Diff for /imach/src/imach.c between versions 1.42 and 1.110

version 1.42, 2002/05/21 18:44:41 version 1.110, 2006/01/25 00:51:50
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.110  2006/01/25 00:51:50  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.109  2006/01/24 19:37:15  brouard
   first survey ("cross") where individuals from different ages are    (Module): Comments (lines starting with a #) are allowed in data.
   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    Revision 1.108  2006/01/19 18:05:42  lievre
   second wave of interviews ("longitudinal") which measure each change    Gnuplot problem appeared...
   (if any) in individual health status.  Health expectancies are    To be fixed
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.107  2006/01/19 16:20:37  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Test existence of gnuplot in imach path
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.106  2006/01/19 13:24:36  brouard
   conditional to be observed in state i at the first wave. Therefore    Some cleaning and links added in html output
   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 1.105  2006/01/05 20:23:19  lievre
   complex model than "constant and age", you should modify the program    *** empty log message ***
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.104  2005/09/30 16:11:43  lievre
   convergence.    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
   The advantage of this computer programme, compared to a simple    that the person is alive, then we can code his/her status as -2
   multinomial logistic model, is clear when the delay between waves is not    (instead of missing=-1 in earlier versions) and his/her
   identical for each individual. Also, if a individual missed an    contributions to the likelihood is 1 - Prob of dying from last
   intermediate interview, the information is lost, but taken into    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   account using an interpolation or extrapolation.      the healthy state at last known wave). Version is 0.98
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.103  2005/09/30 15:54:49  lievre
   conditional to the observed state i at age x. The delay 'h' can be    (Module): sump fixed, loop imx fixed, and simplifications.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.102  2004/09/15 17:31:30  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Add the possibility to read data file including tab characters.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.101  2004/09/15 10:38:38  brouard
   hPijx.    Fix on curr_time
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.100  2004/07/12 18:29:06  brouard
   of the life expectancies. It also computes the prevalence limits.    Add version for Mac OS X. Just define UNIX in Makefile
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.99  2004/06/05 08:57:40  brouard
            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 1.98  2004/05/16 15:05:56  brouard
   It is copyrighted identically to a GNU software product, ie programme and    New version 0.97 . First attempt to estimate force of mortality
   software can be distributed freely for non commercial use. Latest version    directly from the data i.e. without the need of knowing the health
   can be accessed at http://euroreves.ined.fr/imach .    state at each age, but using a Gompertz model: log u =a + b*age .
   **********************************************************************/    This is the basic analysis of mortality and should be done before any
      other analysis, in order to test if the mortality estimated from the
 #include <math.h>    cross-longitudinal survey is different from the mortality estimated
 #include <stdio.h>    from other sources like vital statistic data.
 #include <stdlib.h>  
 #include <unistd.h>    The same imach parameter file can be used but the option for mle should be -3.
   
 #define MAXLINE 256    Agnès, who wrote this part of the code, tried to keep most of the
 #define GNUPLOTPROGRAM "gnuplot"    former routines in order to include the new code within the former code.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    The output is very simple: only an estimate of the intercept and of
 /*#define DEBUG*/    the slope with 95% confident intervals.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Current limitations:
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    B) There is no computation of Life Expectancy nor Life Table.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.97  2004/02/20 13:25:42  lievre
 #define NINTERVMAX 8    Version 0.96d. Population forecasting command line is (temporarily)
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    suppressed.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.96  2003/07/15 15:38:55  brouard
 #define MAXN 20000    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define YEARM 12. /* Number of months per year */    rewritten within the same printf. Workaround: many printfs.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 int erreur; /* Error number */    matrix (cov(a12,c31) instead of numbers.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.94  2003/06/27 13:00:02  brouard
 int npar=NPARMAX;    Just cleaning
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.93  2003/06/25 16:33:55  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): On windows (cygwin) function asctime_r doesn't
 int popbased=0;    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.92  2003/06/25 16:30:45  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): On windows (cygwin) function asctime_r doesn't
 int mle, weightopt;    exist so I changed back to asctime which exists.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.91  2003/06/25 15:30:29  brouard
 double jmean; /* Mean space between 2 waves */    * imach.c (Repository): Duplicated warning errors corrected.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Repository): Elapsed time after each iteration is now output. It
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    helps to forecast when convergence will be reached. Elapsed time
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    is stamped in powell.  We created a new html file for the graphs
 FILE *ficgp,*ficresprob,*ficpop;    concerning matrix of covariance. It has extension -cov.htm.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.90  2003/06/24 12:34:15  brouard
  FILE  *ficresvij;    (Module): Some bugs corrected for windows. Also, when
   char fileresv[FILENAMELENGTH];    mle=-1 a template is output in file "or"mypar.txt with the design
  FILE  *ficresvpl;    of the covariance matrix to be input.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.89  2003/06/24 12:30:52  brouard
 #define NR_END 1    (Module): Some bugs corrected for windows. Also, when
 #define FREE_ARG char*    mle=-1 a template is output in file "or"mypar.txt with the design
 #define FTOL 1.0e-10    of the covariance matrix to be input.
   
 #define NRANSI    Revision 1.88  2003/06/23 17:54:56  brouard
 #define ITMAX 200    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
 #define TOL 2.0e-4    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.86  2003/06/17 20:04:08  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.85  2003/06/17 13:12:43  brouard
 #define TINY 1.0e-20    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 static double maxarg1,maxarg2;    prior to the death. In this case, dh was negative and likelihood
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    was wrong (infinity). We still send an "Error" but patch by
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    assuming that the date of death was just one stepm after the
      interview.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Repository): Because some people have very long ID (first column)
 #define rint(a) floor(a+0.5)    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 static double sqrarg;    truncation)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Repository): No more line truncation errors.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.84  2003/06/13 21:44:43  brouard
 int imx;    * imach.c (Repository): Replace "freqsummary" at a correct
 int stepm;    place. It differs from routine "prevalence" which may be called
 /* Stepm, step in month: minimum step interpolation*/    many times. Probs is memory consuming and must be used with
     parcimony.
 int estepm;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.83  2003/06/10 13:39:11  lievre
 int m,nb;    *** empty log message ***
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.82  2003/06/05 15:57:20  brouard
 double **pmmij, ***probs, ***mobaverage;    Add log in  imach.c and  fullversion number is now printed.
 double dateintmean=0;  
   */
 double *weight;  /*
 int **s; /* Status */     Interpolated Markov Chain
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Short summary of the programme:
     
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    This program computes Healthy Life Expectancies from
 double ftolhess; /* Tolerance for computing hessian */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 /**************** split *************************/    interviewed on their health status or degree of disability (in the
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    case of a health survey which is our main interest) -2- at least a
 {    second wave of interviews ("longitudinal") which measure each change
    char *s;                             /* pointer */    (if any) in individual health status.  Health expectancies are
    int  l1, l2;                         /* length counters */    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
    l1 = strlen( path );                 /* length of path */    Maximum Likelihood of the parameters involved in the model.  The
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    simplest model is the multinomial logistic model where pij is the
 #ifdef windows    probability to be observed in state j at the second wave
    s = strrchr( path, '\\' );           /* find last / */    conditional to be observed in state i at the first wave. Therefore
 #else    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    s = strrchr( path, '/' );            /* find last / */    'age' is age and 'sex' is a covariate. If you want to have a more
 #endif    complex model than "constant and age", you should modify the program
    if ( s == NULL ) {                   /* no directory, so use current */    where the markup *Covariates have to be included here again* invites
 #if     defined(__bsd__)                /* get current working directory */    you to do it.  More covariates you add, slower the
       extern char       *getwd( );    convergence.
   
       if ( getwd( dirc ) == NULL ) {    The advantage of this computer programme, compared to a simple
 #else    multinomial logistic model, is clear when the delay between waves is not
       extern char       *getcwd( );    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    account using an interpolation or extrapolation.  
 #endif  
          return( GLOCK_ERROR_GETCWD );    hPijx is the probability to be observed in state i at age x+h
       }    conditional to the observed state i at age x. The delay 'h' can be
       strcpy( name, path );             /* we've got it */    split into an exact number (nh*stepm) of unobserved intermediate
    } else {                             /* strip direcotry from path */    states. This elementary transition (by month, quarter,
       s++;                              /* after this, the filename */    semester or year) is modelled as a multinomial logistic.  The hPx
       l2 = strlen( s );                 /* length of filename */    matrix is simply the matrix product of nh*stepm elementary matrices
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    and the contribution of each individual to the likelihood is simply
       strcpy( name, s );                /* save file name */    hPijx.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Also this programme outputs the covariance matrix of the parameters but also
    }    of the life expectancies. It also computes the stable prevalence. 
    l1 = strlen( dirc );                 /* length of directory */    
 #ifdef windows    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }             Institut national d'études démographiques, Paris.
 #else    This software have been partly granted by Euro-REVES, a concerted action
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    from the European Union.
 #endif    It is copyrighted identically to a GNU software product, ie programme and
    s = strrchr( name, '.' );            /* find last / */    software can be distributed freely for non commercial use. Latest version
    s++;    can be accessed at http://euroreves.ined.fr/imach .
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    l2= strlen( s)+1;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    strncpy( finame, name, l1-l2);    
    finame[l1-l2]= 0;    **********************************************************************/
    return( 0 );                         /* we're done */  /*
 }    main
     read parameterfile
     read datafile
 /******************************************/    concatwav
     freqsummary
 void replace(char *s, char*t)    if (mle >= 1)
 {      mlikeli
   int i;    print results files
   int lg=20;    if mle==1 
   i=0;       computes hessian
   lg=strlen(t);    read end of parameter file: agemin, agemax, bage, fage, estepm
   for(i=0; i<= lg; i++) {        begin-prev-date,...
     (s[i] = t[i]);    open gnuplot file
     if (t[i]== '\\') s[i]='/';    open html file
   }    stable prevalence
 }     for age prevalim()
     h Pij x
 int nbocc(char *s, char occ)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   int i,j=0;    health expectancies
   int lg=20;    Variance-covariance of DFLE
   i=0;    prevalence()
   lg=strlen(s);     movingaverage()
   for(i=0; i<= lg; i++) {    varevsij() 
   if  (s[i] == occ ) j++;    if popbased==1 varevsij(,popbased)
   }    total life expectancies
   return j;    Variance of stable prevalence
 }   end
   */
 void cutv(char *u,char *v, char*t, char occ)  
 {  
   int i,lg,j,p=0;  
   i=0;   
   for(j=0; j<=strlen(t)-1; j++) {  #include <math.h>
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #include <stdio.h>
   }  #include <stdlib.h>
   #include <string.h>
   lg=strlen(t);  #include <unistd.h>
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  #include <limits.h>
   }  #include <sys/types.h>
      u[p]='\0';  #include <sys/stat.h>
   #include <errno.h>
    for(j=0; j<= lg; j++) {  extern int errno;
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 /********************** nrerror ********************/  
   /* #include <libintl.h> */
 void nrerror(char error_text[])  /* #define _(String) gettext (String) */
 {  
   fprintf(stderr,"ERREUR ...\n");  #define MAXLINE 256
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /*********************** vector *******************/  #define FILENAMELENGTH 132
 double *vector(int nl, int nh)  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   double *v;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   return v-nl+NR_END;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /************************ free vector ******************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 void free_vector(double*v, int nl, int nh)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 {  #define NCOVMAX 8 /* Maximum number of covariates */
   free((FREE_ARG)(v+nl-NR_END));  #define MAXN 20000
 }  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 /************************ivector *******************************/  #define AGEBASE 40
 int *ivector(long nl,long nh)  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 {  #ifdef UNIX
   int *v;  #define DIRSEPARATOR '/'
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define CHARSEPARATOR "/"
   if (!v) nrerror("allocation failure in ivector");  #define ODIRSEPARATOR '\\'
   return v-nl+NR_END;  #else
 }  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
 /******************free ivector **************************/  #define ODIRSEPARATOR '/'
 void free_ivector(int *v, long nl, long nh)  #endif
 {  
   free((FREE_ARG)(v+nl-NR_END));  /* $Id$ */
 }  /* $State$ */
   
 /******************* imatrix *******************************/  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
 int **imatrix(long nrl, long nrh, long ncl, long nch)  char fullversion[]="$Revision$ $Date$"; 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int **m;  int npar=NPARMAX;
    int nlstate=2; /* Number of live states */
   /* allocate pointers to rows */  int ndeath=1; /* Number of dead states */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   if (!m) nrerror("allocation failure 1 in matrix()");  int popbased=0;
   m += NR_END;  
   m -= nrl;  int *wav; /* Number of waves for this individuual 0 is possible */
    int maxwav; /* Maxim number of waves */
    int jmin, jmax; /* min, max spacing between 2 waves */
   /* allocate rows and set pointers to them */  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int gipmx, gsw; /* Global variables on the number of contributions 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");                     to the likelihood and the sum of weights (done by funcone)*/
   m[nrl] += NR_END;  int mle, weightopt;
   m[nrl] -= ncl;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
   /* return pointer to array of pointers to rows */  double jmean; /* Mean space between 2 waves */
   return m;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 /****************** free_imatrix *************************/  FILE *ficlog, *ficrespow;
 void free_imatrix(m,nrl,nrh,ncl,nch)  int globpr; /* Global variable for printing or not */
       int **m;  double fretone; /* Only one call to likelihood */
       long nch,ncl,nrh,nrl;  long ipmx; /* Number of contributions */
      /* free an int matrix allocated by imatrix() */  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG) (m+nrl-NR_END));  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /******************* matrix *******************************/  FILE *fichtm, *fichtmcov; /* Html File */
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  FILE  *ficresvij;
   double **m;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileresvpl[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char title[MAXLINE];
   m += NR_END;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m -= nrl;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char command[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int  outcmd=0;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char filelog[FILENAMELENGTH]; /* Log file */
   return m;  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   free((FREE_ARG)(m+nrl-NR_END));  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /******************* ma3x *******************************/  long time_value;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  extern long time();
 {  char strcurr[80], strfor[80];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  char *endptr;
   long lval;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NR_END 1
   m += NR_END;  #define FREE_ARG char*
   m -= nrl;  #define FTOL 1.0e-10
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define NRANSI 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define ITMAX 200 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #define TOL 2.0e-4 
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  #define GOLD 1.618034 
   m[nrl][ncl] -= nll;  #define GLIMIT 100.0 
   for (j=ncl+1; j<=nch; j++)  #define TINY 1.0e-20 
     m[nrl][j]=m[nrl][j-1]+nlay;  
    static double maxarg1,maxarg2;
   for (i=nrl+1; i<=nrh; i++) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     for (j=ncl+1; j<=nch; j++)    
       m[i][j]=m[i][j-1]+nlay;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   }  #define rint(a) floor(a+0.5)
   return m;  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /*************************free ma3x ************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int agegomp= AGEGOMP;
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int imx; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int stepm=1;
   free((FREE_ARG)(m+nrl-NR_END));  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /***************** f1dim *************************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 extern int ncom;  
 extern double *pcom,*xicom;  int m,nb;
 extern double (*nrfunc)(double []);  long *num;
    int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double f1dim(double x)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 {  double **pmmij, ***probs;
   int j;  double *ageexmed,*agecens;
   double f;  double dateintmean=0;
   double *xt;  
    double *weight;
   xt=vector(1,ncom);  int **s; /* Status */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double *agedc, **covar, idx;
   f=(*nrfunc)(xt);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free_vector(xt,1,ncom);  double *lsurv, *lpop, *tpop;
   return f;  
 }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int iter;  {
   double a,b,d,etemp;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double fu,fv,fw,fx;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double ftemp;    */ 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    char  *ss;                            /* pointer */
   double e=0.0;    int   l1, l2;                         /* length counters */
    
   a=(ax < cx ? ax : cx);    l1 = strlen(path );                   /* length of path */
   b=(ax > cx ? ax : cx);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   x=w=v=bx;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   fw=fv=fx=(*f)(x);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for (iter=1;iter<=ITMAX;iter++) {      strcpy( name, path );               /* we got the fullname name because no directory */
     xm=0.5*(a+b);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      /* get current working directory */
     printf(".");fflush(stdout);      /*    extern  char* getcwd ( char *buf , int len);*/
 #ifdef DEBUG      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     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);        return( GLOCK_ERROR_GETCWD );
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      }
 #endif      /* got dirc from getcwd*/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      printf(" DIRC = %s \n",dirc);
       *xmin=x;    } else {                              /* strip direcotry from path */
       return fx;      ss++;                               /* after this, the filename */
     }      l2 = strlen( ss );                  /* length of filename */
     ftemp=fu;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (fabs(e) > tol1) {      strcpy( name, ss );         /* save file name */
       r=(x-w)*(fx-fv);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       q=(x-v)*(fx-fw);      dirc[l1-l2] = 0;                    /* add zero */
       p=(x-v)*q-(x-w)*r;      printf(" DIRC2 = %s \n",dirc);
       q=2.0*(q-r);    }
       if (q > 0.0) p = -p;    /* We add a separator at the end of dirc if not exists */
       q=fabs(q);    l1 = strlen( dirc );                  /* length of directory */
       etemp=e;    if( dirc[l1-1] != DIRSEPARATOR ){
       e=d;      dirc[l1] =  DIRSEPARATOR;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      dirc[l1+1] = 0; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      printf(" DIRC3 = %s \n",dirc);
       else {    }
         d=p/q;    ss = strrchr( name, '.' );            /* find last / */
         u=x+d;    if (ss >0){
         if (u-a < tol2 || b-u < tol2)      ss++;
           d=SIGN(tol1,xm-x);      strcpy(ext,ss);                     /* save extension */
       }      l1= strlen( name);
     } else {      l2= strlen(ss)+1;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      strncpy( finame, name, l1-l2);
     }      finame[l1-l2]= 0;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    }
     fu=(*f)(u);  
     if (fu <= fx) {    return( 0 );                          /* we're done */
       if (u >= x) a=x; else b=x;  }
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  
         } else {  /******************************************/
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  void replace_back_to_slash(char *s, char*t)
             v=w;  {
             w=u;    int i;
             fv=fw;    int lg=0;
             fw=fu;    i=0;
           } else if (fu <= fv || v == x || v == w) {    lg=strlen(t);
             v=u;    for(i=0; i<= lg; i++) {
             fv=fu;      (s[i] = t[i]);
           }      if (t[i]== '\\') s[i]='/';
         }    }
   }  }
   nrerror("Too many iterations in brent");  
   *xmin=x;  int nbocc(char *s, char occ)
   return fx;  {
 }    int i,j=0;
     int lg=20;
 /****************** mnbrak ***********************/    i=0;
     lg=strlen(s);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    for(i=0; i<= lg; i++) {
             double (*func)(double))    if  (s[i] == occ ) j++;
 {    }
   double ulim,u,r,q, dum;    return j;
   double fu;  }
    
   *fa=(*func)(*ax);  void cutv(char *u,char *v, char*t, char occ)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     SHFT(dum,*ax,*bx,dum)       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       SHFT(dum,*fb,*fa,dum)       gives u="abcedf" and v="ghi2j" */
       }    int i,lg,j,p=0;
   *cx=(*bx)+GOLD*(*bx-*ax);    i=0;
   *fc=(*func)(*cx);    for(j=0; j<=strlen(t)-1; j++) {
   while (*fb > *fc) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     r=(*bx-*ax)*(*fb-*fc);    }
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    lg=strlen(t);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    for(j=0; j<p; j++) {
     ulim=(*bx)+GLIMIT*(*cx-*bx);      (u[j] = t[j]);
     if ((*bx-u)*(u-*cx) > 0.0) {    }
       fu=(*func)(u);       u[p]='\0';
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);     for(j=0; j<= lg; j++) {
       if (fu < *fc) {      if (j>=(p+1))(v[j-p-1] = t[j]);
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    }
           SHFT(*fb,*fc,fu,(*func)(u))  }
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /********************** nrerror ********************/
       u=ulim;  
       fu=(*func)(u);  void nrerror(char error_text[])
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    fprintf(stderr,"ERREUR ...\n");
       fu=(*func)(u);    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     SHFT(*ax,*bx,*cx,u)  }
       SHFT(*fa,*fb,*fc,fu)  /*********************** vector *******************/
       }  double *vector(int nl, int nh)
 }  {
     double *v;
 /*************** linmin ************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 int ncom;    return v-nl+NR_END;
 double *pcom,*xicom;  }
 double (*nrfunc)(double []);  
    /************************ free vector ******************/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  void free_vector(double*v, int nl, int nh)
 {  {
   double brent(double ax, double bx, double cx,    free((FREE_ARG)(v+nl-NR_END));
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /************************ivector *******************************/
               double *fc, double (*func)(double));  int *ivector(long nl,long nh)
   int j;  {
   double xx,xmin,bx,ax;    int *v;
   double fx,fb,fa;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
   ncom=n;    return v-nl+NR_END;
   pcom=vector(1,n);  }
   xicom=vector(1,n);  
   nrfunc=func;  /******************free ivector **************************/
   for (j=1;j<=n;j++) {  void free_ivector(int *v, long nl, long nh)
     pcom[j]=p[j];  {
     xicom[j]=xi[j];    free((FREE_ARG)(v+nl-NR_END));
   }  }
   ax=0.0;  
   xx=1.0;  /************************lvector *******************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  long *lvector(long nl,long nh)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  {
 #ifdef DEBUG    long *v;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #endif    if (!v) nrerror("allocation failure in ivector");
   for (j=1;j<=n;j++) {    return v-nl+NR_END;
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  /******************free lvector **************************/
   free_vector(xicom,1,n);  void free_lvector(long *v, long nl, long nh)
   free_vector(pcom,1,n);  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /******************* imatrix *******************************/
             double (*func)(double []))  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   void linmin(double p[], double xi[], int n, double *fret,  { 
               double (*func)(double []));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   int i,ibig,j;    int **m; 
   double del,t,*pt,*ptt,*xit;    
   double fp,fptt;    /* allocate pointers to rows */ 
   double *xits;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   pt=vector(1,n);    if (!m) nrerror("allocation failure 1 in matrix()"); 
   ptt=vector(1,n);    m += NR_END; 
   xit=vector(1,n);    m -= nrl; 
   xits=vector(1,n);    
   *fret=(*func)(p);    
   for (j=1;j<=n;j++) pt[j]=p[j];    /* allocate rows and set pointers to them */ 
   for (*iter=1;;++(*iter)) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     fp=(*fret);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     ibig=0;    m[nrl] += NR_END; 
     del=0.0;    m[nrl] -= ncl; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    
     for (i=1;i<=n;i++)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       printf(" %d %.12f",i, p[i]);    
     printf("\n");    /* return pointer to array of pointers to rows */ 
     for (i=1;i<=n;i++) {    return m; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  } 
       fptt=(*fret);  
 #ifdef DEBUG  /****************** free_imatrix *************************/
       printf("fret=%lf \n",*fret);  void free_imatrix(m,nrl,nrh,ncl,nch)
 #endif        int **m;
       printf("%d",i);fflush(stdout);        long nch,ncl,nrh,nrl; 
       linmin(p,xit,n,fret,func);       /* free an int matrix allocated by imatrix() */ 
       if (fabs(fptt-(*fret)) > del) {  { 
         del=fabs(fptt-(*fret));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         ibig=i;    free((FREE_ARG) (m+nrl-NR_END)); 
       }  } 
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  /******************* matrix *******************************/
       for (j=1;j<=n;j++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       }    double **m;
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       printf("\n");    if (!m) nrerror("allocation failure 1 in matrix()");
 #endif    m += NR_END;
     }    m -= nrl;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       int k[2],l;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       k[0]=1;    m[nrl] += NR_END;
       k[1]=-1;    m[nrl] -= ncl;
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         printf(" %.12e",p[j]);    return m;
       printf("\n");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       for(l=0;l<=1;l++) {     */
         for (j=1;j<=n;j++) {  }
           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]);  /*************************free matrix ************************/
         }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  {
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #endif    free((FREE_ARG)(m+nrl-NR_END));
   }
   
       free_vector(xit,1,n);  /******************* ma3x *******************************/
       free_vector(xits,1,n);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       return;    double ***m;
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=1;j<=n;j++) {    if (!m) nrerror("allocation failure 1 in matrix()");
       ptt[j]=2.0*p[j]-pt[j];    m += NR_END;
       xit[j]=p[j]-pt[j];    m -= nrl;
       pt[j]=p[j];  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     fptt=(*func)(ptt);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     if (fptt < fp) {    m[nrl] += NR_END;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m[nrl] -= ncl;
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
           xi[j][n]=xit[j];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         }    m[nrl][ncl] += NR_END;
 #ifdef DEBUG    m[nrl][ncl] -= nll;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    for (j=ncl+1; j<=nch; j++) 
         for(j=1;j<=n;j++)      m[nrl][j]=m[nrl][j-1]+nlay;
           printf(" %.12e",xit[j]);    
         printf("\n");    for (i=nrl+1; i<=nrh; i++) {
 #endif      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
   }    }
 }    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 /**** Prevalence limit ****************/             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  }
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /*************************free ma3x ************************/
      matrix by transitions matrix until convergence is reached */  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
   int i, ii,j,k;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double min, max, maxmin, maxmax,sumnew=0.;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double **matprod2();    free((FREE_ARG)(m+nrl-NR_END));
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
   for (ii=1;ii<=nlstate+ndeath;ii++)  {
     for (j=1;j<=nlstate+ndeath;j++){    /* Caution optionfilefiname is hidden */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
    cov[1]=1.;    return tmpout;
    }
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /*************** function subdirf2 ***********/
     newm=savm;  char *subdirf2(char fileres[], char *preop)
     /* Covariates have to be included here again */  {
      cov[2]=agefin;    
      /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovn;k++) {    strcpy(tmpout,optionfilefiname);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    strcat(tmpout,"/");
         /*      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]]);*/    strcat(tmpout,preop);
       }    strcat(tmpout,fileres);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    return tmpout;
       for (k=1; k<=cptcovprod;k++)  }
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /*************** function subdirf3 ***********/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  char *subdirf3(char fileres[], char *preop, char *preop2)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  {
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    
     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,"/");
     oldm=newm;    strcat(tmpout,preop);
     maxmax=0.;    strcat(tmpout,preop2);
     for(j=1;j<=nlstate;j++){    strcat(tmpout,fileres);
       min=1.;    return tmpout;
       max=0.;  }
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /***************** f1dim *************************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  extern int ncom; 
         prlim[i][j]= newm[i][j]/(1-sumnew);  extern double *pcom,*xicom;
         max=FMAX(max,prlim[i][j]);  extern double (*nrfunc)(double []); 
         min=FMIN(min,prlim[i][j]);   
       }  double f1dim(double x) 
       maxmin=max-min;  { 
       maxmax=FMAX(maxmax,maxmin);    int j; 
     }    double f;
     if(maxmax < ftolpl){    double *xt; 
       return prlim;   
     }    xt=vector(1,ncom); 
   }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 }    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
 /*************** transition probabilities ***************/    return f; 
   } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /*****************brent *************************/
   double s1, s2;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   /*double t34;*/  { 
   int i,j,j1, nc, ii, jj;    int iter; 
     double a,b,d,etemp;
     for(i=1; i<= nlstate; i++){    double fu,fv,fw,fx;
     for(j=1; j<i;j++){    double ftemp;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         /*s2 += param[i][j][nc]*cov[nc];*/    double e=0.0; 
         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);*/    a=(ax < cx ? ax : cx); 
       }    b=(ax > cx ? ax : cx); 
       ps[i][j]=s2;    x=w=v=bx; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
     for(j=i+1; j<=nlstate+ndeath;j++){      xm=0.5*(a+b); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
       ps[i][j]=s2;  #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);
     /*ps[3][2]=1;*/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
   for(i=1; i<= nlstate; i++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
      s1=0;        *xmin=x; 
     for(j=1; j<i; j++)        return fx; 
       s1+=exp(ps[i][j]);      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      ftemp=fu;
       s1+=exp(ps[i][j]);      if (fabs(e) > tol1) { 
     ps[i][i]=1./(s1+1.);        r=(x-w)*(fx-fv); 
     for(j=1; j<i; j++)        q=(x-v)*(fx-fw); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        p=(x-v)*q-(x-w)*r; 
     for(j=i+1; j<=nlstate+ndeath; j++)        q=2.0*(q-r); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        if (q > 0.0) p = -p; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        q=fabs(q); 
   } /* end i */        etemp=e; 
         e=d; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for(jj=1; jj<= nlstate+ndeath; jj++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       ps[ii][jj]=0;        else { 
       ps[ii][ii]=1;          d=p/q; 
     }          u=x+d; 
   }          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
         } 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      } else { 
     for(jj=1; jj<= nlstate+ndeath; jj++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      printf("%lf ",ps[ii][jj]);      } 
    }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     printf("\n ");      fu=(*f)(u); 
     }      if (fu <= fx) { 
     printf("\n ");printf("%lf ",cov[2]);*/        if (u >= x) a=x; else b=x; 
 /*        SHFT(v,w,x,u) 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          SHFT(fv,fw,fx,fu) 
   goto end;*/          } else { 
     return ps;            if (u < x) a=u; else b=u; 
 }            if (fu <= fw || w == x) { 
               v=w; 
 /**************** Product of 2 matrices ******************/              w=u; 
               fv=fw; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)              fw=fu; 
 {            } else if (fu <= fv || v == x || v == w) { 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times              v=u; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */              fv=fu; 
   /* in, b, out are matrice of pointers which should have been initialized            } 
      before: only the contents of out is modified. The function returns          } 
      a pointer to pointers identical to out */    } 
   long i, j, k;    nrerror("Too many iterations in brent"); 
   for(i=nrl; i<= nrh; i++)    *xmin=x; 
     for(k=ncolol; k<=ncoloh; k++)    return fx; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  } 
         out[i][k] +=in[i][j]*b[j][k];  
   /****************** mnbrak ***********************/
   return out;  
 }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   { 
 /************* Higher Matrix Product ***************/    double ulim,u,r,q, dum;
     double fu; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )   
 {    *fa=(*func)(*ax); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    *fb=(*func)(*bx); 
      duration (i.e. until    if (*fb > *fa) { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      SHFT(dum,*ax,*bx,dum) 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        SHFT(dum,*fb,*fa,dum) 
      (typically every 2 years instead of every month which is too big).        } 
      Model is determined by parameters x and covariates have to be    *cx=(*bx)+GOLD*(*bx-*ax); 
      included manually here.    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
      */      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   int i, j, d, h, k;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double **out, cov[NCOVMAX];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double **newm;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
   /* Hstepm could be zero and should return the unit matrix */        fu=(*func)(u); 
   for (i=1;i<=nlstate+ndeath;i++)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     for (j=1;j<=nlstate+ndeath;j++){        fu=(*func)(u); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        if (fu < *fc) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }            SHFT(*fb,*fc,fu,(*func)(u)) 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */            } 
   for(h=1; h <=nhstepm; h++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for(d=1; d <=hstepm; d++){        u=ulim; 
       newm=savm;        fu=(*func)(u); 
       /* Covariates have to be included here again */      } else { 
       cov[1]=1.;        u=(*cx)+GOLD*(*cx-*bx); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        fu=(*func)(u); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      } 
       for (k=1; k<=cptcovage;k++)      SHFT(*ax,*bx,*cx,u) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        SHFT(*fa,*fb,*fc,fu) 
       for (k=1; k<=cptcovprod;k++)        } 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  } 
   
   /*************** linmin ************************/
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  int ncom; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  double *pcom,*xicom;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  double (*nrfunc)(double []); 
       savm=oldm;   
       oldm=newm;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     }  { 
     for(i=1; i<=nlstate+ndeath; i++)    double brent(double ax, double bx, double cx, 
       for(j=1;j<=nlstate+ndeath;j++) {                 double (*f)(double), double tol, double *xmin); 
         po[i][j][h]=newm[i][j];    double f1dim(double x); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
          */                double *fc, double (*func)(double)); 
       }    int j; 
   } /* end h */    double xx,xmin,bx,ax; 
   return po;    double fx,fb,fa;
 }   
     ncom=n; 
     pcom=vector(1,n); 
 /*************** log-likelihood *************/    xicom=vector(1,n); 
 double func( double *x)    nrfunc=func; 
 {    for (j=1;j<=n;j++) { 
   int i, ii, j, k, mi, d, kk;      pcom[j]=p[j]; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      xicom[j]=xi[j]; 
   double **out;    } 
   double sw; /* Sum of weights */    ax=0.0; 
   double lli; /* Individual log likelihood */    xx=1.0; 
   long ipmx;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   /*extern weight */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   /* We are differentiating ll according to initial status */  #ifdef DEBUG
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*for(i=1;i<imx;i++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf(" %d\n",s[4][i]);  #endif
   */    for (j=1;j<=n;j++) { 
   cov[1]=1.;      xi[j] *= xmin; 
       p[j] += xi[j]; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    } 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    free_vector(xicom,1,n); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    free_vector(pcom,1,n); 
     for(mi=1; mi<= wav[i]-1; mi++){  } 
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char *asc_diff_time(long time_sec, char ascdiff[])
       for(d=0; d<dh[mi][i]; d++){  {
         newm=savm;    long sec_left, days, hours, minutes;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    days = (time_sec) / (60*60*24);
         for (kk=1; kk<=cptcovage;kk++) {    sec_left = (time_sec) % (60*60*24);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    hours = (sec_left) / (60*60) ;
         }    sec_left = (sec_left) %(60*60);
            minutes = (sec_left) /60;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    sec_left = (sec_left) % (60);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         savm=oldm;    return ascdiff;
         oldm=newm;  }
          
          /*************** powell ************************/
       } /* end mult */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                    double (*func)(double [])) 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    void linmin(double p[], double xi[], int n, double *fret, 
       ipmx +=1;                double (*func)(double [])); 
       sw += weight[i];    int i,ibig,j; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double del,t,*pt,*ptt,*xit;
     } /* end of wave */    double fp,fptt;
   } /* end of individual */    double *xits;
     int niterf, itmp;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    pt=vector(1,n); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    ptt=vector(1,n); 
   return -l;    xit=vector(1,n); 
 }    xits=vector(1,n); 
     *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
 /*********** Maximum Likelihood Estimation ***************/    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      ibig=0; 
 {      del=0.0; 
   int i,j, iter;      last_time=curr_time;
   double **xi,*delti;      (void) gettimeofday(&curr_time,&tzp);
   double fret;      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);
   xi=matrix(1,npar,1,npar);      /*    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);
   for (i=1;i<=npar;i++)      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     for (j=1;j<=npar;j++)      */
       xi[i][j]=(i==j ? 1.0 : 0.0);     for (i=1;i<=n;i++) {
   printf("Powell\n");        printf(" %d %.12f",i, p[i]);
   powell(p,xi,npar,ftol,&iter,&fret,func);        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      printf("\n");
       fprintf(ficlog,"\n");
 }      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
 /**** Computes Hessian and covariance matrix ***/        tm = *localtime(&curr_time.tv_sec);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        strcpy(strcurr,asctime(&tm));
 {  /*       asctime_r(&tm,strcurr); */
   double  **a,**y,*x,pd;        forecast_time=curr_time; 
   double **hess;        itmp = strlen(strcurr);
   int i, j,jk;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   int *indx;          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);
   double hessii(double p[], double delta, int theta, double delti[]);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double hessij(double p[], double delti[], int i, int j);        for(niterf=10;niterf<=30;niterf+=10){
   void lubksb(double **a, int npar, int *indx, double b[]) ;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   void ludcmp(double **a, int npar, int *indx, double *d) ;          tmf = *localtime(&forecast_time.tv_sec);
   /*      asctime_r(&tmf,strfor); */
   hess=matrix(1,npar,1,npar);          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
   printf("\nCalculation of the hessian matrix. Wait...\n");          if(strfor[itmp-1]=='\n')
   for (i=1;i<=npar;i++){          strfor[itmp-1]='\0';
     printf("%d",i);fflush(stdout);          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);
     hess[i][i]=hessii(p,ftolhess,i,delti);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     /*printf(" %f ",p[i]);*/        }
     /*printf(" %lf ",hess[i][i]);*/      }
   }      for (i=1;i<=n;i++) { 
          for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   for (i=1;i<=npar;i++) {        fptt=(*fret); 
     for (j=1;j<=npar;j++)  {  #ifdef DEBUG
       if (j>i) {        printf("fret=%lf \n",*fret);
         printf(".%d%d",i,j);fflush(stdout);        fprintf(ficlog,"fret=%lf \n",*fret);
         hess[i][j]=hessij(p,delti,i,j);  #endif
         hess[j][i]=hess[i][j];            printf("%d",i);fflush(stdout);
         /*printf(" %lf ",hess[i][j]);*/        fprintf(ficlog,"%d",i);fflush(ficlog);
       }        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
   printf("\n");          ibig=i; 
         } 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  #ifdef DEBUG
          printf("%d %.12e",i,(*fret));
   a=matrix(1,npar,1,npar);        fprintf(ficlog,"%d %.12e",i,(*fret));
   y=matrix(1,npar,1,npar);        for (j=1;j<=n;j++) {
   x=vector(1,npar);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   indx=ivector(1,npar);          printf(" x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=npar;i++)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   for (j=1;j<=npar;j++) {          fprintf(ficlog," p=%.12e",p[j]);
     for (i=1;i<=npar;i++) x[i]=0;        }
     x[j]=1;        printf("\n");
     lubksb(a,npar,indx,x);        fprintf(ficlog,"\n");
     for (i=1;i<=npar;i++){  #endif
       matcov[i][j]=x[i];      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   }  #ifdef DEBUG
         int k[2],l;
   printf("\n#Hessian matrix#\n");        k[0]=1;
   for (i=1;i<=npar;i++) {        k[1]=-1;
     for (j=1;j<=npar;j++) {        printf("Max: %.12e",(*func)(p));
       printf("%.3e ",hess[i][j]);        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
     printf("\n");          printf(" %.12e",p[j]);
   }          fprintf(ficlog," %.12e",p[j]);
         }
   /* Recompute Inverse */        printf("\n");
   for (i=1;i<=npar;i++)        fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        for(l=0;l<=1;l++) {
   ludcmp(a,npar,indx,&pd);          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   /*  printf("\n#Hessian matrix recomputed#\n");            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (j=1;j<=npar;j++) {          }
     for (i=1;i<=npar;i++) x[i]=0;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     x[j]=1;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     lubksb(a,npar,indx,x);        }
     for (i=1;i<=npar;i++){  #endif
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  
     }        free_vector(xit,1,n); 
     printf("\n");        free_vector(xits,1,n); 
   }        free_vector(ptt,1,n); 
   */        free_vector(pt,1,n); 
         return; 
   free_matrix(a,1,npar,1,npar);      } 
   free_matrix(y,1,npar,1,npar);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   free_vector(x,1,npar);      for (j=1;j<=n;j++) { 
   free_ivector(indx,1,npar);        ptt[j]=2.0*p[j]-pt[j]; 
   free_matrix(hess,1,npar,1,npar);        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
       } 
 }      fptt=(*func)(ptt); 
       if (fptt < fp) { 
 /*************** hessian matrix ****************/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 double hessii( double x[], double delta, int theta, double delti[])        if (t < 0.0) { 
 {          linmin(p,xit,n,fret,func); 
   int i;          for (j=1;j<=n;j++) { 
   int l=1, lmax=20;            xi[j][ibig]=xi[j][n]; 
   double k1,k2;            xi[j][n]=xit[j]; 
   double p2[NPARMAX+1];          }
   double res;  #ifdef DEBUG
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double fx;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int k=0,kmax=10;          for(j=1;j<=n;j++){
   double l1;            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   fx=func(x);          }
   for (i=1;i<=npar;i++) p2[i]=x[i];          printf("\n");
   for(l=0 ; l <=lmax; l++){          fprintf(ficlog,"\n");
     l1=pow(10,l);  #endif
     delts=delt;        }
     for(k=1 ; k <kmax; k=k+1){      } 
       delt = delta*(l1*k);    } 
       p2[theta]=x[theta] +delt;  } 
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  /**** Prevalence limit (stable prevalence)  ****************/
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  {
          /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 #ifdef DEBUG       matrix by transitions matrix until convergence is reached */
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif    int i, ii,j,k;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double min, max, maxmin, maxmax,sumnew=0.;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    double **matprod2();
         k=kmax;    double **out, cov[NCOVMAX], **pmij();
       }    double **newm;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    double agefin, delaymax=50 ; /* Max number of years to converge */
         k=kmax; l=lmax*10.;  
       }    for (ii=1;ii<=nlstate+ndeath;ii++)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (j=1;j<=nlstate+ndeath;j++){
         delts=delt;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }      }
     }  
   }     cov[1]=1.;
   delti[theta]=delts;   
   return res;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
 double hessij( double x[], double delti[], int thetai,int thetaj)       cov[2]=agefin;
 {    
   int i;        for (k=1; k<=cptcovn;k++) {
   int l=1, l1, lmax=20;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double k1,k2,k3,k4,res,fx;          /*      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]]);*/
   double p2[NPARMAX+1];        }
   int k;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   fx=func(x);          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<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     p2[thetai]=x[thetai]+delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     k1=func(p2)-fx;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
    
     p2[thetai]=x[thetai]+delti[thetai]/k;      savm=oldm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      oldm=newm;
     k2=func(p2)-fx;      maxmax=0.;
        for(j=1;j<=nlstate;j++){
     p2[thetai]=x[thetai]-delti[thetai]/k;        min=1.;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        max=0.;
     k3=func(p2)-fx;        for(i=1; i<=nlstate; i++) {
            sumnew=0;
     p2[thetai]=x[thetai]-delti[thetai]/k;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          prlim[i][j]= newm[i][j]/(1-sumnew);
     k4=func(p2)-fx;          max=FMAX(max,prlim[i][j]);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          min=FMIN(min,prlim[i][j]);
 #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);        maxmin=max-min;
 #endif        maxmax=FMAX(maxmax,maxmin);
   }      }
   return res;      if(maxmax < ftolpl){
 }        return prlim;
       }
 /************** Inverse of matrix **************/    }
 void ludcmp(double **a, int n, int *indx, double *d)  }
 {  
   int i,imax,j,k;  /*************** transition probabilities ***************/ 
   double big,dum,sum,temp;  
   double *vv;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    {
   vv=vector(1,n);    double s1, s2;
   *d=1.0;    /*double t34;*/
   for (i=1;i<=n;i++) {    int i,j,j1, nc, ii, jj;
     big=0.0;  
     for (j=1;j<=n;j++)      for(i=1; i<= nlstate; i++){
       if ((temp=fabs(a[i][j])) > big) big=temp;        for(j=1; j<i;j++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     vv[i]=1.0/big;            /*s2 += param[i][j][nc]*cov[nc];*/
   }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for (j=1;j<=n;j++) {  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     for (i=1;i<j;i++) {          }
       sum=a[i][j];          ps[i][j]=s2;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       a[i][j]=sum;        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
     big=0.0;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for (i=j;i<=n;i++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       sum=a[i][j];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       for (k=1;k<j;k++)          }
         sum -= a[i][k]*a[k][j];          ps[i][j]=s2;
       a[i][j]=sum;        }
       if ( (dum=vv[i]*fabs(sum)) >= big) {      }
         big=dum;      /*ps[3][2]=1;*/
         imax=i;      
       }      for(i=1; i<= nlstate; i++){
     }        s1=0;
     if (j != imax) {        for(j=1; j<i; j++)
       for (k=1;k<=n;k++) {          s1+=exp(ps[i][j]);
         dum=a[imax][k];        for(j=i+1; j<=nlstate+ndeath; j++)
         a[imax][k]=a[j][k];          s1+=exp(ps[i][j]);
         a[j][k]=dum;        ps[i][i]=1./(s1+1.);
       }        for(j=1; j<i; j++)
       *d = -(*d);          ps[i][j]= exp(ps[i][j])*ps[i][i];
       vv[imax]=vv[j];        for(j=i+1; j<=nlstate+ndeath; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     indx[j]=imax;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     if (a[j][j] == 0.0) a[j][j]=TINY;      } /* end i */
     if (j != n) {      
       dum=1.0/(a[j][j]);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(jj=1; jj<= nlstate+ndeath; jj++){
     }          ps[ii][jj]=0;
   }          ps[ii][ii]=1;
   free_vector(vv,1,n);  /* Doesn't work */        }
 ;      }
 }      
   
 void lubksb(double **a, int n, int *indx, double b[])  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   int i,ii=0,ip,j;  /*         printf("ddd %lf ",ps[ii][jj]); */
   double sum;  /*       } */
    /*       printf("\n "); */
   for (i=1;i<=n;i++) {  /*        } */
     ip=indx[i];  /*        printf("\n ");printf("%lf ",cov[2]); */
     sum=b[ip];         /*
     b[ip]=b[i];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     if (ii)        goto end;*/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      return ps;
     else if (sum) ii=i;  }
     b[i]=sum;  
   }  /**************** Product of 2 matrices ******************/
   for (i=n;i>=1;i--) {  
     sum=b[i];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  {
     b[i]=sum/a[i][i];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 }    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
 /************ Frequencies ********************/       a pointer to pointers identical to out */
 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)    long i, j, k;
 {  /* Some frequencies */    for(i=nrl; i<= nrh; i++)
        for(k=ncolol; k<=ncoloh; k++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double ***freq; /* Frequencies */          out[i][k] +=in[i][j]*b[j][k];
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;    return out;
   FILE *ficresp;  }
   char fileresp[FILENAMELENGTH];  
    
   pp=vector(1,nlstate);  /************* Higher Matrix Product ***************/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   strcat(fileresp,fileres);  {
   if((ficresp=fopen(fileresp,"w"))==NULL) {    /* Computes the transition matrix starting at age 'age' over 
     printf("Problem with prevalence resultfile: %s\n", fileresp);       'nhstepm*hstepm*stepm' months (i.e. until
     exit(0);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   }       nhstepm*hstepm matrices. 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   j1=0;       (typically every 2 years instead of every month which is too big 
         for the memory).
   j=cptcoveff;       Model is determined by parameters x and covariates have to be 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       included manually here. 
    
   for(k1=1; k1<=j;k1++){       */
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;    int i, j, d, h, k;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double **out, cov[NCOVMAX];
         scanf("%d", i);*/    double **newm;
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      /* Hstepm could be zero and should return the unit matrix */
           for(m=agemin; m <= agemax+3; m++)    for (i=1;i<=nlstate+ndeath;i++)
             freq[i][jk][m]=0;      for (j=1;j<=nlstate+ndeath;j++){
              oldm[i][j]=(i==j ? 1.0 : 0.0);
       dateintsum=0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       k2cpt=0;      }
       for (i=1; i<=imx; i++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         bool=1;    for(h=1; h <=nhstepm; h++){
         if  (cptcovn>0) {      for(d=1; d <=hstepm; d++){
           for (z1=1; z1<=cptcoveff; z1++)        newm=savm;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        /* Covariates have to be included here again */
               bool=0;        cov[1]=1.;
         }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         if (bool==1) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           for(m=firstpass; m<=lastpass; m++){        for (k=1; k<=cptcovage;k++)
             k2=anint[m][i]+(mint[m][i]/12.);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (k=1; k<=cptcovprod;k++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
               }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                                   pmij(pmmij,cov,ncovmodel,x,nlstate));
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        savm=oldm;
                 dateintsum=dateintsum+k2;        oldm=newm;
                 k2cpt++;      }
               }      for(i=1; i<=nlstate+ndeath; i++)
             }        for(j=1;j<=nlstate+ndeath;j++) {
           }          po[i][j][h]=newm[i][j];
         }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       }           */
                }
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    } /* end h */
     return po;
       if  (cptcovn>0) {  }
         fprintf(ficresp, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresp, "**********\n#");  /*************** log-likelihood *************/
       }  double func( double *x)
       for(i=1; i<=nlstate;i++)  {
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    int i, ii, j, k, mi, d, kk;
       fprintf(ficresp, "\n");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
          double **out;
       for(i=(int)agemin; i <= (int)agemax+3; i++){    double sw; /* Sum of weights */
         if(i==(int)agemax+3)    double lli; /* Individual log likelihood */
           printf("Total");    int s1, s2;
         else    double bbh, survp;
           printf("Age %d", i);    long ipmx;
         for(jk=1; jk <=nlstate ; jk++){    /*extern weight */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /* We are differentiating ll according to initial status */
             pp[jk] += freq[jk][m][i];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         }    /*for(i=1;i<imx;i++) 
         for(jk=1; jk <=nlstate ; jk++){      printf(" %d\n",s[4][i]);
           for(m=-1, pos=0; m <=0 ; m++)    */
             pos += freq[jk][m][i];    cov[1]=1.;
           if(pp[jk]>=1.e-10)  
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for(k=1; k<=nlstate; k++) ll[k]=0.;
           else  
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    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 ; jk++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             pp[jk] += freq[jk][m][i];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1,pos=0; jk <=nlstate ; jk++)            }
           pos += pp[jk];          for(d=0; d<dh[mi][i]; d++){
         for(jk=1; jk <=nlstate ; jk++){            newm=savm;
           if(pos>=1.e-5)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            for (kk=1; kk<=cptcovage;kk++) {
           else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            }
           if( i <= (int) agemax){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             if(pos>=1.e-5){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            savm=oldm;
               probs[i][jk][j1]= pp[jk]/pos;            oldm=newm;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          } /* end mult */
             }        
             else          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          /* But now since version 0.9 we anticipate for bias at large stepm.
           }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
                   * the nearest (and in case of equal distance, to the lowest) interval but now
         for(jk=-1; jk <=nlstate+ndeath; jk++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           for(m=-1; m <=nlstate+ndeath; m++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);           * probability in order to take into account the bias as a fraction of the way
         if(i <= (int) agemax)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           fprintf(ficresp,"\n");           * -stepm/2 to stepm/2 .
         printf("\n");           * 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. 
     }           */
   }          s1=s[mw[mi][i]][i];
   dateintmean=dateintsum/k2cpt;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   fclose(ficresp);          /* bias bh is positive if real duration
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * is higher than the multiple of stepm and negative otherwise.
   free_vector(pp,1,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]));*/
   /* End of Freq */          if( s2 > nlstate){ 
 }            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
 /************ Prevalence ********************/               die between last step unit time and current  step unit time, 
 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)               which is also equal to probability to die before dh 
 {  /* Some frequencies */               minus probability to die before dh-stepm . 
                 In version up to 0.92 likelihood was computed
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          as if date of death was unknown. Death was treated as any other
   double ***freq; /* Frequencies */          health state: the date of the interview describes the actual state
   double *pp;          and not the date of a change in health state. The former idea was
   double pos, k2;          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
   pp=vector(1,nlstate);          introduced the exact date of death then we should have modified
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          the contribution of an exact death to the likelihood. This new
            contribution is smaller and very dependent of the step unit
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          stepm. It is no more the probability to die between last interview
   j1=0;          and month of death but the probability to survive from last
            interview up to one month before death multiplied by the
   j=cptcoveff;          probability to die within a month. Thanks to Chris
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          Jackson for correcting this bug.  Former versions increased
            mortality artificially. The bad side is that we add another loop
   for(k1=1; k1<=j;k1++){          which slows down the processing. The difference can be up to 10%
     for(i1=1; i1<=ncodemax[k1];i1++){          lower mortality.
       j1++;            */
                  lli=log(out[s1][s2] - savm[s1][s2]);
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)          } else if  (s2==-2) {
             freq[i][jk][m]=0;            for (j=1,survp=0. ; j<=nlstate; j++) 
                    survp += out[s1][j];
       for (i=1; i<=imx; i++) {            lli= survp;
         bool=1;          }
         if  (cptcovn>0) {          
           for (z1=1; z1<=cptcoveff; z1++)          else if  (s2==-4) {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            for (j=3,survp=0. ; j<=nlstate; j++) 
               bool=0;              survp += out[s1][j];
         }            lli= survp;
         if (bool==1) {          }
           for(m=firstpass; m<=lastpass; m++){          
             k2=anint[m][i]+(mint[m][i]/12.);          else if  (s2==-5) {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (j=1,survp=0. ; j<=2; j++) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;              survp += out[s1][j];
               if(agev[m][i]==1) agev[m][i]=agemax+2;            lli= survp;
               if (m<lastpass) {          }
                 if (calagedate>0)  
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  
                 else          else{
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
               }          } 
             }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           }          /*if(lli ==000.0)*/
         }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       }          ipmx +=1;
       for(i=(int)agemin; i <= (int)agemax+3; i++){          sw += weight[i];
         for(jk=1; jk <=nlstate ; jk++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        } /* end of wave */
             pp[jk] += freq[jk][m][i];      } /* end of individual */
         }    }  else if(mle==2){
         for(jk=1; jk <=nlstate ; jk++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(m=-1, pos=0; m <=0 ; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             pos += freq[jk][m][i];        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
                    for (j=1;j<=nlstate+ndeath;j++){
         for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             pp[jk] += freq[jk][m][i];            }
         }          for(d=0; d<=dh[mi][i]; d++){
                    newm=savm;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
         for(jk=1; jk <=nlstate ; jk++){                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if( i <= (int) agemax){            }
             if(pos>=1.e-5){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               probs[i][jk][j1]= pp[jk]/pos;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             }            savm=oldm;
           }            oldm=newm;
         }          } /* end mult */
                
       }          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            ipmx +=1;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          sw += weight[i];
   free_vector(pp,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
 }  /* End of Freq */      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
 /************* Waves Concatenation ***************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        for(mi=1; mi<= wav[i]-1; mi++){
 {          for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for (j=1;j<=nlstate+ndeath;j++){
      Death is a valid wave (if date is known).              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            }
      and mw[mi+1][i]. dh depends on stepm.          for(d=0; d<dh[mi][i]; d++){
      */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, mi, m;            for (kk=1; kk<=cptcovage;kk++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      double sum=0., jmean=0.;*/            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int j, k=0,jk, ju, jl;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double sum=0.;            savm=oldm;
   jmin=1e+5;            oldm=newm;
   jmax=-1;          } /* end mult */
   jmean=0.;        
   for(i=1; i<=imx; i++){          s1=s[mw[mi][i]][i];
     mi=0;          s2=s[mw[mi+1][i]][i];
     m=firstpass;          bbh=(double)bh[mi][i]/(double)stepm; 
     while(s[m][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(s[m][i]>=1)          ipmx +=1;
         mw[++mi][i]=m;          sw += weight[i];
       if(m >=lastpass)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         break;        } /* end of wave */
       else      } /* end of individual */
         m++;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     }/* end while */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (s[m][i] > nlstate){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       mi++;     /* Death is another wave */        for(mi=1; mi<= wav[i]-1; mi++){
       /* if(mi==0)  never been interviewed correctly before death */          for (ii=1;ii<=nlstate+ndeath;ii++)
          /* Only death is a correct wave */            for (j=1;j<=nlstate+ndeath;j++){
       mw[mi][i]=m;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     wav[i]=mi;          for(d=0; d<dh[mi][i]; d++){
     if(mi==0)            newm=savm;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            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];
   for(i=1; i<=imx; i++){            }
     for(mi=1; mi<wav[i];mi++){          
       if (stepm <=0)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         dh[mi][i]=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       else{            savm=oldm;
         if (s[mw[mi+1][i]][i] > nlstate) {            oldm=newm;
           if (agedc[i] < 2*AGESUP) {          } /* end mult */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        
           if(j==0) j=1;  /* Survives at least one month after exam */          s1=s[mw[mi][i]][i];
           k=k+1;          s2=s[mw[mi+1][i]][i];
           if (j >= jmax) jmax=j;          if( s2 > nlstate){ 
           if (j <= jmin) jmin=j;            lli=log(out[s1][s2] - savm[s1][s2]);
           sum=sum+j;          }else{
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }          }
         }          ipmx +=1;
         else{          sw += weight[i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           k=k+1;  /*      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 (j >= jmax) jmax=j;        } /* end of wave */
           else if (j <= jmin)jmin=j;      } /* end of individual */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           sum=sum+j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         jk= j/stepm;        for(mi=1; mi<= wav[i]-1; mi++){
         jl= j -jk*stepm;          for (ii=1;ii<=nlstate+ndeath;ii++)
         ju= j -(jk+1)*stepm;            for (j=1;j<=nlstate+ndeath;j++){
         if(jl <= -ju)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=jk;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         else            }
           dh[mi][i]=jk+1;          for(d=0; d<dh[mi][i]; d++){
         if(dh[mi][i]==0)            newm=savm;
           dh[mi][i]=1; /* At least one step */            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];
   }            }
   jmean=sum/k;          
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*********** Tricode ****************************/            savm=oldm;
 void tricode(int *Tvar, int **nbcode, int imx)            oldm=newm;
 {          } /* end mult */
   int Ndum[20],ij=1, k, j, i;        
   int cptcode=0;          s1=s[mw[mi][i]][i];
   cptcoveff=0;          s2=s[mw[mi+1][i]][i];
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for (k=0; k<19; k++) Ndum[k]=0;          ipmx +=1;
   for (k=1; k<=7; k++) ncodemax[k]=0;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     for (i=1; i<=imx; i++) {        } /* end of wave */
       ij=(int)(covar[Tvar[j]][i]);      } /* end of individual */
       Ndum[ij]++;    } /* End of if */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       if (ij > cptcode) cptcode=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;
     for (i=0; i<=cptcode; i++) {  }
       if(Ndum[i]!=0) ncodemax[j]++;  
     }  /*************** log-likelihood *************/
     ij=1;  double funcone( double *x)
   {
     /* Same as likeli but slower because of a lot of printf and if */
     for (i=1; i<=ncodemax[j]; i++) {    int i, ii, j, k, mi, d, kk;
       for (k=0; k<=19; k++) {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if (Ndum[k] != 0) {    double **out;
           nbcode[Tvar[j]][ij]=k;    double lli; /* Individual log likelihood */
              double llt;
           ij++;    int s1, s2;
         }    double bbh, survp;
         if (ij > ncodemax[j]) break;    /*extern weight */
       }      /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }      /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
  for (k=0; k<19; k++) Ndum[k]=0;    */
     cov[1]=1.;
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
       Ndum[ij]++;  
     }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  ij=1;      for(mi=1; mi<= wav[i]-1; mi++){
  for (i=1; i<=10; i++) {        for (ii=1;ii<=nlstate+ndeath;ii++)
    if((Ndum[i]!=0) && (i<=ncovcol)){          for (j=1;j<=nlstate+ndeath;j++){
      Tvaraff[ij]=i;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      ij++;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
    }          }
  }        for(d=0; d<dh[mi][i]; d++){
            newm=savm;
     cptcoveff=ij-1;          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];
 /*********** Health Expectancies ****************/          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 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 )                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
 {          oldm=newm;
   /* Health expectancies */        } /* end mult */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        
   double age, agelim, hf;        s1=s[mw[mi][i]][i];
   double ***p3mat,***varhe;        s2=s[mw[mi+1][i]][i];
   double **dnewm,**doldm;        bbh=(double)bh[mi][i]/(double)stepm; 
   double *xp;        /* bias is positive if real duration
   double **gp, **gm;         * is higher than the multiple of stepm and negative otherwise.
   double ***gradg, ***trgradg;         */
   int theta;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        } else if (mle==1){
   xp=vector(1,npar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   dnewm=matrix(1,nlstate*2,1,npar);        } else if(mle==2){
   doldm=matrix(1,nlstate*2,1,nlstate*2);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
          } else if(mle==3){  /* exponential inter-extrapolation */
   fprintf(ficreseij,"# Health expectancies\n");          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 */
   fprintf(ficreseij,"# Age");        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for(i=1; i<=nlstate;i++)          lli=log(out[s1][s2]); /* Original formula */
     for(j=1; j<=nlstate;j++)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          lli=log(out[s1][s2]); /* Original formula */
   fprintf(ficreseij,"\n");        } /* End of if */
         ipmx +=1;
   if(estepm < stepm){        sw += weight[i];
     printf ("Problem %d lower than %d\n",estepm, stepm);        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]); */
   else  hstepm=estepm;          if(globpr){
   /* We compute the life expectancy from trapezoids spaced every estepm months          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    * This is mainly to measure the difference between two models: for example   %10.6f %10.6f %10.6f ", \
    * if stepm=24 months pijx are given only every 2 years and by summing them                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
    * we are calculating an estimate of the Life Expectancy assuming a linear                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
    * progression inbetween and thus overestimating or underestimating according          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
    * to the curvature of the survival function. If, for the same date, we            llt +=ll[k]*gipmx/gsw;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
    * to compare the new estimate of Life expectancy with the same linear          }
    * hypothesis. A more precise result, taking into account a more precise          fprintf(ficresilk," %10.6f\n", -llt);
    * curvature will be obtained if estepm is as small as stepm. */        }
       } /* end of wave */
   /* For example we decided to compute the life expectancy with the smallest unit */    } /* end of individual */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      nhstepm is the number of hstepm from age to agelim    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      nstepm is the number of stepm from age to agelin.    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      Look at hpijx to understand the reason of that which relies in memory size    if(globpr==0){ /* First time we count the contributions and weights */
      and note for a fixed period like estepm months */      gipmx=ipmx;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      gsw=sw;
      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    return -l;
      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.  
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   agelim=AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* This routine should help understanding what is done with 
     /* nhstepm age range expressed in number of stepm */       the selection of individuals/waves and
     nstepm=(int) rint((agelim-age)*YEARM/stepm);       to check the exact contribution to the likelihood.
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */       Plotting could be done.
     /* if (stepm >= YEARM) hstepm=1;*/     */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    int k;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    if(*globpri !=0){ /* Just counts and sums, no printings */
     gp=matrix(0,nhstepm,1,nlstate*2);      strcpy(fileresilk,"ilk"); 
     gm=matrix(0,nhstepm,1,nlstate*2);      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        printf("Problem with resultfile: %s\n", fileresilk);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     hpxij(p3mat,nhstepm,age,hstepm,x,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 ");
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
     /* Computing Variances of health expectancies */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      for(theta=1; theta <=npar; theta++){    }
       for(i=1; i<=npar; i++){  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    *fretone=(*funcone)(p);
       }    if(*globpri !=0){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fclose(ficresilk);
        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       cptj=0;      fflush(fichtm); 
       for(j=1; j<= nlstate; j++){    } 
         for(i=1; i<=nlstate; i++){    return;
           cptj=cptj+1;  }
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  /*********** Maximum Likelihood Estimation ***************/
         }  
       }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
        {
          int i,j, iter;
       for(i=1; i<=npar; i++)    double **xi;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double fret;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double fretone; /* Only one call to likelihood */
          /*  char filerespow[FILENAMELENGTH];*/
       cptj=0;    xi=matrix(1,npar,1,npar);
       for(j=1; j<= nlstate; j++){    for (i=1;i<=npar;i++)
         for(i=1;i<=nlstate;i++){      for (j=1;j<=npar;j++)
           cptj=cptj+1;        xi[i][j]=(i==j ? 1.0 : 0.0);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    strcpy(filerespow,"pow"); 
           }    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(j=1; j<= nlstate*2; j++)    for (i=1;i<=nlstate;i++)
         for(h=0; h<=nhstepm-1; h++){      for(j=1;j<=nlstate+ndeath;j++)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         }    fprintf(ficrespow,"\n");
   
      }    powell(p,xi,npar,ftol,&iter,&fret,func);
      
 /* End theta */    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
      for(h=0; h<=nhstepm-1; h++)  
       for(j=1; j<=nlstate*2;j++)  }
         for(theta=1; theta <=npar; theta++)  
         trgradg[h][j][theta]=gradg[h][theta][j];  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
      for(i=1;i<=nlstate*2;i++)    double  **a,**y,*x,pd;
       for(j=1;j<=nlstate*2;j++)    double **hess;
         varhe[i][j][(int)age] =0.;    int i, j,jk;
     int *indx;
      printf("%d||",(int)age);fflush(stdout);  
     for(h=0;h<=nhstepm-1;h++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(k=0;k<=nhstepm-1;k++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    void lubksb(double **a, int npar, int *indx, double b[]) ;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
         for(i=1;i<=nlstate*2;i++)    double gompertz(double p[]);
           for(j=1;j<=nlstate*2;j++)    hess=matrix(1,npar,1,npar);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }    printf("\nCalculation of the hessian matrix. Wait...\n");
     }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
            printf("%d",i);fflush(stdout);
     /* Computing expectancies */      fprintf(ficlog,"%d",i);fflush(ficlog);
     for(i=1; i<=nlstate;i++)     
       for(j=1; j<=nlstate;j++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      /*  printf(" %f ",p[i]);
                    printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
 /* 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<=npar;i++) {
       for (j=1;j<=npar;j++)  {
     fprintf(ficreseij,"%3.0f",age );        if (j>i) { 
     cptj=0;          printf(".%d%d",i,j);fflush(stdout);
     for(i=1; i<=nlstate;i++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       for(j=1; j<=nlstate;j++){          hess[i][j]=hessij(p,delti,i,j,func,npar);
         cptj++;          
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          hess[j][i]=hess[i][j];    
       }          /*printf(" %lf ",hess[i][j]);*/
     fprintf(ficreseij,"\n");        }
          }
     free_matrix(gm,0,nhstepm,1,nlstate*2);    }
     free_matrix(gp,0,nhstepm,1,nlstate*2);    printf("\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    fprintf(ficlog,"\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   free_vector(xp,1,npar);    
   free_matrix(dnewm,1,nlstate*2,1,npar);    a=matrix(1,npar,1,npar);
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    y=matrix(1,npar,1,npar);
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    x=vector(1,npar);
 }    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
 /************ Variance ******************/      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 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)    ludcmp(a,npar,indx,&pd);
 {  
   /* Variance of health expectancies */    for (j=1;j<=npar;j++) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for (i=1;i<=npar;i++) x[i]=0;
   double **newm;      x[j]=1;
   double **dnewm,**doldm;      lubksb(a,npar,indx,x);
   int i, j, nhstepm, hstepm, h, nstepm ;      for (i=1;i<=npar;i++){ 
   int k, cptcode;        matcov[i][j]=x[i];
   double *xp;      }
   double **gp, **gm;    }
   double ***gradg, ***trgradg;  
   double ***p3mat;    printf("\n#Hessian matrix#\n");
   double age,agelim, hf;    fprintf(ficlog,"\n#Hessian matrix#\n");
   int theta;    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
    fprintf(ficresvij,"# Covariances of life expectancies\n");        printf("%.3e ",hess[i][j]);
   fprintf(ficresvij,"# Age");        fprintf(ficlog,"%.3e ",hess[i][j]);
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      printf("\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      fprintf(ficlog,"\n");
   fprintf(ficresvij,"\n");    }
   
   xp=vector(1,npar);    /* Recompute Inverse */
   dnewm=matrix(1,nlstate,1,npar);    for (i=1;i<=npar;i++)
   doldm=matrix(1,nlstate,1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      ludcmp(a,npar,indx,&pd);
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);    /*  printf("\n#Hessian matrix recomputed#\n");
   }  
   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        y[i][j]=x[i];
      and note for a fixed period like k years */        printf("%.3e ",y[i][j]);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        fprintf(ficlog,"%.3e ",y[i][j]);
      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");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      fprintf(ficlog,"\n");
      results. So we changed our mind and took the option of the best precision.    }
   */    */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
   agelim = AGESUP;    free_matrix(a,1,npar,1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_matrix(y,1,npar,1,npar);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_vector(x,1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    free_ivector(indx,1,npar);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(hess,1,npar,1,npar);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /*************** hessian matrix ****************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    int i;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int l=1, lmax=20;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double k1,k2;
     double p2[NPARMAX+1];
       if (popbased==1) {    double res;
         for(i=1; i<=nlstate;i++)    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           prlim[i][i]=probs[(int)age][i][ij];    double fx;
       }    int k=0,kmax=10;
      double l1;
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    fx=func(x);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for(l=0 ; l <=lmax; l++){
         }      l1=pow(10,l);
       }      delts=delt;
          for(k=1 ; k <kmax; k=k+1){
       for(i=1; i<=npar; i++) /* Computes gradient */        delt = delta*(l1*k);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        p2[theta]=x[theta] +delt;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          k1=func(p2)-fx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
       if (popbased==1) {        /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(i=1; i<=nlstate;i++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           prlim[i][i]=probs[(int)age][i][ij];        
       }  #ifdef DEBUG
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       for(j=1; j<= nlstate; j++){        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for(h=0; h<=nhstepm; h++){  #endif
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         }          k=kmax;
       }        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(j=1; j<= nlstate; j++)          k=kmax; l=lmax*10.;
         for(h=0; h<=nhstepm; h++){        }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         }          delts=delt;
     } /* End theta */        }
       }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    }
     delti[theta]=delts;
     for(h=0; h<=nhstepm; h++)    return res; 
       for(j=1; j<=nlstate;j++)    
         for(theta=1; theta <=npar; theta++)  }
           trgradg[h][j][theta]=gradg[h][theta][j];  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  {
     for(i=1;i<=nlstate;i++)    int i;
       for(j=1;j<=nlstate;j++)    int l=1, l1, lmax=20;
         vareij[i][j][(int)age] =0.;    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
     for(h=0;h<=nhstepm;h++){    int k;
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    fx=func(x);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    for (k=1; k<=2; k++) {
         for(i=1;i<=nlstate;i++)      for (i=1;i<=npar;i++) p2[i]=x[i];
           for(j=1;j<=nlstate;j++)      p2[thetai]=x[thetai]+delti[thetai]/k;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k1=func(p2)-fx;
     }    
       p2[thetai]=x[thetai]+delti[thetai]/k;
     fprintf(ficresvij,"%.0f ",age );      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1; i<=nlstate;i++)      k2=func(p2)-fx;
       for(j=1; j<=nlstate;j++){    
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fprintf(ficresvij,"\n");      k3=func(p2)-fx;
     free_matrix(gp,0,nhstepm,1,nlstate);    
     free_matrix(gm,0,nhstepm,1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      k4=func(p2)-fx;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   } /* End age */  #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);
   free_vector(xp,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);
   free_matrix(doldm,1,nlstate,1,npar);  #endif
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
     return res;
 }  }
   
 /************ Variance of prevlim ******************/  /************** Inverse of matrix **************/
 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)  void ludcmp(double **a, int n, int *indx, double *d) 
 {  { 
   /* Variance of prevalence limit */    int i,imax,j,k; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double big,dum,sum,temp; 
   double **newm;    double *vv; 
   double **dnewm,**doldm;   
   int i, j, nhstepm, hstepm;    vv=vector(1,n); 
   int k, cptcode;    *d=1.0; 
   double *xp;    for (i=1;i<=n;i++) { 
   double *gp, *gm;      big=0.0; 
   double **gradg, **trgradg;      for (j=1;j<=n;j++) 
   double age,agelim;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   int theta;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
          vv[i]=1.0/big; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    } 
   fprintf(ficresvpl,"# Age");    for (j=1;j<=n;j++) { 
   for(i=1; i<=nlstate;i++)      for (i=1;i<j;i++) { 
       fprintf(ficresvpl," %1d-%1d",i,i);        sum=a[i][j]; 
   fprintf(ficresvpl,"\n");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   xp=vector(1,npar);      } 
   dnewm=matrix(1,nlstate,1,npar);      big=0.0; 
   doldm=matrix(1,nlstate,1,nlstate);      for (i=j;i<=n;i++) { 
          sum=a[i][j]; 
   hstepm=1*YEARM; /* Every year of age */        for (k=1;k<j;k++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          sum -= a[i][k]*a[k][j]; 
   agelim = AGESUP;        a[i][j]=sum; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          big=dum; 
     if (stepm >= YEARM) hstepm=1;          imax=i; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        } 
     gradg=matrix(1,npar,1,nlstate);      } 
     gp=vector(1,nlstate);      if (j != imax) { 
     gm=vector(1,nlstate);        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
     for(theta=1; theta <=npar; theta++){          a[imax][k]=a[j][k]; 
       for(i=1; i<=npar; i++){ /* Computes gradient */          a[j][k]=dum; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } 
       }        *d = -(*d); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        vv[imax]=vv[j]; 
       for(i=1;i<=nlstate;i++)      } 
         gp[i] = prlim[i][i];      indx[j]=imax; 
          if (a[j][j] == 0.0) a[j][j]=TINY; 
       for(i=1; i<=npar; i++) /* Computes gradient */      if (j != n) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        dum=1.0/(a[j][j]); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       for(i=1;i<=nlstate;i++)      } 
         gm[i] = prlim[i][i];    } 
     free_vector(vv,1,n);  /* Doesn't work */
       for(i=1;i<=nlstate;i++)  ;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  } 
     } /* End theta */  
   void lubksb(double **a, int n, int *indx, double b[]) 
     trgradg =matrix(1,nlstate,1,npar);  { 
     int i,ii=0,ip,j; 
     for(j=1; j<=nlstate;j++)    double sum; 
       for(theta=1; theta <=npar; theta++)   
         trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
     for(i=1;i<=nlstate;i++)      sum=b[ip]; 
       varpl[i][(int)age] =0.;      b[ip]=b[i]; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      if (ii) 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     for(i=1;i<=nlstate;i++)      else if (sum) ii=i; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      b[i]=sum; 
     } 
     fprintf(ficresvpl,"%.0f ",age );    for (i=n;i>=1;i--) { 
     for(i=1; i<=nlstate;i++)      sum=b[i]; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     fprintf(ficresvpl,"\n");      b[i]=sum/a[i][i]; 
     free_vector(gp,1,nlstate);    } 
     free_vector(gm,1,nlstate);  } 
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);  /************ Frequencies ********************/
   } /* End age */  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[])
   {  /* Some frequencies */
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   free_matrix(dnewm,1,nlstate,1,nlstate);    int first;
     double ***freq; /* Frequencies */
 }    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
 /************ Variance of one-step probabilities  ******************/    FILE *ficresp;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    char fileresp[FILENAMELENGTH];
 {    
   int i, j, i1, k1, j1, z1;    pp=vector(1,nlstate);
   int k=0, cptcode;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   double **dnewm,**doldm;    strcpy(fileresp,"p");
   double *xp;    strcat(fileresp,fileres);
   double *gp, *gm;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   double **gradg, **trgradg;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   double age,agelim, cov[NCOVMAX];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   int theta;      exit(0);
   char fileresprob[FILENAMELENGTH];    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   strcpy(fileresprob,"prob");    j1=0;
   strcat(fileresprob,fileres);    
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    j=cptcoveff;
     printf("Problem with resultfile: %s\n", fileresprob);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    first=1;
    
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    for(k1=1; k1<=j;k1++){
   fprintf(ficresprob,"# Age");      for(i1=1; i1<=ncodemax[k1];i1++){
   for(i=1; i<=nlstate;i++)        j1++;
     for(j=1; j<=(nlstate+ndeath);j++)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
   fprintf(ficresprob,"\n");            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   
   xp=vector(1,npar);      for (i=1; i<=nlstate; i++)  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(m=iagemin; m <= iagemax+3; m++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          prop[i][m]=0;
          
   cov[1]=1;        dateintsum=0;
   j=cptcoveff;        k2cpt=0;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for (i=1; i<=imx; i++) {
   j1=0;          bool=1;
   for(k1=1; k1<=1;k1++){          if  (cptcovn>0) {
     for(i1=1; i1<=ncodemax[k1];i1++){            for (z1=1; z1<=cptcoveff; z1++) 
     j1++;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
     if  (cptcovn>0) {          }
       fprintf(ficresprob, "\n#********** Variable ");          if (bool==1){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for(m=firstpass; m<=lastpass; m++){
       fprintf(ficresprob, "**********\n#");              k2=anint[m][i]+(mint[m][i]/12.);
     }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for (age=bage; age<=fage; age ++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         cov[2]=age;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         for (k=1; k<=cptcovn;k++) {                if (m<lastpass) {
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];                  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];
         }                }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                
         for (k=1; k<=cptcovprod;k++)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                  dateintsum=dateintsum+k2;
                          k2cpt++;
         gradg=matrix(1,npar,1,9);                }
         trgradg=matrix(1,9,1,npar);                /*}*/
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            }
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
            }
         for(theta=1; theta <=npar; theta++){         
           for(i=1; i<=npar; i++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  fprintf(ficresp, "#Local time at start: %s", strstart);
                  if  (cptcovn>0) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          fprintf(ficresp, "\n#********** Variable "); 
                    for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           k=0;          fprintf(ficresp, "**********\n#");
           for(i=1; i<= (nlstate+ndeath); i++){        }
             for(j=1; j<=(nlstate+ndeath);j++){        for(i=1; i<=nlstate;i++) 
               k=k+1;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
               gp[k]=pmmij[i][j];        fprintf(ficresp, "\n");
             }        
           }        for(i=iagemin; i <= iagemax+3; i++){
                    if(i==iagemax+3){
           for(i=1; i<=npar; i++)            fprintf(ficlog,"Total");
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          }else{
                if(first==1){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              first=0;
           k=0;              printf("See log file for details...\n");
           for(i=1; i<=(nlstate+ndeath); i++){            }
             for(j=1; j<=(nlstate+ndeath);j++){            fprintf(ficlog,"Age %d", i);
               k=k+1;          }
               gm[k]=pmmij[i][j];          for(jk=1; jk <=nlstate ; jk++){
             }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           }              pp[jk] += freq[jk][m][i]; 
                }
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          for(jk=1; jk <=nlstate ; jk++){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              for(m=-1, pos=0; m <=0 ; m++)
         }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              if(first==1){
           for(theta=1; theta <=npar; theta++)              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             trgradg[j][theta]=gradg[theta][j];              }
                      fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            }else{
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              if(first==1)
                        printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         pmij(pmmij,cov,ncovmodel,x,nlstate);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                    }
         k=0;          }
         for(i=1; i<=(nlstate+ndeath); i++){  
           for(j=1; j<=(nlstate+ndeath);j++){          for(jk=1; jk <=nlstate ; jk++){
             k=k+1;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             gm[k]=pmmij[i][j];              pp[jk] += freq[jk][m][i];
           }          }       
         }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                  pos += pp[jk];
      /*printf("\n%d ",(int)age);            posprop += prop[jk][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++){
      }*/            if(pos>=1.e-5){
               if(first==1)
         fprintf(ficresprob,"\n%d ",(int)age);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)            }else{
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }            }
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            if( i <= iagemax){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              if(pos>=1.e-5){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                /*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]);*/
   free_vector(xp,1,npar);              }
   fclose(ficresprob);              else
                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 }            }
           }
 /******************* Printing html file ***********/          
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          for(jk=-1; jk <=nlstate+ndeath; jk++)
  int lastpass, int stepm, int weightopt, char model[],\            for(m=-1; m <=nlstate+ndeath; m++)
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              if(freq[jk][m][i] !=0 ) {
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\              if(first==1)
  char version[], int popforecast, int estepm ){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   int jj1, k1, i1, cpt;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   FILE *fichtm;              }
   /*char optionfilehtm[FILENAMELENGTH];*/          if(i <= iagemax)
             fprintf(ficresp,"\n");
   strcpy(optionfilehtm,optionfile);          if(first==1)
   strcat(optionfilehtm,".htm");            printf("Others in log...\n");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          fprintf(ficlog,"\n");
     printf("Problem with %s \n",optionfilehtm), exit(0);        }
   }      }
     }
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    dateintmean=dateintsum/k2cpt; 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n   
 \n    fclose(ficresp);
 Total number of observations=%d <br>\n    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    free_vector(pp,1,nlstate);
 <hr  size=\"2\" color=\"#EC5E5E\">    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  <ul><li>Outputs files<br>\n    /* End of Freq */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  }
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n  
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  /************ Prevalence ********************/
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
  - 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);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
  fprintf(fichtm,"\n       We still use firstpass and lastpass as another selection.
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    */
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n   
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    double ***freq; /* Frequencies */
  - 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);    double *pp, **prop;
     double pos,posprop; 
  if(popforecast==1) fprintf(fichtm,"\n    double  y2; /* in fractional years */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    int iagemin, iagemax;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    iagemin= (int) agemin;
  else    iagemax= (int) agemax;
    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);    /*pp=vector(1,nlstate);*/
 fprintf(fichtm," <li>Graphs</li><p>");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
  m=cptcoveff;    j1=0;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    
     j=cptcoveff;
  jj1=0;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
  for(k1=1; k1<=m;k1++){    
    for(i1=1; i1<=ncodemax[k1];i1++){    for(k1=1; k1<=j;k1++){
        jj1++;      for(i1=1; i1<=ncodemax[k1];i1++){
        if (cptcovn > 0) {        j1++;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        
          for (cpt=1; cpt<=cptcoveff;cpt++)        for (i=1; i<=nlstate; i++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          for(m=iagemin; m <= iagemax+3; m++)
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            prop[i][m]=0.0;
        }       
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.png<br>        for (i=1; i<=imx; i++) { /* Each individual */
 <img src=\"pe%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              bool=1;
        for(cpt=1; cpt<nlstate;cpt++){          if  (cptcovn>0) {
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.png<br>            for (z1=1; z1<=cptcoveff; z1++) 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        }                bool=0;
     for(cpt=1; cpt<=nlstate;cpt++) {          } 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          if (bool==1) { 
 interval) in state (%d): v%s%d%d.png <br>            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
      }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
      for(cpt=1; cpt<=nlstate;cpt++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                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); 
      }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                  /*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]]);*/
 health expectancies in states (1) and (2): e%s%d.png<br>                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
 fprintf(fichtm,"\n</body>");                } 
    }              }
    }            } /* end selection of waves */
 fclose(fichtm);          }
 }        }
         for(i=iagemin; i <= iagemax+3; i++){  
 /******************* Gnuplot file **************/          
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          } 
   
   strcpy(optionfilegnuplot,optionfilefiname);          for(jk=1; jk <=nlstate ; jk++){     
   strcat(optionfilegnuplot,".gp.txt");            if( i <=  iagemax){ 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              if(posprop>=1.e-5){ 
     printf("Problem with file %s",optionfilegnuplot);                probs[i][jk][j1]= prop[jk][i]/posprop;
   }              } 
             } 
 #ifdef windows          }/* end jk */ 
     fprintf(ficgp,"cd \"%s\" \n",pathc);        }/* end i */ 
 #endif      } /* end i1 */
 m=pow(2,cptcoveff);    } /* end k1 */
      
  /* 1eme*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {    /*free_vector(pp,1,nlstate);*/
    for (k1=1; k1<= m ; k1 ++) {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
 #ifdef windows  
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);  /************* Waves Concatenation ***************/
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);  
 #endif  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)
 #ifdef unix  {
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);       Death is a valid wave (if date is known).
 #endif       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 for (i=1; i<= nlstate ; i ++) {       and mw[mi+1][i]. dh depends on stepm.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    int i, mi, m;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for (i=1; i<= nlstate ; i ++) {       double sum=0., jmean=0.;*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int first;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int j, k=0,jk, ju, jl;
 }    double sum=0.;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    first=0;
      for (i=1; i<= nlstate ; i ++) {    jmin=1e+5;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    jmax=-1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    jmean=0.;
 }      for(i=1; i<=imx; i++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      mi=0;
 #ifdef unix      m=firstpass;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      while(s[m][i] <= nlstate){
 #endif        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
    }          mw[++mi][i]=m;
   }        if(m >=lastpass)
   /*2 eme*/          break;
         else
   for (k1=1; k1<= m ; k1 ++) {          m++;
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n\n",strtok(optionfile, "."),k1);      }/* end while */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
     for (i=1; i<= nlstate+1 ; i ++) {        /* if(mi==0)  never been interviewed correctly before death */
       k=2*i;           /* Only death is a correct wave */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        mw[mi][i]=m;
       for (j=1; j<= nlstate+1 ; j ++) {      }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      wav[i]=mi;
 }        if(mi==0){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        nbwarn++;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        if(first==0){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       for (j=1; j<= nlstate+1 ; j ++) {          first=1;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
         else fprintf(ficgp," \%%*lf (\%%*lf)");        if(first==1){
 }            fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       fprintf(ficgp,"\" t\"\" w l 0,");        }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      } /* end mi==0 */
       for (j=1; j<= nlstate+1 ; j ++) {    } /* End individuals */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(i=1; i<=imx; i++){
 }        for(mi=1; mi<wav[i];mi++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        if (stepm <=0)
       else fprintf(ficgp,"\" t\"\" w l 0,");          dh[mi][i]=1;
     }        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
   /*3eme*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
   for (k1=1; k1<= m ; k1 ++) {              else if(j<0){
     for (cpt=1; cpt<= nlstate ; cpt ++) {                nberr++;
       k=2+nlstate*(2*cpt-2);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);                j=1; /* Temporary Dangerous patch */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);              }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              k=k+1;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              if (j >= jmax){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);                jmax=j;
                 ijmax=i;
 */              }
       for (i=1; i< nlstate ; i ++) {              if (j <= jmin){
         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);                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);*/
   /* CV preval stat */            }
     for (k1=1; k1<= m ; k1 ++) {          }
     for (cpt=1; cpt<nlstate ; cpt ++) {          else{
       k=3;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficgp,"set out \"p%s%d%d.png\" \n\n",strtok(optionfile, "."),cpt,k1);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  
             k=k+1;
       for (i=1; i< nlstate ; i ++)            if (j >= jmax) {
         fprintf(ficgp,"+$%d",k+i+1);              jmax=j;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              ijmax=i;
                  }
       l=3+(nlstate+ndeath)*cpt;            else if (j <= jmin){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              jmin=j;
       for (i=1; i< nlstate ; i ++) {              ijmin=i;
         l=3+(nlstate+ndeath)*cpt;            }
         fprintf(ficgp,"+$%d",l+i+1);            /*        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,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              if(j<0){
     }              nberr++;
   }                printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   /* proba elementaires */            }
    for(i=1,jk=1; i <=nlstate; i++){            sum=sum+j;
     for(k=1; k <=(nlstate+ndeath); k++){          }
       if (k != i) {          jk= j/stepm;
         for(j=1; j <=ncovmodel; j++){          jl= j -jk*stepm;
                  ju= j -(jk+1)*stepm;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           jk++;            if(jl==0){
           fprintf(ficgp,"\n");              dh[mi][i]=jk;
         }              bh[mi][i]=0;
       }            }else{ /* We want a negative bias in order to only have interpolation ie
     }                    * at the price of an extra matrix product in likelihood */
    }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
    for(jk=1; jk <=m; jk++) {            }
      fprintf(ficgp,"\nset out \"pe%s%d.png\" \n\n",strtok(optionfile, "."),jk);          }else{
      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            if(jl <= -ju){
      i=1;              dh[mi][i]=jk;
      for(k2=1; k2<=nlstate; k2++) {              bh[mi][i]=jl;       /* bias is positive if real duration
        k3=i;                                   * is higher than the multiple of stepm and negative otherwise.
        for(k=1; k<=(nlstate+ndeath); k++) {                                   */
          if (k != k2){            }
            fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            else{
            ij=1;              dh[mi][i]=jk+1;
            for(j=3; j <=ncovmodel; j++) {              bh[mi][i]=ju;
              if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            }
                fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(dh[mi][i]==0){
                ij++;              dh[mi][i]=1; /* At least one step */
              }              bh[mi][i]=ju; /* At least one step */
              else              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
                fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            }
            }          } /* end if mle */
            fprintf(ficgp,")/(1");        }
                  } /* end wave */
            for(k1=1; k1 <=nlstate; k1++){      }
              fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    jmean=sum/k;
              ij=1;    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);
              for(j=3; j <=ncovmodel; j++){    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);
                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++;  /*********** Tricode ****************************/
                }  void tricode(int *Tvar, int **nbcode, int imx)
                else  {
                  fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    
              }    int Ndum[20],ij=1, k, j, i, maxncov=19;
              fprintf(ficgp,")");    int cptcode=0;
            }    cptcoveff=0; 
            fprintf(ficgp,") t \"p%d%d\" ", k2,k);   
            if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    for (k=0; k<maxncov; k++) Ndum[k]=0;
            i=i+ncovmodel;    for (k=1; k<=7; k++) ncodemax[k]=0;
          }  
        }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
      }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
    }                                 modality*/ 
            ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
    fclose(ficgp);        Ndum[ij]++; /*store the modality */
 }  /* end gnuplot */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
 /*************** Moving average **************/                                         female is 1, then  cptcode=1.*/
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      }
   
   int i, cpt, cptcod;      for (i=0; i<=cptcode; i++) {
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       for (i=1; i<=nlstate;i++)      }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;      ij=1; 
          for (i=1; i<=ncodemax[j]; i++) {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        for (k=0; k<= maxncov; k++) {
       for (i=1; i<=nlstate;i++){          if (Ndum[k] != 0) {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            nbcode[Tvar[j]][ij]=k; 
           for (cpt=0;cpt<=4;cpt++){            /* 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; */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            
           }            ij++;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          }
         }          if (ij > ncodemax[j]) break; 
       }        }  
     }      } 
        }  
 }  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
   
 /************** Forecasting ******************/   for (i=1; i<=ncovmodel-2; i++) { 
 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){     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       ij=Tvar[i];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;     Ndum[ij]++;
   int *popage;   }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;   ij=1;
   double ***p3mat;   for (i=1; i<= maxncov; i++) {
   char fileresf[FILENAMELENGTH];     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
  agelim=AGESUP;       ij++;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;     }
    }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   
     cptcoveff=ij-1; /*Number of simple covariates*/
    }
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);  /*********** Health Expectancies ****************/
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);  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[] )
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);  {
     /* Health expectancies */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
   if (mobilav==1) {    double ***p3mat,***varhe;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **dnewm,**doldm;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double *xp;
   }    double **gp, **gm;
     double ***gradg, ***trgradg;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int theta;
   if (stepm<=12) stepsize=1;  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   agelim=AGESUP;    xp=vector(1,npar);
      dnewm=matrix(1,nlstate*nlstate,1,npar);
   hstepm=1;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   hstepm=hstepm/stepm;    
   yp1=modf(dateintmean,&yp);    fprintf(ficreseij,"# Local time at start: %s", strstart);
   anprojmean=yp;    fprintf(ficreseij,"# Health expectancies\n");
   yp2=modf((yp1*12),&yp);    fprintf(ficreseij,"# Age");
   mprojmean=yp;    for(i=1; i<=nlstate;i++)
   yp1=modf((yp2*30.5),&yp);      for(j=1; j<=nlstate;j++)
   jprojmean=yp;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   if(jprojmean==0) jprojmean=1;    fprintf(ficreseij,"\n");
   if(mprojmean==0) jprojmean=1;  
      if(estepm < stepm){
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   for(cptcov=1;cptcov<=i2;cptcov++){    else  hstepm=estepm;   
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* We compute the life expectancy from trapezoids spaced every estepm months
       k=k+1;     * This is mainly to measure the difference between two models: for example
       fprintf(ficresf,"\n#******");     * if stepm=24 months pijx are given only every 2 years and by summing them
       for(j=1;j<=cptcoveff;j++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * progression in between and thus overestimating or underestimating according
       }     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficresf,"******\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       fprintf(ficresf,"# StartingAge FinalAge");     * to compare the new estimate of Life expectancy with the same linear 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);     * hypothesis. A more precise result, taking into account a more precise
           * curvature will be obtained if estepm is as small as stepm. */
        
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficresf,"\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       Look at hpijx to understand the reason of that which relies in memory size
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       and note for a fixed period like estepm months */
           nhstepm = nhstepm/hstepm;    /* 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
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       means that if the survival funtion is printed only each two years of age and if
           oldm=oldms;savm=savms;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         results. So we changed our mind and took the option of the best precision.
            */
           for (h=0; h<=nhstepm; h++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    agelim=AGESUP;
             }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             for(j=1; j<=nlstate+ndeath;j++) {      /* nhstepm age range expressed in number of stepm */
               kk1=0.;kk2=0;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
               for(i=1; i<=nlstate;i++) {                    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                 if (mobilav==1)      /* if (stepm >= YEARM) hstepm=1;*/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                 else {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                 }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
                      gm=matrix(0,nhstepm,1,nlstate*nlstate);
               }  
               if (h==(int)(calagedate+12*cpt)){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 fprintf(ficresf," %.3f", kk1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                              hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
               }   
             }  
           }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      /* Computing  Variances of health expectancies */
       }  
     }       for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ 
                  xp[i] = x[i] + (i==theta ?delti[theta]:0);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fclose(ficresf);    
 }        cptj=0;
 /************** Forecasting ******************/        for(j=1; j<= nlstate; j++){
 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){          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   int *popage;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }
   double *popeffectif,*popcount;          }
   double ***p3mat,***tabpop,***tabpopprev;        }
   char filerespop[FILENAMELENGTH];       
        
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1; i<=npar; i++) 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   agelim=AGESUP;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        
          cptj=0;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(j=1; j<= nlstate; j++){
            for(i=1;i<=nlstate;i++){
              cptj=cptj+1;
   strcpy(filerespop,"pop");            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     printf("Problem with forecast resultfile: %s\n", filerespop);            }
   }          }
   printf("Computing forecasting: result on file '%s' \n", filerespop);        }
         for(j=1; j<= nlstate*nlstate; j++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if (mobilav==1) {          }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       } 
     movingaverage(agedeb, fage, ageminpar, mobaverage);     
   }  /* End theta */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   if (stepm<=12) stepsize=1;  
         for(h=0; h<=nhstepm-1; h++)
   agelim=AGESUP;        for(j=1; j<=nlstate*nlstate;j++)
            for(theta=1; theta <=npar; theta++)
   hstepm=1;            trgradg[h][j][theta]=gradg[h][theta][j];
   hstepm=hstepm/stepm;       
    
   if (popforecast==1) {       for(i=1;i<=nlstate*nlstate;i++)
     if((ficpop=fopen(popfile,"r"))==NULL) {        for(j=1;j<=nlstate*nlstate;j++)
       printf("Problem with population file : %s\n",popfile);exit(0);          varhe[i][j][(int)age] =0.;
     }  
     popage=ivector(0,AGESUP);       printf("%d|",(int)age);fflush(stdout);
     popeffectif=vector(0,AGESUP);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     popcount=vector(0,AGESUP);       for(h=0;h<=nhstepm-1;h++){
            for(k=0;k<=nhstepm-1;k++){
     i=1;            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
              for(i=1;i<=nlstate*nlstate;i++)
     imx=i;            for(j=1;j<=nlstate*nlstate;j++)
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   }        }
       }
   for(cptcov=1;cptcov<=i2;cptcov++){      /* Computing expectancies */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(i=1; i<=nlstate;i++)
       k=k+1;        for(j=1; j<=nlstate;j++)
       fprintf(ficrespop,"\n#******");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for(j=1;j<=cptcoveff;j++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            
       }  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");          }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");      fprintf(ficreseij,"%3.0f",age );
            cptj=0;
       for (cpt=0; cpt<=0;cpt++) {      for(i=1; i<=nlstate;i++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for(j=1; j<=nlstate;j++){
                  cptj++;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }
           nhstepm = nhstepm/hstepm;      fprintf(ficreseij,"\n");
               
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           oldm=oldms;savm=savms;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
              free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           for (h=0; h<=nhstepm; h++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             if (h==(int) (calagedate+YEARM*cpt)) {    }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    printf("\n");
             }    fprintf(ficlog,"\n");
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    free_vector(xp,1,npar);
               for(i=1; i<=nlstate;i++) {                  free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                 if (mobilav==1)    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                 else {  }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }  /************ Variance ******************/
               }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
               if (h==(int)(calagedate+12*cpt)){  {
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    /* Variance of health expectancies */
                   /*fprintf(ficrespop," %.3f", kk1);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    /* double **newm;*/
               }    double **dnewm,**doldm;
             }    double **dnewmp,**doldmp;
             for(i=1; i<=nlstate;i++){    int i, j, nhstepm, hstepm, h, nstepm ;
               kk1=0.;    int k, cptcode;
                 for(j=1; j<=nlstate;j++){    double *xp;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double **gp, **gm;  /* for var eij */
                 }    double ***gradg, ***trgradg; /*for var eij */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    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 */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    double ***p3mat;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    double age,agelim, hf;
           }    double ***mobaverage;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int theta;
         }    char digit[4];
       }    char digitp[25];
    
   /******/    char fileresprobmorprev[FILENAMELENGTH];
   
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    if(popbased==1){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        if(mobilav!=0)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        strcpy(digitp,"-populbased-mobilav-");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      else strcpy(digitp,"-populbased-nomobil-");
           nhstepm = nhstepm/hstepm;    }
              else 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      strcpy(digitp,"-stablbased-");
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if (mobilav!=0) {
           for (h=0; h<=nhstepm; h++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             if (h==(int) (calagedate+YEARM*cpt)) {      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             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];        strcpy(fileresprobmorprev,"prmorprev"); 
               }    sprintf(digit,"%-d",ij);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
             }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresprobmorprev,fileres);
         }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
    }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if (popforecast==1) {    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
     free_ivector(popage,0,AGESUP);    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);
     free_vector(popeffectif,0,AGESUP);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     free_vector(popcount,0,AGESUP);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   }      fprintf(ficresprobmorprev," p.%-d SE",j);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1; i<=nlstate;i++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   fclose(ficrespop);    }  
 }    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
 /***********************************************/    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
 /**************** Main Program *****************/    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);
   /*   } */
 int main(int argc, char *argv[])    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 {   fprintf(ficresvij, "#Local time at start: %s", strstart);
     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");
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(ficresvij,"# Age");
   double agedeb, agefin,hf;    for(i=1; i<=nlstate;i++)
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   double fret;    fprintf(ficresvij,"\n");
   double **xi,tmp,delta;  
     xp=vector(1,npar);
   double dum; /* Dummy variable */    dnewm=matrix(1,nlstate,1,npar);
   double ***p3mat;    doldm=matrix(1,nlstate,1,nlstate);
   int *indx;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   char line[MAXLINE], linepar[MAXLINE];    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   char filerest[FILENAMELENGTH];    if(estepm < stepm){
   char fileregp[FILENAMELENGTH];      printf ("Problem %d lower than %d\n",estepm, stepm);
   char popfile[FILENAMELENGTH];    }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    else  hstepm=estepm;   
   int firstobs=1, lastobs=10;    /* For example we decided to compute the life expectancy with the smallest unit */
   int sdeb, sfin; /* Status at beginning and end */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int c,  h , cpt,l;       nhstepm is the number of hstepm from age to agelim 
   int ju,jl, mi;       nstepm is the number of stepm from age to agelin. 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;       Look at hpijx to understand the reason of that which relies in memory size
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;       and note for a fixed period like k years */
   int mobilav=0,popforecast=0;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   int hstepm, nhstepm;       survival function given by stepm (the optimization length). Unfortunately it
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double bage, fage, age, agelim, agebase;       results. So we changed our mind and took the option of the best precision.
   double ftolpl=FTOL;    */
   double **prlim;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double *severity;    agelim = AGESUP;
   double ***param; /* Matrix of parameters */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double  *p;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double **matcov; /* Matrix of covariance */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double ***delti3; /* Scale */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double *delti; /* Scale */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   double ***eij, ***vareij;      gp=matrix(0,nhstepm,1,nlstate);
   double **varpl; /* Variances of prevalence limits by age */      gm=matrix(0,nhstepm,1,nlstate);
   double *epj, vepp;  
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char version[80]="Imach version 0.8d, May 2002, INED-EUROREVES ";        }
   char *alph[]={"a","a","b","c","d","e"}, str[4];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   char z[1]="c", occ;        if (popbased==1) {
 #include <sys/time.h>          if(mobilav ==0){
 #include <time.h>            for(i=1; i<=nlstate;i++)
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   /* long total_usecs;            for(i=1; i<=nlstate;i++)
   struct timeval start_time, end_time;              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
   getcwd(pathcd, size);    
         for(j=1; j<= nlstate; j++){
   printf("\n%s",version);          for(h=0; h<=nhstepm; h++){
   if(argc <=1){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     printf("\nEnter the parameter file name: ");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     scanf("%s",pathtot);          }
   }        }
   else{        /* This for computing probability of death (h=1 means
     strcpy(pathtot,argv[1]);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        */
   /*cygwin_split_path(pathtot,path,optionfile);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   /* cutv(path,optionfile,pathtot,'\\');*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        /* end probability of death */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   replace(pathc,path);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 /*-------- arguments in the command line --------*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   strcpy(fileres,"r");        if (popbased==1) {
   strcat(fileres, optionfilefiname);          if(mobilav ==0){
   strcat(fileres,".txt");    /* Other files have txt extension */            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   /*---------arguments file --------*/          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              prlim[i][i]=mobaverage[(int)age][i][ij];
     printf("Problem with optionfile %s\n",optionfile);          }
     goto end;        }
   }  
         for(j=1; j<= nlstate; j++){
   strcpy(filereso,"o");          for(h=0; h<=nhstepm; h++){
   strcat(filereso,fileres);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   if((ficparo=fopen(filereso,"w"))==NULL) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          }
   }        }
         /* This for computing probability of death (h=1 means
   /* Reads comments: lines beginning with '#' */           computed over hstepm matrices product = hstepm*stepm months) 
   while((c=getc(ficpar))=='#' && c!= EOF){           as a weighted average of prlim.
     ungetc(c,ficpar);        */
     fgets(line, MAXLINE, ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     puts(line);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     fputs(line,ficparo);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   }        }    
   ungetc(c,ficpar);        /* end probability of death */
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        for(j=1; j<= nlstate; j++) /* vareij */
   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);          for(h=0; h<=nhstepm; h++){
   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);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     puts(line);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     fputs(line,ficparo);        }
   }  
   ungetc(c,ficpar);      } /* End theta */
    
          trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;      for(h=0; h<=nhstepm; h++) /* veij */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   ncovmodel=2+cptcovn;            trgradg[h][j][theta]=gradg[h][theta][j];
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   /* Read guess parameters */        for(theta=1; theta <=npar; theta++)
   /* Reads comments: lines beginning with '#' */          trgradgp[j][theta]=gradgp[theta][j];
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     puts(line);      for(i=1;i<=nlstate;i++)
     fputs(line,ficparo);        for(j=1;j<=nlstate;j++)
   }          vareij[i][j][(int)age] =0.;
   ungetc(c,ficpar);  
        for(h=0;h<=nhstepm;h++){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(k=0;k<=nhstepm;k++){
     for(i=1; i <=nlstate; i++)          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     for(j=1; j <=nlstate+ndeath-1; j++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for(i=1;i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);            for(j=1;j<=nlstate;j++)
       printf("%1d%1d",i,j);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);      }
         printf(" %lf",param[i][j][k]);    
         fprintf(ficparo," %lf",param[i][j][k]);      /* pptj */
       }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       fscanf(ficpar,"\n");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       printf("\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       fprintf(ficparo,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     }          varppt[j][i]=doldmp[j][i];
        /* end ppptj */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   p=param[1][1];      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     
   /* Reads comments: lines beginning with '#' */      if (popbased==1) {
   while((c=getc(ficpar))=='#' && c!= EOF){        if(mobilav ==0){
     ungetc(c,ficpar);          for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);            prlim[i][i]=probs[(int)age][i][ij];
     puts(line);        }else{ /* mobilav */ 
     fputs(line,ficparo);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=mobaverage[(int)age][i][ij];
   ungetc(c,ficpar);        }
       }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);               
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      /* This for computing probability of death (h=1 means
   for(i=1; i <=nlstate; i++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     for(j=1; j <=nlstate+ndeath-1; j++){         as a weighted average of prlim.
       fscanf(ficpar,"%1d%1d",&i1,&j1);      */
       printf("%1d%1d",i,j);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficparo,"%1d%1d",i1,j1);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       for(k=1; k<=ncovmodel;k++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         fscanf(ficpar,"%le",&delti3[i][j][k]);      }    
         printf(" %le",delti3[i][j][k]);      /* end probability of death */
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fscanf(ficpar,"\n");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       printf("\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       fprintf(ficparo,"\n");        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   }        }
   delti=delti3[1][1];      } 
        fprintf(ficresprobmorprev,"\n");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresvij,"%.0f ",age );
     ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++){
     puts(line);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     fputs(line,ficparo);        }
   }      fprintf(ficresvij,"\n");
   ungetc(c,ficpar);      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   matcov=matrix(1,npar,1,npar);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   for(i=1; i <=npar; i++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     fscanf(ficpar,"%s",&str);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("%s",str);    } /* End age */
     fprintf(ficparo,"%s",str);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     for(j=1; j <=i; j++){    free_vector(gmp,nlstate+1,nlstate+ndeath);
       fscanf(ficpar," %le",&matcov[i][j]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       printf(" %.5le",matcov[i][j]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fprintf(ficparo," %.5le",matcov[i][j]);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fscanf(ficpar,"\n");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     printf("\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficparo,"\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   for(i=1; i <=npar; i++)    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     for(j=i+1;j<=npar;j++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       matcov[i][j]=matcov[j][i];    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   printf("\n");    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);
   */
     /*-------- Rewriting paramater file ----------*/  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
      strcpy(rfileres,"r");    /* "Rparameterfile */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */    free_vector(xp,1,npar);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    free_matrix(doldm,1,nlstate,1,nlstate);
     if((ficres =fopen(rfileres,"w"))==NULL) {    free_matrix(dnewm,1,nlstate,1,npar);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     fprintf(ficres,"#%s\n",version);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     /*-------- data file ----------*/    fclose(ficresprobmorprev);
     if((fic=fopen(datafile,"r"))==NULL)    {    fflush(ficgp);
       printf("Problem with datafile: %s\n", datafile);goto end;    fflush(fichtm); 
     }  }  /* end varevsij */
   
     n= lastobs;  /************ Variance of prevlim ******************/
     severity = vector(1,maxwav);  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[])
     outcome=imatrix(1,maxwav+1,1,n);  {
     num=ivector(1,n);    /* Variance of prevalence limit */
     moisnais=vector(1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     annais=vector(1,n);    double **newm;
     moisdc=vector(1,n);    double **dnewm,**doldm;
     andc=vector(1,n);    int i, j, nhstepm, hstepm;
     agedc=vector(1,n);    int k, cptcode;
     cod=ivector(1,n);    double *xp;
     weight=vector(1,n);    double *gp, *gm;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **gradg, **trgradg;
     mint=matrix(1,maxwav,1,n);    double age,agelim;
     anint=matrix(1,maxwav,1,n);    int theta;
     s=imatrix(1,maxwav+1,1,n);    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     adl=imatrix(1,maxwav+1,1,n);        fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     tab=ivector(1,NCOVMAX);    fprintf(ficresvpl,"# Age");
     ncodemax=ivector(1,8);    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     i=1;    fprintf(ficresvpl,"\n");
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {    xp=vector(1,npar);
            dnewm=matrix(1,nlstate,1,npar);
         for (j=maxwav;j>=1;j--){    doldm=matrix(1,nlstate,1,nlstate);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    
           strcpy(line,stra);    hstepm=1*YEARM; /* Every year of age */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    agelim = AGESUP;
         }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      if (stepm >= YEARM) hstepm=1;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      gp=vector(1,nlstate);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      gm=vector(1,nlstate);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      for(theta=1; theta <=npar; theta++){
         for (j=ncovcol;j>=1;j--){        for(i=1; i<=npar; i++){ /* Computes gradient */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }        }
         num[i]=atol(stra);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                for(i=1;i<=nlstate;i++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          gp[i] = prlim[i][i];
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/      
         for(i=1; i<=npar; i++) /* Computes gradient */
         i=i+1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }        for(i=1;i<=nlstate;i++)
     /* printf("ii=%d", ij);          gm[i] = prlim[i][i];
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */        for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   /* for (i=1; i<=imx; i++){      } /* End theta */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      trgradg =matrix(1,nlstate,1,npar);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }*/      for(j=1; j<=nlstate;j++)
    /*  for (i=1; i<=imx; i++){        for(theta=1; theta <=npar; theta++)
      if (s[4][i]==9)  s[4][i]=-1;          trgradg[j][theta]=gradg[theta][j];
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/  
        for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] =0.;
   /* Calculation of the number of parameter from char model*/      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   Tvar=ivector(1,15);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   Tprod=ivector(1,15);      for(i=1;i<=nlstate;i++)
   Tvaraff=ivector(1,15);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);            fprintf(ficresvpl,"%.0f ",age );
          for(i=1; i<=nlstate;i++)
   if (strlen(model) >1){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     j=0, j1=0, k1=1, k2=1;      fprintf(ficresvpl,"\n");
     j=nbocc(model,'+');      free_vector(gp,1,nlstate);
     j1=nbocc(model,'*');      free_vector(gm,1,nlstate);
     cptcovn=j+1;      free_matrix(gradg,1,npar,1,nlstate);
     cptcovprod=j1;      free_matrix(trgradg,1,nlstate,1,npar);
        } /* End age */
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    free_vector(xp,1,npar);
       printf("Error. Non available option model=%s ",model);    free_matrix(doldm,1,nlstate,1,npar);
       goto end;    free_matrix(dnewm,1,nlstate,1,nlstate);
     }  
      }
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');  /************ Variance of one-step probabilities  ******************/
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  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("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  {
       /*scanf("%d",i);*/    int i, j=0,  i1, k1, l1, t, tj;
       if (strchr(strb,'*')) {    int k2, l2, j1,  z1;
         cutv(strd,strc,strb,'*');    int k=0,l, cptcode;
         if (strcmp(strc,"age")==0) {    int first=1, first1;
           cptcovprod--;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           cutv(strb,stre,strd,'V');    double **dnewm,**doldm;
           Tvar[i]=atoi(stre);    double *xp;
           cptcovage++;    double *gp, *gm;
             Tage[cptcovage]=i;    double **gradg, **trgradg;
             /*printf("stre=%s ", stre);*/    double **mu;
         }    double age,agelim, cov[NCOVMAX];
         else if (strcmp(strd,"age")==0) {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           cptcovprod--;    int theta;
           cutv(strb,stre,strc,'V');    char fileresprob[FILENAMELENGTH];
           Tvar[i]=atoi(stre);    char fileresprobcov[FILENAMELENGTH];
           cptcovage++;    char fileresprobcor[FILENAMELENGTH];
           Tage[cptcovage]=i;  
         }    double ***varpij;
         else {  
           cutv(strb,stre,strc,'V');    strcpy(fileresprob,"prob"); 
           Tvar[i]=ncovcol+k1;    strcat(fileresprob,fileres);
           cutv(strb,strc,strd,'V');    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           Tprod[k1]=i;      printf("Problem with resultfile: %s\n", fileresprob);
           Tvard[k1][1]=atoi(strc);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           Tvard[k1][2]=atoi(stre);    }
           Tvar[cptcovn+k2]=Tvard[k1][1];    strcpy(fileresprobcov,"probcov"); 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    strcat(fileresprobcov,fileres);
           for (k=1; k<=lastobs;k++)    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      printf("Problem with resultfile: %s\n", fileresprobcov);
           k1++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           k2=k2+2;    }
         }    strcpy(fileresprobcor,"probcor"); 
       }    strcat(fileresprobcor,fileres);
       else {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      printf("Problem with resultfile: %s\n", fileresprobcor);
        /*  scanf("%d",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       cutv(strd,strc,strb,'V');    }
       Tvar[i]=atoi(strc);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       strcpy(modelsav,stra);      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         scanf("%d",i);*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 }    fprintf(ficresprob, "#Local time at start: %s", strstart);
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    fprintf(ficresprob,"# Age");
   printf("cptcovprod=%d ", cptcovprod);    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
   scanf("%d ",i);*/    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fclose(fic);    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     /*  if(mle==1){*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     if (weightopt != 1) { /* Maximisation without weights*/    fprintf(ficresprobcov,"# Age");
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }  
     /*-calculation of age at interview from date of interview and age at death -*/    for(i=1; i<=nlstate;i++)
     agev=matrix(1,maxwav,1,imx);      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     for (i=1; i<=imx; i++) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       for(m=2; (m<= maxwav); m++) {        fprintf(ficresprobcor," p%1d-%1d ",i,j);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      }  
          anint[m][i]=9999;   /* fprintf(ficresprob,"\n");
          s[m][i]=-1;    fprintf(ficresprobcov,"\n");
        }    fprintf(ficresprobcor,"\n");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;   */
       }   xp=vector(1,npar);
     }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     for (i=1; i<=imx; i++)  {    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       for(m=1; (m<= maxwav); m++){    first=1;
         if(s[m][i] >0){    fprintf(ficgp,"\n# Routine varprob");
           if (s[m][i] >= nlstate+1) {    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
             if(agedc[i]>0)    fprintf(fichtm,"\n");
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
            else {    file %s<br>\n",optionfilehtmcov);
               if (andc[i]!=9999){    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  and drawn. It helps understanding how is the covariance between two incidences.\
               agev[m][i]=-1;   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 \
           }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
           else if(s[m][i] !=9){ /* Should no more exist */  standard deviations wide on each axis. <br>\
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
             if(mint[m][i]==99 || anint[m][i]==9999)   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
               agev[m][i]=1;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    cov[1]=1;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    tj=cptcoveff;
             }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
             else if(agev[m][i] >agemax){    j1=0;
               agemax=agev[m][i];    for(t=1; t<=tj;t++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      for(i1=1; i1<=ncodemax[t];i1++){ 
             }        j1++;
             /*agev[m][i]=anint[m][i]-annais[i];*/        if  (cptcovn>0) {
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficresprob, "\n#********** Variable "); 
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           else { /* =9 */          fprintf(ficresprob, "**********\n#\n");
             agev[m][i]=1;          fprintf(ficresprobcov, "\n#********** Variable "); 
             s[m][i]=-1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresprobcov, "**********\n#\n");
         }          
         else /*= 0 Unknown */          fprintf(ficgp, "\n#********** Variable "); 
           agev[m][i]=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficgp, "**********\n#\n");
              
     }          
     for (i=1; i<=imx; i++)  {          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       for(m=1; (m<= maxwav); m++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           printf("Error: Wrong value in nlstate or ndeath\n");            
           goto end;          fprintf(ficresprobcor, "\n#********** Variable ");    
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcor, "**********\n#");    
     }        }
         
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
     free_vector(severity,1,maxwav);          for (k=1; k<=cptcovn;k++) {
     free_imatrix(outcome,1,maxwav+1,1,n);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     free_vector(moisnais,1,n);          }
     free_vector(annais,1,n);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     /* free_matrix(mint,1,maxwav,1,n);          for (k=1; k<=cptcovprod;k++)
        free_matrix(anint,1,maxwav,1,n);*/            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     free_vector(moisdc,1,n);          
     free_vector(andc,1,n);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
              gp=vector(1,(nlstate)*(nlstate+ndeath));
     wav=ivector(1,imx);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++)
     /* Concatenates waves */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
       Tcode=ivector(1,100);            k=0;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            for(i=1; i<= (nlstate); i++){
       ncodemax[1]=1;              for(j=1; j<=(nlstate+ndeath);j++){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                k=k+1;
                      gp[k]=pmmij[i][j];
    codtab=imatrix(1,100,1,10);              }
    h=0;            }
    m=pow(2,cptcoveff);            
              for(i=1; i<=npar; i++)
    for(k=1;k<=cptcoveff; k++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
      for(i=1; i <=(m/pow(2,k));i++){      
        for(j=1; j <= ncodemax[k]; j++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            k=0;
            h++;            for(i=1; i<=(nlstate); i++){
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              for(j=1; j<=(nlstate+ndeath);j++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                k=k+1;
          }                gm[k]=pmmij[i][j];
        }              }
      }            }
    }       
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       codtab[1][2]=1;codtab[2][2]=2; */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
    /* for(i=1; i <=m ;i++){          }
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       }            for(theta=1; theta <=npar; theta++)
       printf("\n");              trgradg[j][theta]=gradg[theta][j];
       }          
       scanf("%d",i);*/          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
              matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
    /* Calculates basic frequencies. Computes observed prevalence at single age          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
        and prints on file fileres'p'. */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
              free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          pmij(pmmij,cov,ncovmodel,x,nlstate);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          k=0;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1; i<=(nlstate); i++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(j=1; j<=(nlstate+ndeath);j++){
                    k=k+1;
     /* For Powell, parameters are in a vector p[] starting at p[1]              mu[k][(int) age]=pmmij[i][j];
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            }
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     if(mle==1){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              varpij[i][j][(int)age] = doldm[i][j];
     }  
              /*printf("\n%d ",(int)age);
     /*--------- results files --------------*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          fprintf(ficresprob,"\n%d ",(int)age);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
    for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresprobcor,"\n%d ",(int)age);
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
          {            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
            printf("%d%d ",i,k);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
            for(j=1; j <=ncovmodel; j++){            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
              printf("%f ",p[jk]);          }
              fprintf(ficres,"%f ",p[jk]);          i=0;
              jk++;          for (k=1; k<=(nlstate);k++){
            }            for (l=1; l<=(nlstate+ndeath);l++){ 
            printf("\n");              i=i++;
            fprintf(ficres,"\n");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
          }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
      }              for (j=1; j<=i;j++){
    }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
  if(mle==1){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     /* Computing hessian and covariance matrix */              }
     ftolhess=ftol; /* Usually correct */            }
     hesscov(matcov, p, npar, delti, ftolhess, func);          }/* end of loop for state */
  }        } /* end of loop for age */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");        /* Confidence intervalle of pij  */
      for(i=1,jk=1; i <=nlstate; i++){        /*
       for(j=1; j <=nlstate+ndeath; j++){          fprintf(ficgp,"\nset noparametric;unset label");
         if (j!=i) {          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficres,"%1d%1d",i,j);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           printf("%1d%1d",i,j);          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);
           for(k=1; k<=ncovmodel;k++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
             printf(" %.5e",delti[jk]);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
             fprintf(ficres," %.5e",delti[jk]);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
             jk++;        */
           }  
           printf("\n");        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           fprintf(ficres,"\n");        first1=1;
         }        for (k2=1; k2<=(nlstate);k2++){
       }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
      }            if(l2==k2) continue;
                j=(k2-1)*(nlstate+ndeath)+l2;
     k=1;            for (k1=1; k1<=(nlstate);k1++){
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     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");                if(l1==k1) continue;
     for(i=1;i<=npar;i++){                i=(k1-1)*(nlstate+ndeath)+l1;
       /*  if (k>nlstate) k=1;                if(i<=j) continue;
       i1=(i-1)/(ncovmodel*nlstate)+1;                for (age=bage; age<=fage; age ++){ 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                  if ((int)age %5==0){
       printf("%s%d%d",alph[k],i1,tab[i]);*/                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficres,"%3d",i);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       printf("%3d",i);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       for(j=1; j<=i;j++){                    mu1=mu[i][(int) age]/stepm*YEARM ;
         fprintf(ficres," %.5e",matcov[i][j]);                    mu2=mu[j][(int) age]/stepm*YEARM;
         printf(" %.5e",matcov[i][j]);                    c12=cv12/sqrt(v1*v2);
       }                    /* Computing eigen value of matrix of covariance */
       fprintf(ficres,"\n");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       printf("\n");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       k++;                    /* Eigen vectors */
     }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                        /*v21=sqrt(1.-v11*v11); *//* error */
     while((c=getc(ficpar))=='#' && c!= EOF){                    v21=(lc1-v1)/cv12*v11;
       ungetc(c,ficpar);                    v12=-v21;
       fgets(line, MAXLINE, ficpar);                    v22=v11;
       puts(line);                    tnalp=v21/v11;
       fputs(line,ficparo);                    if(first1==1){
     }                      first1=0;
     ungetc(c,ficpar);                      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);
     estepm=0;                    }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    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);
     if (estepm==0 || estepm < stepm) estepm=stepm;                    /*printf(fignu*/
     if (fage <= 2) {                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       bage = ageminpar;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       fage = agemaxpar;                    if(first==1){
     }                      first=0;
                          fprintf(ficgp,"\nset parametric;unset label");
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     while((c=getc(ficpar))=='#' && c!= EOF){  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     ungetc(c,ficpar);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     fgets(line, MAXLINE, ficpar);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     puts(line);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     fputs(line,ficparo);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   }                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   ungetc(c,ficpar);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                          }else{
   while((c=getc(ficpar))=='#' && c!= EOF){                      first=0;
     ungetc(c,ficpar);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
     fgets(line, MAXLINE, ficpar);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     puts(line);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     fputs(line,ficparo);                      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),\
   ungetc(c,ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }/* if first */
                   } /* age mod 5 */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                } /* end loop age */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   fscanf(ficpar,"pop_based=%d\n",&popbased);              } /*l12 */
   fprintf(ficparo,"pop_based=%d\n",popbased);              } /* k12 */
   fprintf(ficres,"pop_based=%d\n",popbased);            } /*l1 */
          }/* k1 */
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* loop covariates */
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     puts(line);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     fputs(line,ficparo);    free_vector(xp,1,npar);
   }    fclose(ficresprob);
   ungetc(c,ficpar);    fclose(ficresprobcov);
     fclose(ficresprobcor);
   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);    fflush(ficgp);
 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);    fflush(fichtmcov);
 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);  }
   
   
 while((c=getc(ficpar))=='#' && c!= EOF){  /******************* Printing html file ***********/
     ungetc(c,ficpar);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     fgets(line, MAXLINE, ficpar);                    int lastpass, int stepm, int weightopt, char model[],\
     puts(line);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fputs(line,ficparo);                    int popforecast, int estepm ,\
   }                    double jprev1, double mprev1,double anprev1, \
   ungetc(c,ficpar);                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   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(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
 /*------------ gnuplot -------------*/             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);     fprintf(fichtm,"\
     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
 /*------------ free_vector  -------------*/             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
  chdir(path);     fprintf(fichtm,"\
     - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
  free_ivector(wav,1,imx);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);     fprintf(fichtm,"\
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     - Life expectancies by age and initial health status (estepm=%2d months): \
  free_ivector(num,1,n);     <a href=\"%s\">%s</a> <br>\n</li>",
  free_vector(agedc,1,n);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  
  fclose(ficparo);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  fclose(ficres);  
    m=cptcoveff;
 /*--------- index.htm --------*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);   jj1=0;
    for(k1=1; k1<=m;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   /*--------------- Prevalence limit --------------*/       jj1++;
         if (cptcovn > 0) {
   strcpy(filerespl,"pl");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   strcat(filerespl,fileres);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   }       }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       /* Pij */
   fprintf(ficrespl,"#Prevalence limit\n");       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> \
   fprintf(ficrespl,"#Age ");  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);       /* Quasi-incidences */
   fprintf(ficrespl,"\n");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   prlim=matrix(1,nlstate,1,nlstate);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         /* Stable prevalence in each health state */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for(cpt=1; cpt<nlstate;cpt++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */         }
   k=0;       for(cpt=1; cpt<=nlstate;cpt++) {
   agebase=ageminpar;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   agelim=agemaxpar;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   ftolpl=1.e-10;       }
   i1=cptcoveff;     } /* end i1 */
   if (cptcovn < 1){i1=1;}   }/* End k1 */
    fprintf(fichtm,"</ul>");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;   fprintf(fichtm,"\
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
         fprintf(ficrespl,"\n#******");   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficrespl,"******\n");           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
           fprintf(fichtm,"\
         for (age=agebase; age<=agelim; age++){   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)   fprintf(fichtm,"\
           fprintf(ficrespl," %.5f", prlim[i][i]);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespl,"\n");           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
         }   fprintf(fichtm,"\
       }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
     }           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   fclose(ficrespl);   fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   /*------------- h Pij x at various ages ------------*/           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     fprintf(fichtm,"\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   if((ficrespij=fopen(filerespij,"w"))==NULL) {           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }  /*  if(popforecast==1) fprintf(fichtm,"\n */
   printf("Computing pij: result on file '%s' \n", filerespij);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
    /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*      <br>",fileres,fileres,fileres,fileres); */
   /*if (stepm<=24) stepsize=2;*/  /*  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); */
   agelim=AGESUP;   fflush(fichtm);
   hstepm=stepsize*YEARM; /* Every year of age */   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
     m=cptcoveff;
   k=0;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   jj1=0;
       k=k+1;   for(k1=1; k1<=m;k1++){
         fprintf(ficrespij,"\n#****** ");     for(i1=1; i1<=ncodemax[k1];i1++){
         for(j=1;j<=cptcoveff;j++)       jj1++;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       if (cptcovn > 0) {
         fprintf(ficrespij,"******\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
                 for (cpt=1; cpt<=cptcoveff;cpt++) 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for(cpt=1; cpt<=nlstate;cpt++) {
           oldm=oldms;savm=savms;         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
           fprintf(ficrespij,"# Age");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           for(i=1; i<=nlstate;i++)       }
             for(j=1; j<=nlstate+ndeath;j++)       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
               fprintf(ficrespij," %1d-%1d",i,j);  health expectancies in states (1) and (2): %s%d.png<br>\
           fprintf(ficrespij,"\n");  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
            for (h=0; h<=nhstepm; h++){     } /* end i1 */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );   }/* End k1 */
             for(i=1; i<=nlstate;i++)   fprintf(fichtm,"</ul>");
               for(j=1; j<=nlstate+ndeath;j++)   fflush(fichtm);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  }
             fprintf(ficrespij,"\n");  
              }  /******************* Gnuplot file **************/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           fprintf(ficrespij,"\n");  
         }    char dirfileres[132],optfileres[132];
     }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   }    int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   fclose(ficrespij);  /*   } */
   
     /*#ifdef windows */
   /*---------- Forecasting ------------------*/    fprintf(ficgp,"cd \"%s\" \n",pathc);
   if((stepm == 1) && (strcmp(model,".")==0)){      /*#endif */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    m=pow(2,cptcoveff);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
   }    strcpy(dirfileres,optionfilefiname);
   else{    strcpy(optfileres,"vpl");
     erreur=108;   /* 1eme*/
     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);    for (cpt=1; cpt<= nlstate ; cpt ++) {
   }     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   /*---------- Health expectancies and variances ------------*/       fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   strcpy(filerest,"t");  set ter png small\n\
   strcat(filerest,fileres);  set size 0.65,0.65\n\
   if((ficrest=fopen(filerest,"w"))==NULL) {  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }       for (i=1; i<= nlstate ; i ++) {
   printf("Computing Total LEs with variances: file '%s' \n", filerest);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
   strcpy(filerese,"e");       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);
   strcat(filerese,fileres);       for (i=1; i<= nlstate ; i ++) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       } 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
  strcpy(fileresv,"v");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   strcat(fileresv,fileres);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       }  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
   }     }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    }
   calagedate=-1;    /*2 eme*/
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
     for (k1=1; k1<= m ; k1 ++) { 
   k=0;      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      
       k=k+1;      for (i=1; i<= nlstate+1 ; i ++) {
       fprintf(ficrest,"\n#****** ");        k=2*i;
       for(j=1;j<=cptcoveff;j++)        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (j=1; j<= nlstate+1 ; j ++) {
       fprintf(ficrest,"******\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficreseij,"\n#****** ");        }   
       for(j=1;j<=cptcoveff;j++)        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       fprintf(ficreseij,"******\n");        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 ++) {
       fprintf(ficresvij,"\n#****** ");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       for(j=1;j<=cptcoveff;j++)          else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }   
       fprintf(ficresvij,"******\n");        fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for (j=1; j<= nlstate+1 ; j ++) {
       oldm=oldms;savm=savms;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);            else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       oldm=oldms;savm=savms;        else fprintf(ficgp,"\" t\"\" w l 0,");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      }
        }
     
      /*3eme*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficrest,"\n");      for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
       epj=vector(1,nlstate+1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       for(age=bage; age <=fage ;age++){        fprintf(ficgp,"set ter png small\n\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  set size 0.65,0.65\n\
         if (popbased==1) {  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);
           for(i=1; i<=nlstate;i++)        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             prlim[i][i]=probs[(int)age][i][k];          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                  fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         fprintf(ficrest," %4.0f",age);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           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]);*/        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);
           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];    /* CV preval stable (period) */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    for (k1=1; k1<= m ; k1 ++) { 
         for(j=1;j <=nlstate;j++){      for (cpt=1; cpt<=nlstate ; cpt ++) {
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        k=3;
         }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficrest,"\n");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
       }  set ter png small\nset size 0.65,0.65\n\
     }  unset log y\n\
   }  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
 free_matrix(mint,1,maxwav,1,n);        
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        for (i=1; i< nlstate ; i ++)
     free_vector(weight,1,n);          fprintf(ficgp,"+$%d",k+i+1);
   fclose(ficreseij);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   fclose(ficresvij);        
   fclose(ficrest);        l=3+(nlstate+ndeath)*cpt;
   fclose(ficpar);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   free_vector(epj,1,nlstate+1);        for (i=1; i< nlstate ; i ++) {
            l=3+(nlstate+ndeath)*cpt;
   /*------- Variance limit prevalence------*/            fprintf(ficgp,"+$%d",l+i+1);
         }
   strcpy(fileresvpl,"vpl");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   strcat(fileresvpl,fileres);      } 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    }  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    
     exit(0);    /* proba elementaires */
   }    for(i=1,jk=1; i <=nlstate; i++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
   k=0;          for(j=1; j <=ncovmodel; j++){
   for(cptcov=1;cptcov<=i1;cptcov++){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            jk++; 
       k=k+1;            fprintf(ficgp,"\n");
       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);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       oldm=oldms;savm=savms;       for(jk=1; jk <=m; jk++) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     }         if (ng==2)
  }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
   fclose(ficresvpl);           fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   /*---------- End : free ----------------*/         i=1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);         for(k2=1; k2<=nlstate; k2++) {
             k3=i;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);           for(k=1; k<=(nlstate+ndeath); k++) {
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);             if (k != k2){
                 if(ng==2)
                   fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);               else
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);               ij=1;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);               for(j=3; j <=ncovmodel; j++) {
                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   free_matrix(matcov,1,npar,1,npar);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   free_vector(delti,1,npar);                   ij++;
   free_matrix(agev,1,maxwav,1,imx);                 }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                 else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   if(erreur >0)               }
     printf("End of Imach with error or warning %d\n",erreur);               fprintf(ficgp,")/(1");
   else   printf("End of Imach\n");               
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */               for(k1=1; k1 <=nlstate; k1++){   
                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+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);*/                 ij=1;
   /*printf("Total time was %d uSec.\n", total_usecs);*/                 for(j=3; j <=ncovmodel; j++){
   /*------ End -----------*/                   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++;
  end:                   }
 #ifdef windows                   else
   /* chdir(pathcd);*/                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 #endif                 }
  /*system("wgnuplot graph.plt");*/                 fprintf(ficgp,")");
  /*system("../gp37mgw/wgnuplot graph.plt");*/               }
  /*system("cd ../gp37mgw");*/               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
  strcpy(plotcmd,GNUPLOTPROGRAM);               i=i+ncovmodel;
  strcat(plotcmd," ");             }
  strcat(plotcmd,optionfilegnuplot);           } /* end k */
  system(plotcmd);         } /* end k2 */
        } /* end jk */
 #ifdef windows     } /* end ng */
   while (z[0] != 'q') {     fflush(ficgp); 
     /* chdir(path); */  }  /* end gnuplot */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");  /*************** Moving average **************/
     else if (z[0] == 'e') system(optionfilehtm);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     else if (z[0] == 'g') system(plotcmd);  
     else if (z[0] == 'q') exit(0);    int i, cpt, cptcod;
   }    int modcovmax =1;
 #endif    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];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs)))    {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
           ;
         };
         line[j+1]=0;  /* Trims blanks at end of line */
         if(line[0]=='#'){
           fprintf(ficlog,"Comment line\n%s\n",line);
           printf("Comment line\n%s\n",line);
           continue;
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %d %s for individual %d\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n",lval, i,line,linei,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,".") != 0){
             month=99;
             year=9999;
           }else{
             printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,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,".") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,j);
           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,".") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,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\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, i,line,linei);
             exit(1);
           }
           if(lval <-1 || lval >1){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\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,i,line,linei,j);
             exit(1);
           }
           covar[j][i]=(double)(lval);
           strcpy(line,stra);
         } 
         lstra=strlen(stra);
   
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
     } /* End loop reading  data */
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.1; p[NDIM]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
   #ifndef UNIX
     /*  strcpy(plotcmd,"\""); */
   #endif
     strcpy(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     /*  strcat(plotcmd,"\"");*/
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
   
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     strcat(plotcmd,"\"");
   #endif
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",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.1.42  
changed lines
  Added in v.1.110


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