[i][i];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        for(i=1;i<=nlstate;i++)
       /*scanf("%d",i);*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       if (strchr(strb,'*')) {      } /* End theta */
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {      trgradg =matrix(1,nlstate,1,npar);
           cptcovprod--;  
           cutv(strb,stre,strd,'V');      for(j=1; j<=nlstate;j++)
           Tvar[i]=atoi(stre);        for(theta=1; theta <=npar; theta++)
           cptcovage++;          trgradg[j][theta]=gradg[theta][j];
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/      for(i=1;i<=nlstate;i++)
         }        varpl[i][(int)age] =0.;
         else if (strcmp(strd,"age")==0) {      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           cptcovprod--;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           cutv(strb,stre,strc,'V');      for(i=1;i<=nlstate;i++)
           Tvar[i]=atoi(stre);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           cptcovage++;  
           Tage[cptcovage]=i;      fprintf(ficresvpl,"%.0f ",age );
         }      for(i=1; i<=nlstate;i++)
         else {        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           cutv(strb,stre,strc,'V');      fprintf(ficresvpl,"\n");
           Tvar[i]=ncovcol+k1;      free_vector(gp,1,nlstate);
           cutv(strb,strc,strd,'V');      free_vector(gm,1,nlstate);
           Tprod[k1]=i;      free_matrix(gradg,1,npar,1,nlstate);
           Tvard[k1][1]=atoi(strc);      free_matrix(trgradg,1,nlstate,1,npar);
           Tvard[k1][2]=atoi(stre);    } /* End age */
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    free_vector(xp,1,npar);
           for (k=1; k<=lastobs;k++)    free_matrix(doldm,1,nlstate,1,npar);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    free_matrix(dnewm,1,nlstate,1,nlstate);
           k1++;  
           k2=k2+2;  }
         }  
       }  /************ Variance of one-step probabilities  ******************/
       else {  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[])
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  {
        /*  scanf("%d",i);*/    int i, j=0,  i1, k1, l1, t, tj;
       cutv(strd,strc,strb,'V');    int k2, l2, j1,  z1;
       Tvar[i]=atoi(strc);    int k=0,l, cptcode;
       }    int first=1, first1;
       strcpy(modelsav,stra);      double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    double **dnewm,**doldm;
         scanf("%d",i);*/    double *xp;
     }    double *gp, *gm;
 }    double **gradg, **trgradg;
      double **mu;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double age,agelim, cov[NCOVMAX];
   printf("cptcovprod=%d ", cptcovprod);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   scanf("%d ",i);*/    int theta;
     fclose(fic);    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     /*  if(mle==1){*/    char fileresprobcor[FILENAMELENGTH];
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    double ***varpij;
     }  
     /*-calculation of age at interview from date of interview and age at death -*/    strcpy(fileresprob,"prob"); 
     agev=matrix(1,maxwav,1,imx);    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     for (i=1; i<=imx; i++) {      printf("Problem with resultfile: %s\n", fileresprob);
       for(m=2; (m<= maxwav); m++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    }
          anint[m][i]=9999;    strcpy(fileresprobcov,"probcov"); 
          s[m][i]=-1;    strcat(fileresprobcov,fileres);
        }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      printf("Problem with resultfile: %s\n", fileresprobcov);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }    }
     strcpy(fileresprobcor,"probcor"); 
     for (i=1; i<=imx; i++)  {    strcat(fileresprobcor,fileres);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       for(m=1; (m<= maxwav); m++){      printf("Problem with resultfile: %s\n", fileresprobcor);
         if(s[m][i] >0){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           if (s[m][i] >= nlstate+1) {    }
             if(agedc[i]>0)    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
                 agev[m][i]=agedc[i];    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
            else {    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
               if (andc[i]!=9999){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficresprob, "#Local time at start: %s", strstart);
               agev[m][i]=-1;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
               }    fprintf(ficresprob,"# Age");
             }    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
           }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(ficresprobcov,"# Age");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
               agev[m][i]=1;    fprintf(ficresprobcov,"# Age");
             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);*/    for(i=1; i<=nlstate;i++)
             }      for(j=1; j<=(nlstate+ndeath);j++){
             else if(agev[m][i] >agemax){        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
               agemax=agev[m][i];        fprintf(ficresprobcov," p%1d-%1d ",i,j);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        fprintf(ficresprobcor," p%1d-%1d ",i,j);
             }      }  
             /*agev[m][i]=anint[m][i]-annais[i];*/   /* fprintf(ficresprob,"\n");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficresprobcov,"\n");
           }    fprintf(ficresprobcor,"\n");
           else { /* =9 */   */
             agev[m][i]=1;   xp=vector(1,npar);
             s[m][i]=-1;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         else /*= 0 Unknown */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           agev[m][i]=1;    first=1;
       }    fprintf(ficgp,"\n# Routine varprob");
        fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     }    fprintf(fichtm,"\n");
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
         if (s[m][i] > (nlstate+ndeath)) {    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           printf("Error: Wrong value in nlstate or ndeath\n");      file %s<br>\n",optionfilehtmcov);
           goto end;    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.\
       }   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
     free_vector(severity,1,maxwav);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     free_imatrix(outcome,1,maxwav+1,1,n);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
     free_vector(moisnais,1,n);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);    cov[1]=1;
        free_matrix(anint,1,maxwav,1,n);*/    tj=cptcoveff;
     free_vector(moisdc,1,n);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     free_vector(andc,1,n);    j1=0;
     for(t=1; t<=tj;t++){
          for(i1=1; i1<=ncodemax[t];i1++){ 
     wav=ivector(1,imx);        j1++;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        if  (cptcovn>0) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficresprob, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     /* Concatenates waves */          fprintf(ficresprob, "**********\n#\n");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
       Tcode=ivector(1,100);          
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          fprintf(ficgp, "\n#********** Variable "); 
       ncodemax[1]=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          fprintf(ficgp, "**********\n#\n");
                
    codtab=imatrix(1,100,1,10);          
    h=0;          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
    m=pow(2,cptcoveff);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
    for(k=1;k<=cptcoveff; k++){          
      for(i=1; i <=(m/pow(2,k));i++){          fprintf(ficresprobcor, "\n#********** Variable ");    
        for(j=1; j <= ncodemax[k]; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficresprobcor, "**********\n#");    
            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]);*/        for (age=bage; age<=fage; age ++){ 
          }          cov[2]=age;
        }          for (k=1; k<=cptcovn;k++) {
      }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
    }          }
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       codtab[1][2]=1;codtab[2][2]=2; */          for (k=1; k<=cptcovprod;k++)
    /* for(i=1; i <=m ;i++){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for(k=1; k <=cptcovn; k++){          
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       }          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       printf("\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
       }          gm=vector(1,(nlstate)*(nlstate+ndeath));
       scanf("%d",i);*/      
              for(theta=1; theta <=npar; theta++){
    /* Calculates basic frequencies. Computes observed prevalence at single age            for(i=1; i<=npar; i++)
        and prints on file fileres'p'. */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
                pmij(pmmij,cov,ncovmodel,xp,nlstate);
                
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            k=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(i=1; i<= (nlstate); i++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for(j=1; j<=(nlstate+ndeath);j++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                k=k+1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                gp[k]=pmmij[i][j];
                    }
     /* 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) */            for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     if(mle==1){      
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     }            k=0;
                for(i=1; i<=(nlstate); i++){
     /*--------- results files --------------*/              for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);                k=k+1;
                  gm[k]=pmmij[i][j];
               }
    jk=1;            }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");       
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
    for(i=1,jk=1; i <=nlstate; i++){              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
      for(k=1; k <=(nlstate+ndeath); k++){          }
        if (k != i)  
          {          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
            printf("%d%d ",i,k);            for(theta=1; theta <=npar; theta++)
            fprintf(ficres,"%1d%1d ",i,k);              trgradg[j][theta]=gradg[theta][j];
            for(j=1; j <=ncovmodel; j++){          
              printf("%f ",p[jk]);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
              fprintf(ficres,"%f ",p[jk]);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
              jk++;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
            }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
            printf("\n");          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            fprintf(ficres,"\n");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
          }  
      }          pmij(pmmij,cov,ncovmodel,x,nlstate);
    }          
  if(mle==1){          k=0;
     /* Computing hessian and covariance matrix */          for(i=1; i<=(nlstate); i++){
     ftolhess=ftol; /* Usually correct */            for(j=1; j<=(nlstate+ndeath);j++){
     hesscov(matcov, p, npar, delti, ftolhess, func);              k=k+1;
  }              mu[k][(int) age]=pmmij[i][j];
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            }
     printf("# Scales (for hessian or gradient estimation)\n");          }
      for(i=1,jk=1; i <=nlstate; i++){          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       for(j=1; j <=nlstate+ndeath; j++){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         if (j!=i) {              varpij[i][j][(int)age] = doldm[i][j];
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);          /*printf("\n%d ",(int)age);
           for(k=1; k<=ncovmodel;k++){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf(" %.5e",delti[jk]);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficres," %.5e",delti[jk]);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             jk++;            }*/
           }  
           printf("\n");          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficres,"\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
         }          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]));
     k=1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     for(i=1;i<=npar;i++){          }
       /*  if (k>nlstate) k=1;          i=0;
       i1=(i-1)/(ncovmodel*nlstate)+1;          for (k=1; k<=(nlstate);k++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            for (l=1; l<=(nlstate+ndeath);l++){ 
       printf("%s%d%d",alph[k],i1,tab[i]);*/              i=i++;
       fprintf(ficres,"%3d",i);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       printf("%3d",i);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       for(j=1; j<=i;j++){              for (j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         printf(" %.5e",matcov[i][j]);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       }              }
       fprintf(ficres,"\n");            }
       printf("\n");          }/* end of loop for state */
       k++;        } /* end of loop for age */
     }  
            /* Confidence intervalle of pij  */
     while((c=getc(ficpar))=='#' && c!= EOF){        /*
       ungetc(c,ficpar);          fprintf(ficgp,"\nset noparametric;unset label");
       fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       puts(line);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fputs(line,ficparo);          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(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     ungetc(c,ficpar);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     estepm=0;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     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) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       bage = ageminpar;        first1=1;
       fage = agemaxpar;        for (k2=1; k2<=(nlstate);k2++){
     }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                if(l2==k2) continue;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            j=(k2-1)*(nlstate+ndeath)+l2;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);            for (k1=1; k1<=(nlstate);k1++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                  if(l1==k1) continue;
     while((c=getc(ficpar))=='#' && c!= EOF){                i=(k1-1)*(nlstate+ndeath)+l1;
     ungetc(c,ficpar);                if(i<=j) continue;
     fgets(line, MAXLINE, ficpar);                for (age=bage; age<=fage; age ++){ 
     puts(line);                  if ((int)age %5==0){
     fputs(line,ficparo);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   ungetc(c,ficpar);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      mu1=mu[i][(int) age]/stepm*YEARM ;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    mu2=mu[j][(int) age]/stepm*YEARM;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    c12=cv12/sqrt(v1*v2);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    /* Computing eigen value of matrix of covariance */
                          lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   while((c=getc(ficpar))=='#' && c!= EOF){                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     ungetc(c,ficpar);                    /* Eigen vectors */
     fgets(line, MAXLINE, ficpar);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     puts(line);                    /*v21=sqrt(1.-v11*v11); *//* error */
     fputs(line,ficparo);                    v21=(lc1-v1)/cv12*v11;
   }                    v12=-v21;
   ungetc(c,ficpar);                    v22=v11;
                      tnalp=v21/v11;
                     if(first1==1){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                      first1=0;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                      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);
                     }
   fscanf(ficpar,"pop_based=%d\n",&popbased);                    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);
   fprintf(ficparo,"pop_based=%d\n",popbased);                      /*printf(fignu*/
   fprintf(ficres,"pop_based=%d\n",popbased);                      /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                      /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   while((c=getc(ficpar))=='#' && c!= EOF){                    if(first==1){
     ungetc(c,ficpar);                      first=0;
     fgets(line, MAXLINE, ficpar);                      fprintf(ficgp,"\nset parametric;unset label");
     puts(line);                      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);
     fputs(line,ficparo);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   }                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   ungetc(c,ficpar);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   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);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
 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);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     ungetc(c,ficpar);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     fgets(line, MAXLINE, ficpar);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     puts(line);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fputs(line,ficparo);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   }                    }else{
   ungetc(c,ficpar);                      first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   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(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
 /*------------ gnuplot -------------*/                  } /* age mod 5 */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);                } /* end loop age */
                  fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
 /*------------ free_vector  -------------*/                first=1;
  chdir(path);              } /*l12 */
              } /* k12 */
  free_ivector(wav,1,imx);          } /*l1 */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }/* k1 */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        } /* loop covariates */
  free_ivector(num,1,n);    }
  free_vector(agedc,1,n);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
  fclose(ficparo);    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
  fclose(ficres);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
 /*--------- index.htm --------*/    fclose(ficresprob);
     fclose(ficresprobcov);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    fclose(ficresprobcor);
     fflush(ficgp);
      fflush(fichtmcov);
   /*--------------- Prevalence limit --------------*/  }
    
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);  /******************* Printing html file ***********/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                    int lastpass, int stepm, int weightopt, char model[],\
   }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                    int popforecast, int estepm ,\
   fprintf(ficrespl,"#Prevalence limit\n");                    double jprev1, double mprev1,double anprev1, \
   fprintf(ficrespl,"#Age ");                    double jprev2, double mprev2,double anprev2){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int jj1, k1, i1, cpt;
   fprintf(ficrespl,"\n");  
       fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   prlim=matrix(1,nlstate,1,nlstate);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  </ul>");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     fprintf(fichtm,"\
   k=0;   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   agebase=ageminpar;             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   agelim=agemaxpar;     fprintf(fichtm,"\
   ftolpl=1.e-10;   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
   i1=cptcoveff;             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   if (cptcovn < 1){i1=1;}     fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months) WRONG LINK (to be made): \
   for(cptcov=1;cptcov<=i1;cptcov++){     <a href=\"%s\">%s</a> <br>\n</li>",
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){             estepm,subdirf2(fileres,"le"),subdirf2(fileres,"le"));
         k=k+1;     fprintf(fichtm,"\
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   - Health expectancies by age and initial health status with standard errors (estepm=%2d months): \
         fprintf(ficrespl,"\n#******");     <a href=\"%s\">%s</a> <br>\n</li>",
         for(j=1;j<=cptcoveff;j++)             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     fprintf(fichtm,"\
         fprintf(ficrespl,"******\n");   - Variances and covariances of health expectancies by age and initial health status (estepm=%2d months) TO BE MADE: \
             <a href=\"%s\">%s</a> <br>\n</li>",
         for (age=agebase; age<=agelim; age++){             estepm,subdirf2(fileres,"vch"),subdirf2(fileres,"vch"));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");   m=cptcoveff;
         }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       }  
     }   jj1=0;
   fclose(ficrespl);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   /*------------- h Pij x at various ages ------------*/       jj1++;
         if (cptcovn > 0) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {         for (cpt=1; cpt<=cptcoveff;cpt++) 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   printf("Computing pij: result on file '%s' \n", filerespij);       }
         /* Pij */
   stepsize=(int) (stepm+YEARM-1)/YEARM;       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> \
   /*if (stepm<=24) stepsize=2;*/  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
   agelim=AGESUP;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   hstepm=stepsize*YEARM; /* Every year of age */   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           /* Stable prevalence in each health state */
   k=0;         for(cpt=1; cpt<nlstate;cpt++){
   for(cptcov=1;cptcov<=i1;cptcov++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
       k=k+1;         }
         fprintf(ficrespij,"\n#****** ");       for(cpt=1; cpt<=nlstate;cpt++) {
         for(j=1;j<=cptcoveff;j++)          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         fprintf(ficrespij,"******\n");       }
             } /* end i1 */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */   }/* End k1 */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   fprintf(fichtm,"</ul>");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;   fprintf(fichtm,"\
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
           fprintf(ficrespij,"# Age");   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
               fprintf(ficrespij," %1d-%1d",i,j);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
           fprintf(ficrespij,"\n");   fprintf(fichtm,"\
            for (h=0; h<=nhstepm; h++){   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)   fprintf(fichtm,"\
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             fprintf(ficrespij,"\n");           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
              }   fprintf(fichtm,"\
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   - Variances and covariances of health expectancies by age (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
           fprintf(ficrespij,"\n");           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
         }   fprintf(fichtm,"\
     }   - Life and health expectancies with their standard errors: <a href=\"%s\">%s</a> <br>\n",
   }           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   fclose(ficrespij);  
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*---------- Forecasting ------------------*/  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   if((stepm == 1) && (strcmp(model,".")==0)){  /*      <br>",fileres,fileres,fileres,fileres); */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  /*  else  */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  /*    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);
   else{   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     erreur=108;  
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);   m=cptcoveff;
   }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
    jj1=0;
   /*---------- Health expectancies and variances ------------*/   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   strcpy(filerest,"t");       jj1++;
   strcat(filerest,fileres);       if (cptcovn > 0) {
   if((ficrest=fopen(filerest,"w"))==NULL) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
   strcpy(filerese,"e");         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   strcat(filerese,fileres);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   if((ficreseij=fopen(filerese,"w"))==NULL) {  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       }
   }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
  strcpy(fileresv,"v");     } /* end i1 */
   strcat(fileresv,fileres);   }/* End k1 */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   fprintf(fichtm,"</ul>");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);   fflush(fichtm);
   }  }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   calagedate=-1;  /******************* Gnuplot file **************/
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   k=0;    char dirfileres[132],optfileres[132];
   for(cptcov=1;cptcov<=i1;cptcov++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int ng;
       k=k+1;  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       fprintf(ficrest,"\n#****** ");  /*     printf("Problem with file %s",optionfilegnuplot); */
       for(j=1;j<=cptcoveff;j++)  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   } */
       fprintf(ficrest,"******\n");  
     /*#ifdef windows */
       fprintf(ficreseij,"\n#****** ");    fprintf(ficgp,"cd \"%s\" \n",pathc);
       for(j=1;j<=cptcoveff;j++)      /*#endif */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    m=pow(2,cptcoveff);
       fprintf(ficreseij,"******\n");  
     strcpy(dirfileres,optionfilefiname);
       fprintf(ficresvij,"\n#****** ");    strcpy(optfileres,"vpl");
       for(j=1;j<=cptcoveff;j++)   /* 1eme*/
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (cpt=1; cpt<= nlstate ; cpt ++) {
       fprintf(ficresvij,"******\n");     for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
       oldm=oldms;savm=savms;       fprintf(ficgp,"set xlabel \"Age\" \n\
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    set ylabel \"Probability\" \n\
    set ter png small\n\
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  set size 0.65,0.65\n\
       oldm=oldms;savm=savms;  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);  
           for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");       }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
       fprintf(ficrest,"\n");       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) 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);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         if (popbased==1) {       for (i=1; i<= nlstate ; i ++) {
           for(i=1; i<=nlstate;i++)         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             prlim[i][i]=probs[(int)age][i][k];         else fprintf(ficgp," \%%*lf (\%%*lf)");
         }       }  
               fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
         fprintf(ficrest," %4.0f",age);     }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    /*2 eme*/
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    for (k1=1; k1<= m ; k1 ++) { 
           }      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
           epj[nlstate+1] +=epj[j];      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         }      
       for (i=1; i<= nlstate+1 ; i ++) {
         for(i=1, vepp=0.;i <=nlstate;i++)        k=2*i;
           for(j=1;j <=nlstate;j++)        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
             vepp += vareij[i][j][(int)age];        for (j=1; j<= nlstate+1 ; j ++) {
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         for(j=1;j <=nlstate;j++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        }   
         }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         fprintf(ficrest,"\n");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     }        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 free_matrix(mint,1,maxwav,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        }   
     free_vector(weight,1,n);        fprintf(ficgp,"\" t\"\" w l 0,");
   fclose(ficreseij);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   fclose(ficresvij);        for (j=1; j<= nlstate+1 ; j ++) {
   fclose(ficrest);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   fclose(ficpar);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_vector(epj,1,nlstate+1);        }   
          if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   /*------- Variance limit prevalence------*/          else fprintf(ficgp,"\" t\"\" w l 0,");
       }
   strcpy(fileresvpl,"vpl");    }
   strcat(fileresvpl,fileres);    
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    /*3eme*/
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    
     exit(0);    for (k1=1; k1<= m ; k1 ++) { 
   }      for (cpt=1; cpt<= nlstate ; cpt ++) {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   k=0;        fprintf(ficgp,"set ter png small\n\
   for(cptcov=1;cptcov<=i1;cptcov++){  set size 0.65,0.65\n\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       k=k+1;        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       fprintf(ficresvpl,"\n#****** ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       fprintf(ficresvpl,"******\n");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
                fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       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);        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);
  }          
         } 
   fclose(ficresvpl);      }
     }
   /*---------- End : free ----------------*/    
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    /* CV preval stable (period) */
      for (k1=1; k1<= m ; k1 ++) { 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        k=3;
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  set ter png small\nset size 0.65,0.65\n\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  unset log y\n\
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        
          for (i=1; i< nlstate ; i ++)
   free_matrix(matcov,1,npar,1,npar);          fprintf(ficgp,"+$%d",k+i+1);
   free_vector(delti,1,npar);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   free_matrix(agev,1,maxwav,1,imx);        
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   if(erreur >0)        for (i=1; i< nlstate ; i ++) {
     printf("End of Imach with error or warning %d\n",erreur);          l=3+(nlstate+ndeath)*cpt;
   else   printf("End of Imach\n");          fprintf(ficgp,"+$%d",l+i+1);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        }
          fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+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);*/      } 
   /*printf("Total time was %d uSec.\n", total_usecs);*/    }  
   /*------ End -----------*/    
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
  end:      for(k=1; k <=(nlstate+ndeath); k++){
   /* chdir(pathcd);*/        if (k != i) {
  /*system("wgnuplot graph.plt");*/          for(j=1; j <=ncovmodel; j++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
  /*system("cd ../gp37mgw");*/            jk++; 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            fprintf(ficgp,"\n");
  strcpy(plotcmd,GNUPLOTPROGRAM);          }
  strcat(plotcmd," ");        }
  strcat(plotcmd,optionfilegnuplot);      }
  system(plotcmd);     }
   
  /*#ifdef windows*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   while (z[0] != 'q') {       for(jk=1; jk <=m; jk++) {
     /* chdir(path); */         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");         if (ng==2)
     scanf("%s",z);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     if (z[0] == 'c') system("./imach");         else
     else if (z[0] == 'e') system(optionfilehtm);           fprintf(ficgp,"\nset title \"Probability\"\n");
     else if (z[0] == 'g') system(plotcmd);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     else if (z[0] == 'q') exit(0);         i=1;
   }         for(k2=1; k2<=nlstate; k2++) {
   /*#endif */           k3=i;
 }           for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.41.2.1  
changed lines
  Added in v.1.116


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