Diff for /imach/src/imach.c between versions 1.17 and 1.105

version 1.17, 2002/02/20 17:15:02 version 1.105, 2006/01/05 20:23:19
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.105  2006/01/05 20:23:19  lievre
   individuals from different ages are interviewed on their health status    *** empty log message ***
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.104  2005/09/30 16:11:43  lievre
   Health expectancies are computed from the transistions observed between    (Module): sump fixed, loop imx fixed, and simplifications.
   waves and are computed for each degree of severity of disability (number    (Module): If the status is missing at the last wave but we know
   of life states). More degrees you consider, more time is necessary to    that the person is alive, then we can code his/her status as -2
   reach the Maximum Likelihood of the parameters involved in the model.    (instead of missing=-1 in earlier versions) and his/her
   The simplest model is the multinomial logistic model where pij is    contributions to the likelihood is 1 - Prob of dying from last
   the probabibility to be observed in state j at the second wave conditional    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   to be observed in state i at the first wave. Therefore the model is:    the healthy state at last known wave). Version is 0.98
   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 complex model than "constant and    Revision 1.103  2005/09/30 15:54:49  lievre
   age", you should modify the program where the markup    (Module): sump fixed, loop imx fixed, and simplifications.
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.101  2004/09/15 10:38:38  brouard
   individual missed an interview, the information is not rounded or lost, but    Fix on curr_time
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.100  2004/07/12 18:29:06  brouard
   observed in state i at age x+h conditional to the observed state i at age    Add version for Mac OS X. Just define UNIX in Makefile
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.99  2004/06/05 08:57:40  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    *** empty log message ***
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
   Also this programme outputs the covariance matrix of the parameters but also    directly from the data i.e. without the need of knowing the health
   of the life expectancies. It also computes the prevalence limits.    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
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    other analysis, in order to test if the mortality estimated from the
            Institut national d'études démographiques, Paris.    cross-longitudinal survey is different from the mortality estimated
   This software have been partly granted by Euro-REVES, a concerted action    from other sources like vital statistic data.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    The same imach parameter file can be used but the option for mle should be -3.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Agnès, who wrote this part of the code, tried to keep most of the
   **********************************************************************/    former routines in order to include the new code within the former code.
    
 #include <math.h>    The output is very simple: only an estimate of the intercept and of
 #include <stdio.h>    the slope with 95% confident intervals.
 #include <stdlib.h>  
 #include <unistd.h>    Current limitations:
     A) Even if you enter covariates, i.e. with the
 #define MAXLINE 256    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define FILENAMELENGTH 80    B) There is no computation of Life Expectancy nor Life Table.
 /*#define DEBUG*/  
 #define windows    Revision 1.97  2004/02/20 13:25:42  lievre
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Version 0.96d. Population forecasting command line is (temporarily)
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    suppressed.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.96  2003/07/15 15:38:55  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.95  2003/07/08 07:54:34  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    * imach.c (Repository):
 #define NCOVMAX 8 /* Maximum number of covariates */    (Repository): Using imachwizard code to output a more meaningful covariance
 #define MAXN 20000    matrix (cov(a12,c31) instead of numbers.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.94  2003/06/27 13:00:02  brouard
 #define AGEBASE 40    Just cleaning
   
     Revision 1.93  2003/06/25 16:33:55  brouard
 int nvar;    (Module): On windows (cygwin) function asctime_r doesn't
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    exist so I changed back to asctime which exists.
 int npar=NPARMAX;    (Module): Version 0.96b
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.92  2003/06/25 16:30:45  brouard
 int ncovmodel, ncov;     /* 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.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.91  2003/06/25 15:30:29  brouard
 int maxwav; /* Maxim number of waves */    * imach.c (Repository): Duplicated warning errors corrected.
 int jmin, jmax; /* min, max spacing between 2 waves */    (Repository): Elapsed time after each iteration is now output. It
 int mle, weightopt;    helps to forecast when convergence will be reached. Elapsed time
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    is stamped in powell.  We created a new html file for the graphs
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    concerning matrix of covariance. It has extension -cov.htm.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.90  2003/06/24 12:34:15  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Some bugs corrected for windows. Also, when
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    mle=-1 a template is output in file "or"mypar.txt with the design
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    of the covariance matrix to be input.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.89  2003/06/24 12:30:52  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 1.88  2003/06/23 17:54:56  brouard
 #define NR_END 1    * 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 FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 #define NRANSI  
 #define ITMAX 200    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 #define TOL 2.0e-4    routine fileappend.
   
 #define CGOLD 0.3819660    Revision 1.85  2003/06/17 13:12:43  brouard
 #define ZEPS 1.0e-10    * imach.c (Repository): Check when date of death was earlier that
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 #define GOLD 1.618034    was wrong (infinity). We still send an "Error" but patch by
 #define GLIMIT 100.0    assuming that the date of death was just one stepm after the
 #define TINY 1.0e-20    interview.
     (Repository): Because some people have very long ID (first column)
 static double maxarg1,maxarg2;    we changed int to long in num[] and we added a new lvector for
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    memory allocation. But we also truncated to 8 characters (left
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    truncation)
      (Repository): No more line truncation errors.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 static double sqrarg;    place. It differs from routine "prevalence" which may be called
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    many times. Probs is memory consuming and must be used with
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 int imx;  
 int stepm;    Revision 1.83  2003/06/10 13:39:11  lievre
 /* Stepm, step in month: minimum step interpolation*/    *** empty log message ***
   
 int m,nb;    Revision 1.82  2003/06/05 15:57:20  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Add log in  imach.c and  fullversion number is now printed.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;  */
   /*
 double *weight;     Interpolated Markov Chain
 int **s; /* Status */  
 double *agedc, **covar, idx;    Short summary of the programme:
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    
     This program computes Healthy Life Expectancies from
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 double ftolhess; /* Tolerance for computing hessian */    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 /**************** split *************************/    case of a health survey which is our main interest) -2- at least a
 static  int split( char *path, char *dirc, char *name )    second wave of interviews ("longitudinal") which measure each change
 {    (if any) in individual health status.  Health expectancies are
    char *s;                             /* pointer */    computed from the time spent in each health state according to a
    int  l1, l2;                         /* length counters */    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
    l1 = strlen( path );                 /* length of path */    simplest model is the multinomial logistic model where pij is the
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    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
    if ( s == NULL ) {                   /* no directory, so use current */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #if     defined(__bsd__)                /* get current working directory */    'age' is age and 'sex' is a covariate. If you want to have a more
       extern char       *getwd( );    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
       if ( getwd( dirc ) == NULL ) {    you to do it.  More covariates you add, slower the
 #else    convergence.
       extern char       *getcwd( );  
     The advantage of this computer programme, compared to a simple
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    multinomial logistic model, is clear when the delay between waves is not
 #endif    identical for each individual. Also, if a individual missed an
          return( GLOCK_ERROR_GETCWD );    intermediate interview, the information is lost, but taken into
       }    account using an interpolation or extrapolation.  
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    hPijx is the probability to be observed in state i at age x+h
       s++;                              /* after this, the filename */    conditional to the observed state i at age x. The delay 'h' can be
       l2 = strlen( s );                 /* length of filename */    split into an exact number (nh*stepm) of unobserved intermediate
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    states. This elementary transition (by month, quarter,
       strcpy( name, s );                /* save file name */    semester or year) is modelled as a multinomial logistic.  The hPx
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    matrix is simply the matrix product of nh*stepm elementary matrices
       dirc[l1-l2] = 0;                  /* add zero */    and the contribution of each individual to the likelihood is simply
    }    hPijx.
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Also this programme outputs the covariance matrix of the parameters but also
    return( 0 );                         /* we're done */    of the life expectancies. It also computes the stable prevalence. 
 }    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /******************************************/    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 void replace(char *s, char*t)    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   int i;    can be accessed at http://euroreves.ined.fr/imach .
   int lg=20;  
   i=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   lg=strlen(t);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   for(i=0; i<= lg; i++) {    
     (s[i] = t[i]);    **********************************************************************/
     if (t[i]== '\\') s[i]='/';  /*
   }    main
 }    read parameterfile
     read datafile
 int nbocc(char *s, char occ)    concatwav
 {    freqsummary
   int i,j=0;    if (mle >= 1)
   int lg=20;      mlikeli
   i=0;    print results files
   lg=strlen(s);    if mle==1 
   for(i=0; i<= lg; i++) {       computes hessian
   if  (s[i] == occ ) j++;    read end of parameter file: agemin, agemax, bage, fage, estepm
   }        begin-prev-date,...
   return j;    open gnuplot file
 }    open html file
     stable prevalence
 void cutv(char *u,char *v, char*t, char occ)     for age prevalim()
 {    h Pij x
   int i,lg,j,p=0;    variance of p varprob
   i=0;    forecasting if prevfcast==1 prevforecast call prevalence()
   for(j=0; j<=strlen(t)-1; j++) {    health expectancies
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Variance-covariance of DFLE
   }    prevalence()
      movingaverage()
   lg=strlen(t);    varevsij() 
   for(j=0; j<p; j++) {    if popbased==1 varevsij(,popbased)
     (u[j] = t[j]);    total life expectancies
   }    Variance of stable prevalence
      u[p]='\0';   end
   */
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  
 }   
   #include <math.h>
 /********************** nrerror ********************/  #include <stdio.h>
   #include <stdlib.h>
 void nrerror(char error_text[])  #include <unistd.h>
 {  
   fprintf(stderr,"ERREUR ...\n");  /* #include <sys/time.h> */
   fprintf(stderr,"%s\n",error_text);  #include <time.h>
   exit(1);  #include "timeval.h"
 }  
 /*********************** vector *******************/  /* #include <libintl.h> */
 double *vector(int nl, int nh)  /* #define _(String) gettext (String) */
 {  
   double *v;  #define MAXLINE 256
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define GNUPLOTPROGRAM "gnuplot"
   if (!v) nrerror("allocation failure in vector");  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   return v-nl+NR_END;  #define FILENAMELENGTH 132
 }  /*#define DEBUG*/
   /*#define windows*/
 /************************ free vector ******************/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 void free_vector(double*v, int nl, int nh)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 {  
   free((FREE_ARG)(v+nl-NR_END));  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 /************************ivector *******************************/  #define NINTERVMAX 8
 int *ivector(long nl,long nh)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   int *v;  #define NCOVMAX 8 /* Maximum number of covariates */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define MAXN 20000
   if (!v) nrerror("allocation failure in ivector");  #define YEARM 12. /* Number of months per year */
   return v-nl+NR_END;  #define AGESUP 130
 }  #define AGEBASE 40
   #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 /******************free ivector **************************/  #ifdef UNIX
 void free_ivector(int *v, long nl, long nh)  #define DIRSEPARATOR '/'
 {  #define ODIRSEPARATOR '\\'
   free((FREE_ARG)(v+nl-NR_END));  #else
 }  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 /******************* imatrix *******************************/  #endif
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /* $Id$ */
 {  /* $State$ */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
    char fullversion[]="$Revision$ $Date$"; 
   /* allocate pointers to rows */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int nvar;
   if (!m) nrerror("allocation failure 1 in matrix()");  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m += NR_END;  int npar=NPARMAX;
   m -= nrl;  int nlstate=2; /* Number of live states */
    int ndeath=1; /* Number of dead states */
    int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   /* allocate rows and set pointers to them */  int popbased=0;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int *wav; /* Number of waves for this individuual 0 is possible */
   m[nrl] += NR_END;  int maxwav; /* Maxim number of waves */
   m[nrl] -= ncl;  int jmin, jmax; /* min, max spacing between 2 waves */
    int gipmx, gsw; /* Global variables on the number of contributions 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;                     to the likelihood and the sum of weights (done by funcone)*/
    int mle, weightopt;
   /* return pointer to array of pointers to rows */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   return m;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 }  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. */
 /****************** free_imatrix *************************/  double jmean; /* Mean space between 2 waves */
 void free_imatrix(m,nrl,nrh,ncl,nch)  double **oldm, **newm, **savm; /* Working pointers to matrices */
       int **m;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       long nch,ncl,nrh,nrl;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
      /* free an int matrix allocated by imatrix() */  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  double fretone; /* Only one call to likelihood */
   free((FREE_ARG) (m+nrl-NR_END));  long ipmx; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /******************* matrix *******************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE *ficresilk;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  FILE *ficresprobmorprev;
   double **m;  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char filerese[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE  *ficresvij;
   m += NR_END;  char fileresv[FILENAMELENGTH];
   m -= nrl;  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char title[MAXLINE];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m[nrl] += NR_END;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   m[nrl] -= ncl;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int  outcmd=0;
   return m;  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
 /*************************free matrix ************************/  char filelog[FILENAMELENGTH]; /* Log file */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char popfile[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  
 }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 /******************* ma3x *******************************/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  struct timezone tzp;
 {  extern int gettimeofday();
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double ***m;  long time_value;
   extern long time();
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char strcurr[80], strfor[80];
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define NR_END 1
   m -= nrl;  #define FREE_ARG char*
   #define FTOL 1.0e-10
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NRANSI 
   m[nrl] += NR_END;  #define ITMAX 200 
   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 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define ZEPS 1.0e-10 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  #define GOLD 1.618034 
   for (j=ncl+1; j<=nch; j++)  #define GLIMIT 100.0 
     m[nrl][j]=m[nrl][j-1]+nlay;  #define TINY 1.0e-20 
    
   for (i=nrl+1; i<=nrh; i++) {  static double maxarg1,maxarg2;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     for (j=ncl+1; j<=nch; j++)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       m[i][j]=m[i][j-1]+nlay;    
   }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   return m;  #define rint(a) floor(a+0.5)
 }  
   static double sqrarg;
 /*************************free ma3x ************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  int agegomp= AGEGOMP;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int imx; 
   free((FREE_ARG)(m+nrl-NR_END));  int stepm=1;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /***************** f1dim *************************/  int estepm;
 extern int ncom;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  int m,nb;
    long *num;
 double f1dim(double x)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   int j;  double **pmmij, ***probs;
   double f;  double *ageexmed,*agecens;
   double *xt;  double dateintmean=0;
    
   xt=vector(1,ncom);  double *weight;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int **s; /* Status */
   f=(*nrfunc)(xt);  double *agedc, **covar, idx;
   free_vector(xt,1,ncom);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   return f;  double *lsurv, *lpop, *tpop;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /*****************brent *************************/  double ftolhess; /* Tolerance for computing hessian */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /**************** split *************************/
   int iter;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   double a,b,d,etemp;  {
   double fu,fv,fw,fx;    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   double ftemp;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double p,q,r,tol1,tol2,u,v,w,x,xm;    */ 
   double e=0.0;    char  *ss;                            /* pointer */
      int   l1, l2;                         /* length counters */
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    l1 = strlen(path );                   /* length of path */
   x=w=v=bx;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   fw=fv=fx=(*f)(x);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for (iter=1;iter<=ITMAX;iter++) {    if ( ss == NULL ) {                   /* no directory, so use current */
     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      strcpy( name, path );               /* we've got it */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    } else {                              /* strip direcotry from path */
       *xmin=x;      ss++;                               /* after this, the filename */
       return fx;      l2 = strlen( ss );                  /* length of filename */
     }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     ftemp=fu;      strcpy( name, ss );         /* save file name */
     if (fabs(e) > tol1) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       r=(x-w)*(fx-fv);      dirc[l1-l2] = 0;                    /* add zero */
       q=(x-v)*(fx-fw);    }
       p=(x-v)*q-(x-w)*r;    l1 = strlen( dirc );                  /* length of directory */
       q=2.0*(q-r);    /*#ifdef windows
       if (q > 0.0) p = -p;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
       q=fabs(q);  #else
       etemp=e;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
       e=d;  #endif
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    ss = strrchr( name, '.' );            /* find last / */
       else {    if (ss >0){
         d=p/q;      ss++;
         u=x+d;      strcpy(ext,ss);                     /* save extension */
         if (u-a < tol2 || b-u < tol2)      l1= strlen( name);
           d=SIGN(tol1,xm-x);      l2= strlen(ss)+1;
       }      strncpy( finame, name, l1-l2);
     } else {      finame[l1-l2]= 0;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    }
     }    return( 0 );                          /* we're done */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  }
     fu=(*f)(u);  
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  /******************************************/
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  void replace_back_to_slash(char *s, char*t)
         } else {  {
           if (u < x) a=u; else b=u;    int i;
           if (fu <= fw || w == x) {    int lg=0;
             v=w;    i=0;
             w=u;    lg=strlen(t);
             fv=fw;    for(i=0; i<= lg; i++) {
             fw=fu;      (s[i] = t[i]);
           } else if (fu <= fv || v == x || v == w) {      if (t[i]== '\\') s[i]='/';
             v=u;    }
             fv=fu;  }
           }  
         }  int nbocc(char *s, char occ)
   }  {
   nrerror("Too many iterations in brent");    int i,j=0;
   *xmin=x;    int lg=20;
   return fx;    i=0;
 }    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 /****************** mnbrak ***********************/    if  (s[i] == occ ) j++;
     }
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    return j;
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  void cutv(char *u,char *v, char*t, char occ)
   double fu;  {
      /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   *fa=(*func)(*ax);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   *fb=(*func)(*bx);       gives u="abcedf" and v="ghi2j" */
   if (*fb > *fa) {    int i,lg,j,p=0;
     SHFT(dum,*ax,*bx,dum)    i=0;
       SHFT(dum,*fb,*fa,dum)    for(j=0; j<=strlen(t)-1; j++) {
       }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   *cx=(*bx)+GOLD*(*bx-*ax);    }
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    lg=strlen(t);
     r=(*bx-*ax)*(*fb-*fc);    for(j=0; j<p; j++) {
     q=(*bx-*cx)*(*fb-*fa);      (u[j] = t[j]);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    }
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));       u[p]='\0';
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {     for(j=0; j<= lg; j++) {
       fu=(*func)(u);      if (j>=(p+1))(v[j-p-1] = t[j]);
     } else if ((*cx-u)*(u-ulim) > 0.0) {    }
       fu=(*func)(u);  }
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /********************** nrerror ********************/
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  void nrerror(char error_text[])
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  {
       u=ulim;    fprintf(stderr,"ERREUR ...\n");
       fu=(*func)(u);    fprintf(stderr,"%s\n",error_text);
     } else {    exit(EXIT_FAILURE);
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  /*********************** vector *******************/
     }  double *vector(int nl, int nh)
     SHFT(*ax,*bx,*cx,u)  {
       SHFT(*fa,*fb,*fc,fu)    double *v;
       }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /*************** linmin ************************/  }
   
 int ncom;  /************************ free vector ******************/
 double *pcom,*xicom;  void free_vector(double*v, int nl, int nh)
 double (*nrfunc)(double []);  {
      free((FREE_ARG)(v+nl-NR_END));
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  }
 {  
   double brent(double ax, double bx, double cx,  /************************ivector *******************************/
                double (*f)(double), double tol, double *xmin);  int *ivector(long nl,long nh)
   double f1dim(double x);  {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    int *v;
               double *fc, double (*func)(double));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   int j;    if (!v) nrerror("allocation failure in ivector");
   double xx,xmin,bx,ax;    return v-nl+NR_END;
   double fx,fb,fa;  }
    
   ncom=n;  /******************free ivector **************************/
   pcom=vector(1,n);  void free_ivector(int *v, long nl, long nh)
   xicom=vector(1,n);  {
   nrfunc=func;    free((FREE_ARG)(v+nl-NR_END));
   for (j=1;j<=n;j++) {  }
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /************************lvector *******************************/
   }  long *lvector(long nl,long nh)
   ax=0.0;  {
   xx=1.0;    long *v;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  /******************free lvector **************************/
     xi[j] *= xmin;  void free_lvector(long *v, long nl, long nh)
     p[j] += xi[j];  {
   }    free((FREE_ARG)(v+nl-NR_END));
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  
 }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
 /*************** powell ************************/       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  { 
             double (*func)(double []))    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {    int **m; 
   void linmin(double p[], double xi[], int n, double *fret,    
               double (*func)(double []));    /* allocate pointers to rows */ 
   int i,ibig,j;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double del,t,*pt,*ptt,*xit;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double fp,fptt;    m += NR_END; 
   double *xits;    m -= nrl; 
   pt=vector(1,n);    
   ptt=vector(1,n);    
   xit=vector(1,n);    /* allocate rows and set pointers to them */ 
   xits=vector(1,n);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   *fret=(*func)(p);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (j=1;j<=n;j++) pt[j]=p[j];    m[nrl] += NR_END; 
   for (*iter=1;;++(*iter)) {    m[nrl] -= ncl; 
     fp=(*fret);    
     ibig=0;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     del=0.0;    
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    /* return pointer to array of pointers to rows */ 
     for (i=1;i<=n;i++)    return m; 
       printf(" %d %.12f",i, p[i]);  } 
     printf("\n");  
     for (i=1;i<=n;i++) {  /****************** free_imatrix *************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  void free_imatrix(m,nrl,nrh,ncl,nch)
       fptt=(*fret);        int **m;
 #ifdef DEBUG        long nch,ncl,nrh,nrl; 
       printf("fret=%lf \n",*fret);       /* free an int matrix allocated by imatrix() */ 
 #endif  { 
       printf("%d",i);fflush(stdout);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       linmin(p,xit,n,fret,func);    free((FREE_ARG) (m+nrl-NR_END)); 
       if (fabs(fptt-(*fret)) > del) {  } 
         del=fabs(fptt-(*fret));  
         ibig=i;  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
 #ifdef DEBUG  {
       printf("%d %.12e",i,(*fret));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       for (j=1;j<=n;j++) {    double **m;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
       for(j=1;j<=n;j++)    m += NR_END;
         printf(" p=%.12e",p[j]);    m -= nrl;
       printf("\n");  
 #endif    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m[nrl] += NR_END;
 #ifdef DEBUG    m[nrl] -= ncl;
       int k[2],l;  
       k[0]=1;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       k[1]=-1;    return m;
       printf("Max: %.12e",(*func)(p));    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       for (j=1;j<=n;j++)     */
         printf(" %.12e",p[j]);  }
       printf("\n");  
       for(l=0;l<=1;l++) {  /*************************free matrix ************************/
         for (j=1;j<=n;j++) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
           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((FREE_ARG)(m[nrl]+ncl-NR_END));
         }    free((FREE_ARG)(m+nrl-NR_END));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  }
       }  
 #endif  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
       free_vector(xit,1,n);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       free_vector(xits,1,n);    double ***m;
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       return;    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m -= nrl;
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       xit[j]=p[j]-pt[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       pt[j]=p[j];    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
     fptt=(*func)(ptt);  
     if (fptt < fp) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         linmin(p,xit,n,fret,func);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         for (j=1;j<=n;j++) {    m[nrl][ncl] += NR_END;
           xi[j][ibig]=xi[j][n];    m[nrl][ncl] -= nll;
           xi[j][n]=xit[j];    for (j=ncl+1; j<=nch; j++) 
         }      m[nrl][j]=m[nrl][j-1]+nlay;
 #ifdef DEBUG    
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    for (i=nrl+1; i<=nrh; i++) {
         for(j=1;j<=n;j++)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
           printf(" %.12e",xit[j]);      for (j=ncl+1; j<=nch; j++) 
         printf("\n");        m[i][j]=m[i][j-1]+nlay;
 #endif    }
       }    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 }    */
   }
 /**** Prevalence limit ****************/  
   /*************************free ma3x ************************/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
      matrix by transitions matrix until convergence is reached */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   int i, ii,j,k;  }
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  /*************** function subdirf ***********/
   double **out, cov[NCOVMAX], **pmij();  char *subdirf(char fileres[])
   double **newm;  {
   double agefin, delaymax=50 ; /* Max number of years to converge */    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   for (ii=1;ii<=nlstate+ndeath;ii++)    strcat(tmpout,"/"); /* Add to the right */
     for (j=1;j<=nlstate+ndeath;j++){    strcat(tmpout,fileres);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return tmpout;
     }  }
   
    cov[1]=1.;  /*************** function subdirf2 ***********/
    char *subdirf2(char fileres[], char *preop)
  /* 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;    /* Caution optionfilefiname is hidden */
     /* Covariates have to be included here again */    strcpy(tmpout,optionfilefiname);
      cov[2]=agefin;    strcat(tmpout,"/");
      strcat(tmpout,preop);
       for (k=1; k<=cptcovn;k++) {    strcat(tmpout,fileres);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    return tmpout;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  }
       }  
       for (k=1; k<=cptcovage;k++)  /*************** function subdirf3 ***********/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (k=1; k<=cptcovprod;k++)  {
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    
     /* Caution optionfilefiname is hidden */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    strcpy(tmpout,optionfilefiname);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    strcat(tmpout,"/");
     strcat(tmpout,preop);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
     savm=oldm;    return tmpout;
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /***************** f1dim *************************/
       min=1.;  extern int ncom; 
       max=0.;  extern double *pcom,*xicom;
       for(i=1; i<=nlstate; i++) {  extern double (*nrfunc)(double []); 
         sumnew=0;   
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double f1dim(double x) 
         prlim[i][j]= newm[i][j]/(1-sumnew);  { 
         max=FMAX(max,prlim[i][j]);    int j; 
         min=FMIN(min,prlim[i][j]);    double f;
       }    double *xt; 
       maxmin=max-min;   
       maxmax=FMAX(maxmax,maxmin);    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     if(maxmax < ftolpl){    f=(*nrfunc)(xt); 
       return prlim;    free_vector(xt,1,ncom); 
     }    return f; 
   }  } 
 }  
   /*****************brent *************************/
 /*************** transition probabilities ***************/  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    int iter; 
 {    double a,b,d,etemp;
   double s1, s2;    double fu,fv,fw,fx;
   /*double t34;*/    double ftemp;
   int i,j,j1, nc, ii, jj;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
     for(i=1; i<= nlstate; i++){   
     for(j=1; j<i;j++){    a=(ax < cx ? ax : cx); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    b=(ax > cx ? ax : cx); 
         /*s2 += param[i][j][nc]*cov[nc];*/    x=w=v=bx; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    fw=fv=fx=(*f)(x); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    for (iter=1;iter<=ITMAX;iter++) { 
       }      xm=0.5*(a+b); 
       ps[i][j]=s2;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     }      printf(".");fflush(stdout);
     for(j=i+1; j<=nlstate+ndeath;j++){      fprintf(ficlog,".");fflush(ficlog);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #ifdef DEBUG
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      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);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       ps[i][j]=(s2);  #endif
     }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   }        *xmin=x; 
     /*ps[3][2]=1;*/        return fx; 
       } 
   for(i=1; i<= nlstate; i++){      ftemp=fu;
      s1=0;      if (fabs(e) > tol1) { 
     for(j=1; j<i; j++)        r=(x-w)*(fx-fv); 
       s1+=exp(ps[i][j]);        q=(x-v)*(fx-fw); 
     for(j=i+1; j<=nlstate+ndeath; j++)        p=(x-v)*q-(x-w)*r; 
       s1+=exp(ps[i][j]);        q=2.0*(q-r); 
     ps[i][i]=1./(s1+1.);        if (q > 0.0) p = -p; 
     for(j=1; j<i; j++)        q=fabs(q); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        etemp=e; 
     for(j=i+1; j<=nlstate+ndeath; j++)        e=d; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   } /* end i */        else { 
           d=p/q; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          u=x+d; 
     for(jj=1; jj<= nlstate+ndeath; jj++){          if (u-a < tol2 || b-u < tol2) 
       ps[ii][jj]=0;            d=SIGN(tol1,xm-x); 
       ps[ii][ii]=1;        } 
     }      } else { 
   }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      fu=(*f)(u); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (fu <= fx) { 
      printf("%lf ",ps[ii][jj]);        if (u >= x) a=x; else b=x; 
    }        SHFT(v,w,x,u) 
     printf("\n ");          SHFT(fv,fw,fx,fu) 
     }          } else { 
     printf("\n ");printf("%lf ",cov[2]);*/            if (u < x) a=u; else b=u; 
 /*            if (fu <= fw || w == x) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);              v=w; 
   goto end;*/              w=u; 
     return ps;              fv=fw; 
 }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 /**************** Product of 2 matrices ******************/              v=u; 
               fv=fu; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)            } 
 {          } 
   /* 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(...) */    nrerror("Too many iterations in brent"); 
   /* in, b, out are matrice of pointers which should have been initialized    *xmin=x; 
      before: only the contents of out is modified. The function returns    return fx; 
      a pointer to pointers identical to out */  } 
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /****************** mnbrak ***********************/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         out[i][k] +=in[i][j]*b[j][k];              double (*func)(double)) 
   { 
   return out;    double ulim,u,r,q, dum;
 }    double fu; 
    
     *fa=(*func)(*ax); 
 /************* Higher Matrix Product ***************/    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      SHFT(dum,*ax,*bx,dum) 
 {        SHFT(dum,*fb,*fa,dum) 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        } 
      duration (i.e. until    *cx=(*bx)+GOLD*(*bx-*ax); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    *fc=(*func)(*cx); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    while (*fb > *fc) { 
      (typically every 2 years instead of every month which is too big).      r=(*bx-*ax)*(*fb-*fc); 
      Model is determined by parameters x and covariates have to be      q=(*bx-*cx)*(*fb-*fa); 
      included manually here.      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
      */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
   int i, j, d, h, k;        fu=(*func)(u); 
   double **out, cov[NCOVMAX];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double **newm;        fu=(*func)(u); 
         if (fu < *fc) { 
   /* Hstepm could be zero and should return the unit matrix */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   for (i=1;i<=nlstate+ndeath;i++)            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (j=1;j<=nlstate+ndeath;j++){            } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        u=ulim; 
     }        fu=(*func)(u); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } else { 
   for(h=1; h <=nhstepm; h++){        u=(*cx)+GOLD*(*cx-*bx); 
     for(d=1; d <=hstepm; d++){        fu=(*func)(u); 
       newm=savm;      } 
       /* Covariates have to be included here again */      SHFT(*ax,*bx,*cx,u) 
       cov[1]=1.;        SHFT(*fa,*fb,*fc,fu) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*************** linmin ************************/
       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]]];  int ncom; 
   double *pcom,*xicom;
   double (*nrfunc)(double []); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/   
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double brent(double ax, double bx, double cx, 
       savm=oldm;                 double (*f)(double), double tol, double *xmin); 
       oldm=newm;    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     for(i=1; i<=nlstate+ndeath; i++)                double *fc, double (*func)(double)); 
       for(j=1;j<=nlstate+ndeath;j++) {    int j; 
         po[i][j][h]=newm[i][j];    double xx,xmin,bx,ax; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double fx,fb,fa;
          */   
       }    ncom=n; 
   } /* end h */    pcom=vector(1,n); 
   return po;    xicom=vector(1,n); 
 }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
 /*************** log-likelihood *************/      xicom[j]=xi[j]; 
 double func( double *x)    } 
 {    ax=0.0; 
   int i, ii, j, k, mi, d, kk;    xx=1.0; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double **out;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double sw; /* Sum of weights */  #ifdef DEBUG
   double lli; /* Individual log likelihood */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   long ipmx;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*extern weight */  #endif
   /* We are differentiating ll according to initial status */    for (j=1;j<=n;j++) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      xi[j] *= xmin; 
   /*for(i=1;i<imx;i++)      p[j] += xi[j]; 
     printf(" %d\n",s[4][i]);    } 
   */    free_vector(xicom,1,n); 
   cov[1]=1.;    free_vector(pcom,1,n); 
   } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  char *asc_diff_time(long time_sec, char ascdiff[])
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
     for(mi=1; mi<= wav[i]-1; mi++){    long sec_left, days, hours, minutes;
       for (ii=1;ii<=nlstate+ndeath;ii++)    days = (time_sec) / (60*60*24);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    sec_left = (time_sec) % (60*60*24);
       for(d=0; d<dh[mi][i]; d++){    hours = (sec_left) / (60*60) ;
         newm=savm;    sec_left = (sec_left) %(60*60);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    minutes = (sec_left) /60;
         for (kk=1; kk<=cptcovage;kk++) {    sec_left = (sec_left) % (60);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         }    return ascdiff;
          }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*************** powell ************************/
         savm=oldm;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         oldm=newm;              double (*func)(double [])) 
          { 
            void linmin(double p[], double xi[], int n, double *fret, 
       } /* end mult */                double (*func)(double [])); 
          int i,ibig,j; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double del,t,*pt,*ptt,*xit;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double fp,fptt;
       ipmx +=1;    double *xits;
       sw += weight[i];    int niterf, itmp;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */    pt=vector(1,n); 
   } /* end of individual */    ptt=vector(1,n); 
     xit=vector(1,n); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    xits=vector(1,n); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    *fret=(*func)(p); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    for (j=1;j<=n;j++) pt[j]=p[j]; 
   return -l;    for (*iter=1;;++(*iter)) { 
 }      fp=(*fret); 
       ibig=0; 
       del=0.0; 
 /*********** Maximum Likelihood Estimation ***************/      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 {      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   int i,j, iter;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   double **xi,*delti;      */
   double fret;     for (i=1;i<=n;i++) {
   xi=matrix(1,npar,1,npar);        printf(" %d %.12f",i, p[i]);
   for (i=1;i<=npar;i++)        fprintf(ficlog," %d %.12lf",i, p[i]);
     for (j=1;j<=npar;j++)        fprintf(ficrespow," %.12lf", p[i]);
       xi[i][j]=(i==j ? 1.0 : 0.0);      }
   printf("Powell\n");      printf("\n");
   powell(p,xi,npar,ftol,&iter,&fret,func);      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      if(*iter <=3){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
 }  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
 /**** Computes Hessian and covariance matrix ***/        itmp = strlen(strcurr);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 {          strcurr[itmp-1]='\0';
   double  **a,**y,*x,pd;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double **hess;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int i, j,jk;        for(niterf=10;niterf<=30;niterf+=10){
   int *indx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   double hessii(double p[], double delta, int theta, double delti[]);  /*      asctime_r(&tmf,strfor); */
   double hessij(double p[], double delti[], int i, int j);          strcpy(strfor,asctime(&tmf));
   void lubksb(double **a, int npar, int *indx, double b[]) ;          itmp = strlen(strfor);
   void ludcmp(double **a, int npar, int *indx, double *d) ;          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
   hess=matrix(1,npar,1,npar);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
           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("\nCalculation of the hessian matrix. Wait...\n");        }
   for (i=1;i<=npar;i++){      }
     printf("%d",i);fflush(stdout);      for (i=1;i<=n;i++) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     /*printf(" %f ",p[i]);*/        fptt=(*fret); 
     /*printf(" %lf ",hess[i][i]);*/  #ifdef DEBUG
   }        printf("fret=%lf \n",*fret);
          fprintf(ficlog,"fret=%lf \n",*fret);
   for (i=1;i<=npar;i++) {  #endif
     for (j=1;j<=npar;j++)  {        printf("%d",i);fflush(stdout);
       if (j>i) {        fprintf(ficlog,"%d",i);fflush(ficlog);
         printf(".%d%d",i,j);fflush(stdout);        linmin(p,xit,n,fret,func); 
         hess[i][j]=hessij(p,delti,i,j);        if (fabs(fptt-(*fret)) > del) { 
         hess[j][i]=hess[i][j];              del=fabs(fptt-(*fret)); 
         /*printf(" %lf ",hess[i][j]);*/          ibig=i; 
       }        } 
     }  #ifdef DEBUG
   }        printf("%d %.12e",i,(*fret));
   printf("\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            printf(" x(%d)=%.12e",j,xit[j]);
   a=matrix(1,npar,1,npar);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   y=matrix(1,npar,1,npar);        }
   x=vector(1,npar);        for(j=1;j<=n;j++) {
   indx=ivector(1,npar);          printf(" p=%.12e",p[j]);
   for (i=1;i<=npar;i++)          fprintf(ficlog," p=%.12e",p[j]);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);        printf("\n");
         fprintf(ficlog,"\n");
   for (j=1;j<=npar;j++) {  #endif
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     lubksb(a,npar,indx,x);  #ifdef DEBUG
     for (i=1;i<=npar;i++){        int k[2],l;
       matcov[i][j]=x[i];        k[0]=1;
     }        k[1]=-1;
   }        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   printf("\n#Hessian matrix#\n");        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) {          printf(" %.12e",p[j]);
     for (j=1;j<=npar;j++) {          fprintf(ficlog," %.12e",p[j]);
       printf("%.3e ",hess[i][j]);        }
     }        printf("\n");
     printf("\n");        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   /* Recompute Inverse */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for (i=1;i<=npar;i++)            printf("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++) a[i][j]=matcov[i][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]);
   ludcmp(a,npar,indx,&pd);          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /*  printf("\n#Hessian matrix recomputed#\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   for (j=1;j<=npar;j++) {  #endif
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  
     lubksb(a,npar,indx,x);        free_vector(xit,1,n); 
     for (i=1;i<=npar;i++){        free_vector(xits,1,n); 
       y[i][j]=x[i];        free_vector(ptt,1,n); 
       printf("%.3e ",y[i][j]);        free_vector(pt,1,n); 
     }        return; 
     printf("\n");      } 
   }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   */      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
   free_matrix(a,1,npar,1,npar);        xit[j]=p[j]-pt[j]; 
   free_matrix(y,1,npar,1,npar);        pt[j]=p[j]; 
   free_vector(x,1,npar);      } 
   free_ivector(indx,1,npar);      fptt=(*func)(ptt); 
   free_matrix(hess,1,npar,1,npar);      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
 }          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
 /*************** hessian matrix ****************/            xi[j][ibig]=xi[j][n]; 
 double hessii( double x[], double delta, int theta, double delti[])            xi[j][n]=xit[j]; 
 {          }
   int i;  #ifdef DEBUG
   int l=1, lmax=20;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double k1,k2;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double p2[NPARMAX+1];          for(j=1;j<=n;j++){
   double res;            printf(" %.12e",xit[j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            fprintf(ficlog," %.12e",xit[j]);
   double fx;          }
   int k=0,kmax=10;          printf("\n");
   double l1;          fprintf(ficlog,"\n");
   #endif
   fx=func(x);        }
   for (i=1;i<=npar;i++) p2[i]=x[i];      } 
   for(l=0 ; l <=lmax; l++){    } 
     l1=pow(10,l);  } 
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  /**** Prevalence limit (stable prevalence)  ****************/
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       k1=func(p2)-fx;  {
       p2[theta]=x[theta]-delt;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       k2=func(p2)-fx;       matrix by transitions matrix until convergence is reached */
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int i, ii,j,k;
          double min, max, maxmin, maxmax,sumnew=0.;
 #ifdef DEBUG    double **matprod2();
       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);    double **out, cov[NCOVMAX], **pmij();
 #endif    double **newm;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double agefin, delaymax=50 ; /* Max number of years to converge */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    for (ii=1;ii<=nlstate+ndeath;ii++)
       }      for (j=1;j<=nlstate+ndeath;j++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         k=kmax; l=lmax*10.;      }
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){     cov[1]=1.;
         delts=delt;   
       }   /* 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;
   delti[theta]=delts;      /* Covariates have to be included here again */
   return res;       cov[2]=agefin;
      
 }        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 double hessij( double x[], double delti[], int thetai,int thetaj)          /*      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]]);*/
 {        }
   int i;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int l=1, l1, lmax=20;        for (k=1; k<=cptcovprod;k++)
   double k1,k2,k3,k4,res,fx;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double p2[NPARMAX+1];  
   int k;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   fx=func(x);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   for (k=1; k<=2; k++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;      savm=oldm;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      oldm=newm;
     k1=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.;
     k2=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);
     k3=func(p2)-fx;          max=FMAX(max,prlim[i][j]);
            min=FMIN(min,prlim[i][j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        maxmin=max-min;
     k4=func(p2)-fx;        maxmax=FMAX(maxmax,maxmin);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      }
 #ifdef DEBUG      if(maxmax < ftolpl){
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        return prlim;
 #endif      }
   }    }
   return res;  }
 }  
   /*************** transition probabilities ***************/ 
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   int i,imax,j,k;    double s1, s2;
   double big,dum,sum,temp;    /*double t34;*/
   double *vv;    int i,j,j1, nc, ii, jj;
    
   vv=vector(1,n);      for(i=1; i<= nlstate; i++){
   *d=1.0;        for(j=1; j<i;j++){
   for (i=1;i<=n;i++) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     big=0.0;            /*s2 += param[i][j][nc]*cov[nc];*/
     for (j=1;j<=n;j++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          }
     vv[i]=1.0/big;          ps[i][j]=s2;
   }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   for (j=1;j<=n;j++) {        }
     for (i=1;i<j;i++) {        for(j=i+1; j<=nlstate+ndeath;j++){
       sum=a[i][j];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       a[i][j]=sum;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     }          }
     big=0.0;          ps[i][j]=s2;
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];      }
       for (k=1;k<j;k++)      /*ps[3][2]=1;*/
         sum -= a[i][k]*a[k][j];      
       a[i][j]=sum;      for(i=1; i<= nlstate; i++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {        s1=0;
         big=dum;        for(j=1; j<i; j++)
         imax=i;          s1+=exp(ps[i][j]);
       }        for(j=i+1; j<=nlstate+ndeath; j++)
     }          s1+=exp(ps[i][j]);
     if (j != imax) {        ps[i][i]=1./(s1+1.);
       for (k=1;k<=n;k++) {        for(j=1; j<i; j++)
         dum=a[imax][k];          ps[i][j]= exp(ps[i][j])*ps[i][i];
         a[imax][k]=a[j][k];        for(j=i+1; j<=nlstate+ndeath; j++)
         a[j][k]=dum;          ps[i][j]= exp(ps[i][j])*ps[i][i];
       }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       *d = -(*d);      } /* end i */
       vv[imax]=vv[j];      
     }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     indx[j]=imax;        for(jj=1; jj<= nlstate+ndeath; jj++){
     if (a[j][j] == 0.0) a[j][j]=TINY;          ps[ii][jj]=0;
     if (j != n) {          ps[ii][ii]=1;
       dum=1.0/(a[j][j]);        }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      }
     }      
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 ;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 }  /*         printf("ddd %lf ",ps[ii][jj]); */
   /*       } */
 void lubksb(double **a, int n, int *indx, double b[])  /*       printf("\n "); */
 {  /*        } */
   int i,ii=0,ip,j;  /*        printf("\n ");printf("%lf ",cov[2]); */
   double sum;         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (i=1;i<=n;i++) {        goto end;*/
     ip=indx[i];      return ps;
     sum=b[ip];  }
     b[ip]=b[i];  
     if (ii)  /**************** Product of 2 matrices ******************/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     b[i]=sum;  {
   }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   for (i=n;i>=1;i--) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     sum=b[i];    /* in, b, out are matrice of pointers which should have been initialized 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];       before: only the contents of out is modified. The function returns
     b[i]=sum/a[i][i];       a pointer to pointers identical to out */
   }    long i, j, k;
 }    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
 /************ Frequencies ********************/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint)          out[i][k] +=in[i][j]*b[j][k];
 {  /* Some frequencies */  
      return out;
   int i, m, jk, k1, k2,i1, j1, bool, z1,z2,j;  }
   double ***freq; /* Frequencies */  
   double *pp;  
   double pos;  /************* Higher Matrix Product ***************/
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
   pp=vector(1,nlstate);    /* Computes the transition matrix starting at age 'age' over 
   probs= ma3x(1,130 ,1,8, 1,8);       'nhstepm*hstepm*stepm' months (i.e. until
   strcpy(fileresp,"p");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   strcat(fileresp,fileres);       nhstepm*hstepm matrices. 
   if((ficresp=fopen(fileresp,"w"))==NULL) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     printf("Problem with prevalence resultfile: %s\n", fileresp);       (typically every 2 years instead of every month which is too big 
     exit(0);       for the memory).
   }       Model is determined by parameters x and covariates have to be 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       included manually here. 
   j1=0;  
        */
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   for(k1=1; k1<=j;k1++){    double **newm;
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;    /* Hstepm could be zero and should return the unit matrix */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for (i=1;i<=nlstate+ndeath;i++)
          scanf("%d", i);*/      for (j=1;j<=nlstate+ndeath;j++){
         for (i=-1; i<=nlstate+ndeath; i++)          oldm[i][j]=(i==j ? 1.0 : 0.0);
          for (jk=-1; jk<=nlstate+ndeath; jk++)          po[i][j][0]=(i==j ? 1.0 : 0.0);
            for(m=agemin; m <= agemax+3; m++)      }
              freq[i][jk][m]=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
            for(h=1; h <=nhstepm; h++){
        for (i=1; i<=imx; i++) {      for(d=1; d <=hstepm; d++){
          bool=1;        newm=savm;
          if  (cptcovn>0) {        /* Covariates have to be included here again */
            for (z1=1; z1<=cptcoveff; z1++)        cov[1]=1.;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                bool=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          }        for (k=1; k<=cptcovage;k++)
           if (bool==1) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             for(m=fprev1; m<=lprev1; m++){        for (k=1; k<=cptcovprod;k++)
              k2=anint[m][i]+(mint[m][i]/12.);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
              if ((k2>=1984) && (k2<=1988.5)) {  
              if(agev[m][i]==0) agev[m][i]=agemax+1;  
              if(agev[m][i]==1) agev[m][i]=agemax+2;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
              }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
             }        savm=oldm;
           }        oldm=newm;
        }      }
         if  (cptcovn>0) {      for(i=1; i<=nlstate+ndeath; i++)
          fprintf(ficresp, "\n#********** Variable ");        for(j=1;j<=nlstate+ndeath;j++) {
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          po[i][j][h]=newm[i][j];
        fprintf(ficresp, "**********\n#");          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         }           */
        for(i=1; i<=nlstate;i++)        }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    } /* end h */
        fprintf(ficresp, "\n");    return po;
          }
   for(i=(int)agemin; i <= (int)agemax+3; i++){  
     if(i==(int)agemax+3)  
       printf("Total");  /*************** log-likelihood *************/
     else  double func( double *x)
       printf("Age %d", i);  {
     for(jk=1; jk <=nlstate ; jk++){    int i, ii, j, k, mi, d, kk;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         pp[jk] += freq[jk][m][i];    double **out;
     }    double sw; /* Sum of weights */
     for(jk=1; jk <=nlstate ; jk++){    double lli; /* Individual log likelihood */
       for(m=-1, pos=0; m <=0 ; m++)    int s1, s2;
         pos += freq[jk][m][i];    double bbh, survp;
       if(pp[jk]>=1.e-10)    long ipmx;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /*extern weight */
       else    /* We are differentiating ll according to initial status */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
      for(jk=1; jk <=nlstate ; jk++){    */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    cov[1]=1.;
         pp[jk] += freq[jk][m][i];  
      }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
     for(jk=1,pos=0; jk <=nlstate ; jk++)    if(mle==1){
       pos += pp[jk];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if(pos>=1.e-5)        for(mi=1; mi<= wav[i]-1; mi++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          for (ii=1;ii<=nlstate+ndeath;ii++)
       else            for (j=1;j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if( i <= (int) agemax){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if(pos>=1.e-5){            }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          for(d=0; d<dh[mi][i]; d++){
           probs[i][jk][j1]= pp[jk]/pos;            newm=savm;
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
       else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(jk=-1; jk <=nlstate+ndeath; jk++)            savm=oldm;
       for(m=-1; m <=nlstate+ndeath; m++)            oldm=newm;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          } /* end mult */
     if(i <= (int) agemax)        
       fprintf(ficresp,"\n");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     printf("\n");          /* 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
             * we keep into memory the bias bh[mi][i] and also the previous matrix product
   fclose(ficresp);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * probability in order to take into account the bias as a fraction of the way
   free_vector(pp,1,nlstate);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
 }  /* End of Freq */           * 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. 
 /************ Prevalence ********************/           */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)          s1=s[mw[mi][i]][i];
 {  /* Some frequencies */          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          /* bias bh is positive if real duration
   double ***freq; /* Frequencies */           * is higher than the multiple of stepm and negative otherwise.
   double *pp;           */
   double pos;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   pp=vector(1,nlstate);            /* i.e. if s2 is a death state and if the date of death is known 
   probs= ma3x(1,130 ,1,8, 1,8);               then the contribution to the likelihood is the probability to 
                 die between last step unit time and current  step unit time, 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);               which is also equal to probability to die before dh 
   j1=0;               minus probability to die before dh-stepm . 
                 In version up to 0.92 likelihood was computed
   j=cptcoveff;          as if date of death was unknown. Death was treated as any other
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
  for(k1=1; k1<=j;k1++){          to consider that at each interview the state was recorded
     for(i1=1; i1<=ncodemax[k1];i1++){          (healthy, disable or death) and IMaCh was corrected; but when we
       j1++;          introduced the exact date of death then we should have modified
            the contribution of an exact death to the likelihood. This new
       for (i=-1; i<=nlstate+ndeath; i++)            contribution is smaller and very dependent of the step unit
         for (jk=-1; jk<=nlstate+ndeath; jk++)            stepm. It is no more the probability to die between last interview
           for(m=agemin; m <= agemax+3; m++)          and month of death but the probability to survive from last
           freq[i][jk][m]=0;          interview up to one month before death multiplied by the
                probability to die within a month. Thanks to Chris
       for (i=1; i<=imx; i++) {          Jackson for correcting this bug.  Former versions increased
         bool=1;          mortality artificially. The bad side is that we add another loop
         if  (cptcovn>0) {          which slows down the processing. The difference can be up to 10%
           for (z1=1; z1<=cptcoveff; z1++)          lower mortality.
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            */
               bool=0;            lli=log(out[s1][s2] - savm[s1][s2]);
               }  
         if (bool==1) {  
           for(m=fprev1; m<=lprev1; m++){          } else if  (s2==-2) {
             if(agev[m][i]==0) agev[m][i]=agemax+1;            for (j=1,survp=0. ; j<=nlstate; j++) 
             if(agev[m][i]==1) agev[m][i]=agemax+2;              survp += out[s1][j];
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            lli= survp;
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          }
           }          
         }          else if  (s2==-4) {
       }            for (j=3,survp=0. ; j<=nlstate; j++) 
        for(i=(int)agemin; i <= (int)agemax+3; i++){              survp += out[s1][j];
         for(jk=1; jk <=nlstate ; jk++){            lli= survp;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          }
             pp[jk] += freq[jk][m][i];          
         }          else if  (s2==-5) {
         for(jk=1; jk <=nlstate ; jk++){            for (j=1,survp=0. ; j<=2; j++) 
           for(m=-1, pos=0; m <=0 ; m++)              survp += out[s1][j];
             pos += freq[jk][m][i];            lli= survp;
         }          }
          
          for(jk=1; jk <=nlstate ; jk++){  
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          else{
              pp[jk] += freq[jk][m][i];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                    } 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
          for(jk=1; jk <=nlstate ; jk++){                    /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            if( i <= (int) agemax){          ipmx +=1;
              if(pos>=1.e-5){          sw += weight[i];
                probs[i][jk][j1]= pp[jk]/pos;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              }        } /* end of wave */
            }      } /* end of individual */
          }    }  else if(mle==2){
                for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(pp,1,nlstate);            }
            for(d=0; d<=dh[mi][i]; d++){
 }  /* End of Freq */            newm=savm;
 /************* Waves Concatenation ***************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      Death is a valid wave (if date is known).                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            savm=oldm;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            oldm=newm;
      and mw[mi+1][i]. dh depends on stepm.          } /* end mult */
      */        
           s1=s[mw[mi][i]][i];
   int i, mi, m;          s2=s[mw[mi+1][i]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          bbh=(double)bh[mi][i]/(double)stepm; 
      double sum=0., jmean=0.;*/          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
   int j, k=0,jk, ju, jl;          sw += weight[i];
   double sum=0.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   jmin=1e+5;        } /* end of wave */
   jmax=-1;      } /* end of individual */
   jmean=0.;    }  else if(mle==3){  /* exponential inter-extrapolation */
   for(i=1; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     mi=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     m=firstpass;        for(mi=1; mi<= wav[i]-1; mi++){
     while(s[m][i] <= nlstate){          for (ii=1;ii<=nlstate+ndeath;ii++)
       if(s[m][i]>=1)            for (j=1;j<=nlstate+ndeath;j++){
         mw[++mi][i]=m;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(m >=lastpass)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         break;            }
       else          for(d=0; d<dh[mi][i]; d++){
         m++;            newm=savm;
     }/* end while */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (s[m][i] > nlstate){            for (kk=1; kk<=cptcovage;kk++) {
       mi++;     /* Death is another wave */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       /* if(mi==0)  never been interviewed correctly before death */            }
          /* Only death is a correct wave */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       mw[mi][i]=m;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
             oldm=newm;
     wav[i]=mi;          } /* end mult */
     if(mi==0)        
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   for(i=1; i<=imx; i++){          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for(mi=1; mi<wav[i];mi++){          ipmx +=1;
       if (stepm <=0)          sw += weight[i];
         dh[mi][i]=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       else{        } /* end of wave */
         if (s[mw[mi+1][i]][i] > nlstate) {      } /* end of individual */
           if (agedc[i] < 2*AGESUP) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if(j==0) j=1;  /* Survives at least one month after exam */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           k=k+1;        for(mi=1; mi<= wav[i]-1; mi++){
           if (j >= jmax) jmax=j;          for (ii=1;ii<=nlstate+ndeath;ii++)
           if (j <= jmin) jmin=j;            for (j=1;j<=nlstate+ndeath;j++){
           sum=sum+j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           /* if (j<10) printf("j=%d num=%d ",j,i); */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
         }          for(d=0; d<dh[mi][i]; d++){
         else{            newm=savm;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           k=k+1;            for (kk=1; kk<=cptcovage;kk++) {
           if (j >= jmax) jmax=j;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           else if (j <= jmin)jmin=j;            }
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          
           sum=sum+j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         jk= j/stepm;            savm=oldm;
         jl= j -jk*stepm;            oldm=newm;
         ju= j -(jk+1)*stepm;          } /* end mult */
         if(jl <= -ju)        
           dh[mi][i]=jk;          s1=s[mw[mi][i]][i];
         else          s2=s[mw[mi+1][i]][i];
           dh[mi][i]=jk+1;          if( s2 > nlstate){ 
         if(dh[mi][i]==0)            lli=log(out[s1][s2] - savm[s1][s2]);
           dh[mi][i]=1; /* At least one step */          }else{
       }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     }          }
   }          ipmx +=1;
   jmean=sum/k;          sw += weight[i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          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]); */
 /*********** Tricode ****************************/        } /* end of wave */
 void tricode(int *Tvar, int **nbcode, int imx)      } /* end of individual */
 {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   int Ndum[20],ij=1, k, j, i;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int cptcode=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   cptcoveff=0;        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   for (k=0; k<19; k++) Ndum[k]=0;            for (j=1;j<=nlstate+ndeath;j++){
   for (k=1; k<=7; k++) ncodemax[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            }
     for (i=1; i<=imx; i++) {          for(d=0; d<dh[mi][i]; d++){
       ij=(int)(covar[Tvar[j]][i]);            newm=savm;
       Ndum[ij]++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            for (kk=1; kk<=cptcovage;kk++) {
       if (ij > cptcode) cptcode=ij;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
           
     for (i=0; i<=cptcode; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(Ndum[i]!=0) ncodemax[j]++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     ij=1;            oldm=newm;
           } /* end mult */
         
     for (i=1; i<=ncodemax[j]; i++) {          s1=s[mw[mi][i]][i];
       for (k=0; k<=19; k++) {          s2=s[mw[mi+1][i]][i];
         if (Ndum[k] != 0) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           nbcode[Tvar[j]][ij]=k;          ipmx +=1;
           ij++;          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if (ij > ncodemax[j]) break;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       }          } /* end of wave */
     }      } /* end of individual */
   }      } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  for (k=0; k<19; k++) Ndum[k]=0;    /* 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 */
  for (i=1; i<=ncovmodel-2; i++) {    return -l;
       ij=Tvar[i];  }
       Ndum[ij]++;  
     }  /*************** log-likelihood *************/
   double funcone( double *x)
  ij=1;  {
  for (i=1; i<=10; i++) {    /* Same as likeli but slower because of a lot of printf and if */
    if((Ndum[i]!=0) && (i<=ncov)){    int i, ii, j, k, mi, d, kk;
      Tvaraff[ij]=i;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      ij++;    double **out;
    }    double lli; /* Individual log likelihood */
  }    double llt;
      int s1, s2;
     cptcoveff=ij-1;    double bbh, survp;
 }    /*extern weight */
     /* We are differentiating ll according to initial status */
 /*********** Health Expectancies ****************/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      printf(" %d\n",s[4][i]);
 {    */
   /* Health expectancies */    cov[1]=1.;
   int i, j, nhstepm, hstepm, h;  
   double age, agelim,hf;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double ***p3mat;  
      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficreseij,"# Health expectancies\n");      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficreseij,"# Age");      for(mi=1; mi<= wav[i]-1; mi++){
   for(i=1; i<=nlstate;i++)        for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<=nlstate;j++)          for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficreseij," %1d-%1d",i,j);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"\n");            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   hstepm=1*YEARM; /*  Every j years of age (in month) */        for(d=0; d<dh[mi][i]; d++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   agelim=AGESUP;          for (kk=1; kk<=cptcovage;kk++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /* nhstepm age range expressed in number of stepm */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* Typically if 20 years = 20*12/6=40 stepm */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     if (stepm >= YEARM) hstepm=1;          savm=oldm;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          oldm=newm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /* end mult */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        s1=s[mw[mi][i]][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
     for(i=1; i<=nlstate;i++)         * is higher than the multiple of stepm and negative otherwise.
       for(j=1; j<=nlstate;j++)         */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           eij[i][j][(int)age] +=p3mat[i][j][h];          lli=log(out[s1][s2] - savm[s1][s2]);
         }        } else if (mle==1){
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     hf=1;        } else if(mle==2){
     if (stepm >= YEARM) hf=stepm/YEARM;          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 */
     fprintf(ficreseij,"%.0f",age );        } else if(mle==3){  /* exponential inter-extrapolation */
     for(i=1; i<=nlstate;i++)          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       for(j=1; j<=nlstate;j++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          lli=log(out[s1][s2]); /* Original formula */
       }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     fprintf(ficreseij,"\n");          lli=log(out[s1][s2]); /* Original formula */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /* End of if */
   }        ipmx +=1;
 }        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************ Variance ******************/  /*       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]); */
 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)        if(globpr){
 {          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   /* Variance of health expectancies */   %10.6f %10.6f %10.6f ", \
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double **newm;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double **dnewm,**doldm;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   int i, j, nhstepm, hstepm, h;            llt +=ll[k]*gipmx/gsw;
   int k, cptcode;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double *xp;          }
   double **gp, **gm;          fprintf(ficresilk," %10.6f\n", -llt);
   double ***gradg, ***trgradg;        }
   double ***p3mat;      } /* end of wave */
   double age,agelim;    } /* end of individual */
   int theta;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
    fprintf(ficresvij,"# Covariances of life expectancies\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficresvij,"# Age");    if(globpr==0){ /* First time we count the contributions and weights */
   for(i=1; i<=nlstate;i++)      gipmx=ipmx;
     for(j=1; j<=nlstate;j++)      gsw=sw;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    }
   fprintf(ficresvij,"\n");    return -l;
   }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  /*************** function likelione ***********/
    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   hstepm=1*YEARM; /* Every year of age */  {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* This routine should help understanding what is done with 
   agelim = AGESUP;       the selection of individuals/waves and
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       to check the exact contribution to the likelihood.
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       Plotting could be done.
     if (stepm >= YEARM) hstepm=1;     */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int k;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    if(*globpri !=0){ /* Just counts and sums, no printings */
     gp=matrix(0,nhstepm,1,nlstate);      strcpy(fileresilk,"ilk"); 
     gm=matrix(0,nhstepm,1,nlstate);      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     for(theta=1; theta <=npar; theta++){        printf("Problem with resultfile: %s\n", fileresilk);
       for(i=1; i<=npar; i++){ /* Computes gradient */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
       }      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");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /*  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++) 
       if (popbased==1) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         for(i=1; i<=nlstate;i++)      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           prlim[i][i]=probs[(int)age][i][ij];    }
       }  
          *fretone=(*funcone)(p);
       for(j=1; j<= nlstate; j++){    if(*globpri !=0){
         for(h=0; h<=nhstepm; h++){      fclose(ficresilk);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      fflush(fichtm); 
         }    } 
       }    return;
      }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /*********** Maximum Likelihood Estimation ***************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       if (popbased==1) {  {
         for(i=1; i<=nlstate;i++)    int i,j, iter;
           prlim[i][i]=probs[(int)age][i][ij];    double **xi;
       }    double fret;
     double fretone; /* Only one call to likelihood */
       for(j=1; j<= nlstate; j++){    /*  char filerespow[FILENAMELENGTH];*/
         for(h=0; h<=nhstepm; h++){    xi=matrix(1,npar,1,npar);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    for (i=1;i<=npar;i++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      for (j=1;j<=npar;j++)
         }        xi[i][j]=(i==j ? 1.0 : 0.0);
       }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
       for(j=1; j<= nlstate; j++)    strcat(filerespow,fileres);
         for(h=0; h<=nhstepm; h++){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      printf("Problem with resultfile: %s\n", filerespow);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     } /* End theta */    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
     for(h=0; h<=nhstepm; h++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       for(j=1; j<=nlstate;j++)    fprintf(ficrespow,"\n");
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];    powell(p,xi,npar,ftol,&iter,&fret,func);
   
     for(i=1;i<=nlstate;i++)    fclose(ficrespow);
       for(j=1;j<=nlstate;j++)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         vareij[i][j][(int)age] =0.;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(h=0;h<=nhstepm;h++){    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)  /**** Computes Hessian and covariance matrix ***/
           for(j=1;j<=nlstate;j++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
             vareij[i][j][(int)age] += doldm[i][j];  {
       }    double  **a,**y,*x,pd;
     }    double **hess;
     h=1;    int i, j,jk;
     if (stepm >= YEARM) h=stepm/YEARM;    int *indx;
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(j=1; j<=nlstate;j++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    void lubksb(double **a, int npar, int *indx, double b[]) ;
       }    void ludcmp(double **a, int npar, int *indx, double *d) ;
     fprintf(ficresvij,"\n");    double gompertz(double p[]);
     free_matrix(gp,0,nhstepm,1,nlstate);    hess=matrix(1,npar,1,npar);
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    printf("\nCalculation of the hessian matrix. Wait...\n");
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++){
   } /* End age */      printf("%d",i);fflush(stdout);
        fprintf(ficlog,"%d",i);fflush(ficlog);
   free_vector(xp,1,npar);     
   free_matrix(doldm,1,nlstate,1,npar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);      
       /*  printf(" %f ",p[i]);
 }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
 /************ Variance of prevlim ******************/    
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    for (i=1;i<=npar;i++) {
 {      for (j=1;j<=npar;j++)  {
   /* Variance of prevalence limit */        if (j>i) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          printf(".%d%d",i,j);fflush(stdout);
   double **newm;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double **dnewm,**doldm;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   int i, j, nhstepm, hstepm;          
   int k, cptcode;          hess[j][i]=hess[i][j];    
   double *xp;          /*printf(" %lf ",hess[i][j]);*/
   double *gp, *gm;        }
   double **gradg, **trgradg;      }
   double age,agelim;    }
   int theta;    printf("\n");
        fprintf(ficlog,"\n");
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficresvpl," %1d-%1d",i,i);    
   fprintf(ficresvpl,"\n");    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
   xp=vector(1,npar);    x=vector(1,npar);
   dnewm=matrix(1,nlstate,1,npar);    indx=ivector(1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   hstepm=1*YEARM; /* Every year of age */    ludcmp(a,npar,indx,&pd);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;    for (j=1;j<=npar;j++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1;i<=npar;i++) x[i]=0;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      x[j]=1;
     if (stepm >= YEARM) hstepm=1;      lubksb(a,npar,indx,x);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=1;i<=npar;i++){ 
     gradg=matrix(1,npar,1,nlstate);        matcov[i][j]=x[i];
     gp=vector(1,nlstate);      }
     gm=vector(1,nlstate);    }
   
     for(theta=1; theta <=npar; theta++){    printf("\n#Hessian matrix#\n");
       for(i=1; i<=npar; i++){ /* Computes gradient */    fprintf(ficlog,"\n#Hessian matrix#\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++) { 
       }      for (j=1;j<=npar;j++) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        printf("%.3e ",hess[i][j]);
       for(i=1;i<=nlstate;i++)        fprintf(ficlog,"%.3e ",hess[i][j]);
         gp[i] = prlim[i][i];      }
          printf("\n");
       for(i=1; i<=npar; i++) /* Computes gradient */      fprintf(ficlog,"\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    /* Recompute Inverse */
         gm[i] = prlim[i][i];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       for(i=1;i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */    /*  printf("\n#Hessian matrix recomputed#\n");
   
     trgradg =matrix(1,nlstate,1,npar);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
     for(j=1; j<=nlstate;j++)      x[j]=1;
       for(theta=1; theta <=npar; theta++)      lubksb(a,npar,indx,x);
         trgradg[j][theta]=gradg[theta][j];      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
     for(i=1;i<=nlstate;i++)        printf("%.3e ",y[i][j]);
       varpl[i][(int)age] =0.;        fprintf(ficlog,"%.3e ",y[i][j]);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      printf("\n");
     for(i=1;i<=nlstate;i++)      fprintf(ficlog,"\n");
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    }
     */
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    free_matrix(a,1,npar,1,npar);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    free_matrix(y,1,npar,1,npar);
     fprintf(ficresvpl,"\n");    free_vector(x,1,npar);
     free_vector(gp,1,nlstate);    free_ivector(indx,1,npar);
     free_vector(gm,1,nlstate);    free_matrix(hess,1,npar,1,npar);
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  }
   
   free_vector(xp,1,npar);  /*************** hessian matrix ****************/
   free_matrix(doldm,1,nlstate,1,npar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   free_matrix(dnewm,1,nlstate,1,nlstate);  {
     int i;
 }    int l=1, lmax=20;
     double k1,k2;
 /************ Variance of one-step probabilities  ******************/    double p2[NPARMAX+1];
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double res;
 {    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   int i, j;    double fx;
   int k=0, cptcode;    int k=0,kmax=10;
   double **dnewm,**doldm;    double l1;
   double *xp;  
   double *gp, *gm;    fx=func(x);
   double **gradg, **trgradg;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double age,agelim, cov[NCOVMAX];    for(l=0 ; l <=lmax; l++){
   int theta;      l1=pow(10,l);
   char fileresprob[FILENAMELENGTH];      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
   strcpy(fileresprob,"prob");        delt = delta*(l1*k);
   strcat(fileresprob,fileres);        p2[theta]=x[theta] +delt;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        k1=func(p2)-fx;
     printf("Problem with resultfile: %s\n", fileresprob);        p2[theta]=x[theta]-delt;
   }        k2=func(p2)-fx;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   xp=vector(1,npar);  #ifdef DEBUG
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        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);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    #endif
   cov[1]=1;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   for (age=bage; age<=fage; age ++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     cov[2]=age;          k=kmax;
     gradg=matrix(1,npar,1,9);        }
     trgradg=matrix(1,9,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          k=kmax; l=lmax*10.;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        }
            else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for(theta=1; theta <=npar; theta++){          delts=delt;
       for(i=1; i<=npar; i++)        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
          }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    delti[theta]=delts;
        return res; 
       k=0;    
       for(i=1; i<= (nlstate+ndeath); i++){  }
         for(j=1; j<=(nlstate+ndeath);j++){  
            k=k+1;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           gp[k]=pmmij[i][j];  {
         }    int i;
       }    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
       for(i=1; i<=npar; i++)    double p2[NPARMAX+1];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int k;
      
     fx=func(x);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    for (k=1; k<=2; k++) {
       k=0;      for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=1; i<=(nlstate+ndeath); i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
         for(j=1; j<=(nlstate+ndeath);j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           k=k+1;      k1=func(p2)-fx;
           gm[k]=pmmij[i][j];    
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            k2=func(p2)-fx;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        p2[thetai]=x[thetai]-delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    
       for(theta=1; theta <=npar; theta++)      p2[thetai]=x[thetai]-delti[thetai]/k;
       trgradg[j][theta]=gradg[theta][j];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  #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);
      pmij(pmmij,cov,ncovmodel,x,nlstate);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
      k=0;    }
      for(i=1; i<=(nlstate+ndeath); i++){    return res;
        for(j=1; j<=(nlstate+ndeath);j++){  }
          k=k+1;  
          gm[k]=pmmij[i][j];  /************** Inverse of matrix **************/
         }  void ludcmp(double **a, int n, int *indx, double *d) 
      }  { 
          int i,imax,j,k; 
      /*printf("\n%d ",(int)age);    double big,dum,sum,temp; 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double *vv; 
           
     vv=vector(1,n); 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    *d=1.0; 
      }*/    for (i=1;i<=n;i++) { 
       big=0.0; 
   fprintf(ficresprob,"\n%d ",(int)age);      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      vv[i]=1.0/big; 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    } 
   }    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        sum=a[i][j]; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        a[i][j]=sum; 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      } 
 }      big=0.0; 
  free_vector(xp,1,npar);      for (i=j;i<=n;i++) { 
 fclose(ficresprob);        sum=a[i][j]; 
  exit(0);        for (k=1;k<j;k++) 
 }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
 /***********************************************/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 /**************** Main Program *****************/          big=dum; 
 /***********************************************/          imax=i; 
         } 
 /*int main(int argc, char *argv[])*/      } 
 int main()      if (j != imax) { 
 {        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          a[imax][k]=a[j][k]; 
   double agedeb, agefin,hf;          a[j][k]=dum; 
   double agemin=1.e20, agemax=-1.e20;        } 
         *d = -(*d); 
   double fret;        vv[imax]=vv[j]; 
   double **xi,tmp,delta;      } 
       indx[j]=imax; 
   double dum; /* Dummy variable */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double ***p3mat;      if (j != n) { 
   int *indx;        dum=1.0/(a[j][j]); 
   char line[MAXLINE], linepar[MAXLINE];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   char title[MAXLINE];      } 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    } 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    free_vector(vv,1,n);  /* Doesn't work */
   char filerest[FILENAMELENGTH];  ;
   char fileregp[FILENAMELENGTH];  } 
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  void lubksb(double **a, int n, int *indx, double b[]) 
   int firstobs=1, lastobs=10;  { 
   int sdeb, sfin; /* Status at beginning and end */    int i,ii=0,ip,j; 
   int c,  h , cpt,l;    double sum; 
   int ju,jl, mi;   
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    for (i=1;i<=n;i++) { 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      ip=indx[i]; 
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;      sum=b[ip]; 
   int hstepm, nhstepm;      b[ip]=b[i]; 
   int *popage;      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double bage, fage, age, agelim, agebase;      else if (sum) ii=i; 
   double ftolpl=FTOL;      b[i]=sum; 
   double **prlim;    } 
   double *severity;    for (i=n;i>=1;i--) { 
   double ***param; /* Matrix of parameters */      sum=b[i]; 
   double  *p;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double **matcov; /* Matrix of covariance */      b[i]=sum/a[i][i]; 
   double ***delti3; /* Scale */    } 
   double *delti; /* Scale */  } 
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  /************ Frequencies ********************/
   double *epj, vepp;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   double kk1, kk2;  {  /* Some frequencies */
   double *popeffectif,*popcount;    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    int first;
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double ***freq; /* Frequencies */
     double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   char z[1]="c", occ;    FILE *ficresp;
 #include <sys/time.h>    char fileresp[FILENAMELENGTH];
 #include <time.h>    
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    pp=vector(1,nlstate);
   /* long total_usecs;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   struct timeval start_time, end_time;    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   printf("\nIMACH, Version 0.7");      exit(0);
   printf("\nEnter the parameter file name: ");    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 #ifdef windows    j1=0;
   scanf("%s",pathtot);    
   getcwd(pathcd, size);    j=cptcoveff;
   /*cygwin_split_path(pathtot,path,optionfile);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/    first=1;
   
 split(pathtot, path,optionfile);    for(k1=1; k1<=j;k1++){
   chdir(path);      for(i1=1; i1<=ncodemax[k1];i1++){
   replace(pathc,path);        j1++;
 #endif        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 #ifdef unix          scanf("%d", i);*/
   scanf("%s",optionfile);        for (i=-5; i<=nlstate+ndeath; i++)  
 #endif          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
 /*-------- arguments in the command line --------*/              freq[i][jk][m]=0;
   
   strcpy(fileres,"r");      for (i=1; i<=nlstate; i++)  
   strcat(fileres, optionfile);        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
   /*---------arguments file --------*/        
         dateintsum=0;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        k2cpt=0;
     printf("Problem with optionfile %s\n",optionfile);        for (i=1; i<=imx; i++) {
     goto end;          bool=1;
   }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   strcpy(filereso,"o");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   strcat(filereso,fileres);                bool=0;
   if((ficparo=fopen(filereso,"w"))==NULL) {          }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          if (bool==1){
   }            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   /* Reads comments: lines beginning with '#' */              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   while((c=getc(ficpar))=='#' && c!= EOF){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     ungetc(c,ficpar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fgets(line, MAXLINE, ficpar);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     puts(line);                if (m<lastpass) {
     fputs(line,ficparo);                  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];
   ungetc(c,ficpar);                }
                 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);                  dateintsum=dateintsum+k2;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);                  k2cpt++;
 while((c=getc(ficpar))=='#' && c!= EOF){                }
     ungetc(c,ficpar);                /*}*/
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }
     fputs(line,ficparo);        }
   }         
   ungetc(c,ficpar);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
    fprintf(ficresp, "#Local time at start: %s", strstart);
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);        if  (cptcovn>0) {
   fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresp, "**********\n#");
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=nlstate;i++) 
     puts(line);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fputs(line,ficparo);        fprintf(ficresp, "\n");
   }        
   ungetc(c,ficpar);        for(i=iagemin; i <= iagemax+3; i++){
            if(i==iagemax+3){
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);            fprintf(ficlog,"Total");
   fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);          }else{
                  if(first==1){
                first=0;
 while((c=getc(ficpar))=='#' && c!= EOF){              printf("See log file for details...\n");
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);            fprintf(ficlog,"Age %d", i);
     puts(line);          }
     fputs(line,ficparo);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   ungetc(c,ficpar);              pp[jk] += freq[jk][m][i]; 
            }
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pos=0; m <=0 ; m++)
   covar=matrix(0,NCOVMAX,1,n);              pos += freq[jk][m][i];
   cptcovn=0;            if(pp[jk]>=1.e-10){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   ncovmodel=2+cptcovn;              }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }else{
   /* Read guess parameters */              if(first==1)
   /* Reads comments: lines beginning with '#' */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   while((c=getc(ficpar))=='#' && c!= EOF){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          }
     puts(line);  
     fputs(line,ficparo);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   ungetc(c,ficpar);              pp[jk] += freq[jk][m][i];
            }       
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     for(i=1; i <=nlstate; i++)            pos += pp[jk];
     for(j=1; j <=nlstate+ndeath-1; j++){            posprop += prop[jk][i];
       fscanf(ficpar,"%1d%1d",&i1,&j1);          }
       fprintf(ficparo,"%1d%1d",i1,j1);          for(jk=1; jk <=nlstate ; jk++){
       printf("%1d%1d",i,j);            if(pos>=1.e-5){
       for(k=1; k<=ncovmodel;k++){              if(first==1)
         fscanf(ficpar," %lf",&param[i][j][k]);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         printf(" %lf",param[i][j][k]);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         fprintf(ficparo," %lf",param[i][j][k]);            }else{
       }              if(first==1)
       fscanf(ficpar,"\n");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       printf("\n");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficparo,"\n");            }
     }            if( i <= iagemax){
                if(pos>=1.e-5){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
   p=param[1][1];                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                }
   /* Reads comments: lines beginning with '#' */              else
   while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          }
     puts(line);          
     fputs(line,ficparo);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   }            for(m=-1; m <=nlstate+ndeath; m++)
   ungetc(c,ficpar);              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   for(i=1; i <=nlstate; i++){              }
     for(j=1; j <=nlstate+ndeath-1; j++){          if(i <= iagemax)
       fscanf(ficpar,"%1d%1d",&i1,&j1);            fprintf(ficresp,"\n");
       printf("%1d%1d",i,j);          if(first==1)
       fprintf(ficparo,"%1d%1d",i1,j1);            printf("Others in log...\n");
       for(k=1; k<=ncovmodel;k++){          fprintf(ficlog,"\n");
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);      }
         fprintf(ficparo," %le",delti3[i][j][k]);    }
       }    dateintmean=dateintsum/k2cpt; 
       fscanf(ficpar,"\n");   
       printf("\n");    fclose(ficresp);
       fprintf(ficparo,"\n");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     }    free_vector(pp,1,nlstate);
   }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   delti=delti3[1][1];    /* End of Freq */
    }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /************ Prevalence ********************/
     ungetc(c,ficpar);  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)
     fgets(line, MAXLINE, ficpar);  {  
     puts(line);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     fputs(line,ficparo);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   }       We still use firstpass and lastpass as another selection.
   ungetc(c,ficpar);    */
     
   matcov=matrix(1,npar,1,npar);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   for(i=1; i <=npar; i++){    double ***freq; /* Frequencies */
     fscanf(ficpar,"%s",&str);    double *pp, **prop;
     printf("%s",str);    double pos,posprop; 
     fprintf(ficparo,"%s",str);    double  y2; /* in fractional years */
     for(j=1; j <=i; j++){    int iagemin, iagemax;
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);    iagemin= (int) agemin;
       fprintf(ficparo," %.5le",matcov[i][j]);    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
     fscanf(ficpar,"\n");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     printf("\n");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     fprintf(ficparo,"\n");    j1=0;
   }    
   for(i=1; i <=npar; i++)    j=cptcoveff;
     for(j=i+1;j<=npar;j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       matcov[i][j]=matcov[j][i];    
        for(k1=1; k1<=j;k1++){
   printf("\n");      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
         
     /*-------- data file ----------*/        for (i=1; i<=nlstate; i++)  
     if((ficres =fopen(fileres,"w"))==NULL) {          for(m=iagemin; m <= iagemax+3; m++)
       printf("Problem with resultfile: %s\n", fileres);goto end;            prop[i][m]=0.0;
     }       
     fprintf(ficres,"#%s\n",version);        for (i=1; i<=imx; i++) { /* Each individual */
              bool=1;
     if((fic=fopen(datafile,"r"))==NULL)    {          if  (cptcovn>0) {
       printf("Problem with datafile: %s\n", datafile);goto end;            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
     n= lastobs;          } 
     severity = vector(1,maxwav);          if (bool==1) { 
     outcome=imatrix(1,maxwav+1,1,n);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     num=ivector(1,n);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     moisnais=vector(1,n);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     annais=vector(1,n);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     moisdc=vector(1,n);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     andc=vector(1,n);                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); 
     agedc=vector(1,n);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     cod=ivector(1,n);                  /*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]]);*/
     weight=vector(1,n);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                  prop[s[m][i]][iagemax+3] += weight[i]; 
     mint=matrix(1,maxwav,1,n);                } 
     anint=matrix(1,maxwav,1,n);              }
     s=imatrix(1,maxwav+1,1,n);            } /* end selection of waves */
     adl=imatrix(1,maxwav+1,1,n);              }
     tab=ivector(1,NCOVMAX);        }
     ncodemax=ivector(1,8);        for(i=iagemin; i <= iagemax+3; i++){  
           
     i=1;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     while (fgets(line, MAXLINE, fic) != NULL)    {            posprop += prop[jk][i]; 
       if ((i >= firstobs) && (i <=lastobs)) {          } 
          
         for (j=maxwav;j>=1;j--){          for(jk=1; jk <=nlstate ; jk++){     
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            if( i <=  iagemax){ 
           strcpy(line,stra);              if(posprop>=1.e-5){ 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                probs[i][jk][j1]= prop[jk][i]/posprop;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              } 
         }            } 
                  }/* end jk */ 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        }/* end i */ 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* end i1 */
     } /* end k1 */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         for (j=ncov;j>=1;j--){  }  /* End of prevalence */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  /************* Waves Concatenation ***************/
         num[i]=atol(stra);  
          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)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  {
           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;}*/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
         i=i+1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     }       and mw[mi+1][i]. dh depends on stepm.
     /* printf("ii=%d", ij);       */
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   /* for (i=1; i<=imx; i++){       double sum=0., jmean=0.;*/
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    int first;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    int j, k=0,jk, ju, jl;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    double sum=0.;
     }    first=0;
     for (i=1; i<=imx; 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]));*/    jmin=1e+5;
     jmax=-1;
   /* Calculation of the number of parameter from char model*/    jmean=0.;
   Tvar=ivector(1,15);    for(i=1; i<=imx; i++){
   Tprod=ivector(1,15);      mi=0;
   Tvaraff=ivector(1,15);      m=firstpass;
   Tvard=imatrix(1,15,1,2);      while(s[m][i] <= nlstate){
   Tage=ivector(1,15);              if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
              mw[++mi][i]=m;
   if (strlen(model) >1){        if(m >=lastpass)
     j=0, j1=0, k1=1, k2=1;          break;
     j=nbocc(model,'+');        else
     j1=nbocc(model,'*');          m++;
     cptcovn=j+1;      }/* end while */
     cptcovprod=j1;      if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
     strcpy(modelsav,model);           /* Only death is a correct wave */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        mw[mi][i]=m;
       printf("Error. Non available option model=%s ",model);      }
       goto end;  
     }      wav[i]=mi;
          if(mi==0){
     for(i=(j+1); i>=1;i--){        nbwarn++;
       cutv(stra,strb,modelsav,'+');        if(first==0){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          first=1;
       /*scanf("%d",i);*/        }
       if (strchr(strb,'*')) {        if(first==1){
         cutv(strd,strc,strb,'*');          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         if (strcmp(strc,"age")==0) {        }
           cptcovprod--;      } /* end mi==0 */
           cutv(strb,stre,strd,'V');    } /* End individuals */
           Tvar[i]=atoi(stre);  
           cptcovage++;    for(i=1; i<=imx; i++){
             Tage[cptcovage]=i;      for(mi=1; mi<wav[i];mi++){
             /*printf("stre=%s ", stre);*/        if (stepm <=0)
         }          dh[mi][i]=1;
         else if (strcmp(strd,"age")==0) {        else{
           cptcovprod--;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           cutv(strb,stre,strc,'V');            if (agedc[i] < 2*AGESUP) {
           Tvar[i]=atoi(stre);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           cptcovage++;              if(j==0) j=1;  /* Survives at least one month after exam */
           Tage[cptcovage]=i;              else if(j<0){
         }                nberr++;
         else {                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]);
           cutv(strb,stre,strc,'V');                j=1; /* Temporary Dangerous patch */
           Tvar[i]=ncov+k1;                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           cutv(strb,strc,strd,'V');                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]);
           Tprod[k1]=i;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           Tvard[k1][1]=atoi(strc);              }
           Tvard[k1][2]=atoi(stre);              k=k+1;
           Tvar[cptcovn+k2]=Tvard[k1][1];              if (j >= jmax) jmax=j;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];              if (j <= jmin) jmin=j;
           for (k=1; k<=lastobs;k++)              sum=sum+j;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           k1++;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           k2=k2+2;            }
         }          }
       }          else{
       else {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  /*        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]); */
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');            k=k+1;
       Tvar[i]=atoi(strc);            if (j >= jmax) jmax=j;
       }            else if (j <= jmin)jmin=j;
       strcpy(modelsav,stra);              /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            /*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]);*/
         scanf("%d",i);*/            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]);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            }
   printf("cptcovprod=%d ", cptcovprod);            sum=sum+j;
   scanf("%d ",i);*/          }
     fclose(fic);          jk= j/stepm;
           jl= j -jk*stepm;
     /*  if(mle==1){*/          ju= j -(jk+1)*stepm;
     if (weightopt != 1) { /* Maximisation without weights*/          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       for(i=1;i<=n;i++) weight[i]=1.0;            if(jl==0){
     }              dh[mi][i]=jk;
     /*-calculation of age at interview from date of interview and age at death -*/              bh[mi][i]=0;
     agev=matrix(1,maxwav,1,imx);            }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
    for (i=1; i<=imx; i++)              dh[mi][i]=jk+1;
      for(m=2; (m<= maxwav); m++)              bh[mi][i]=ju;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            }
          anint[m][i]=9999;          }else{
          s[m][i]=-1;            if(jl <= -ju){
        }              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
     for (i=1; i<=imx; i++)  {                                   * is higher than the multiple of stepm and negative otherwise.
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                                   */
       for(m=1; (m<= maxwav); m++){            }
         if(s[m][i] >0){            else{
           if (s[m][i] == nlstate+1) {              dh[mi][i]=jk+1;
             if(agedc[i]>0)              bh[mi][i]=ju;
               if(moisdc[i]!=99 && andc[i]!=9999)            }
               agev[m][i]=agedc[i];            if(dh[mi][i]==0){
             else {              dh[mi][i]=1; /* At least one step */
               if (andc[i]!=9999){              bh[mi][i]=ju; /* At least one step */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
               agev[m][i]=-1;            }
               }          } /* end if mle */
             }        }
           }      } /* end wave */
           else if(s[m][i] !=9){ /* Should no more exist */    }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    jmean=sum/k;
             if(mint[m][i]==99 || anint[m][i]==9999)    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
               agev[m][i]=1;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
             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);*/  /*********** Tricode ****************************/
             }  void tricode(int *Tvar, int **nbcode, int imx)
             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);*/    int Ndum[20],ij=1, k, j, i, maxncov=19;
             }    int cptcode=0;
             /*agev[m][i]=anint[m][i]-annais[i];*/    cptcoveff=0; 
             /*   agev[m][i] = age[i]+2*m;*/   
           }    for (k=0; k<maxncov; k++) Ndum[k]=0;
           else { /* =9 */    for (k=1; k<=7; k++) ncodemax[k]=0;
             agev[m][i]=1;  
             s[m][i]=-1;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         }                                 modality*/ 
         else /*= 0 Unknown */        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           agev[m][i]=1;        Ndum[ij]++; /*store the modality */
       }        /*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 
     for (i=1; i<=imx; i++)  {                                         female is 1, then  cptcode=1.*/
       for(m=1; (m<= maxwav); m++){      }
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");        for (i=0; i<=cptcode; i++) {
           goto end;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
         }      }
       }  
     }      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
     free_vector(severity,1,maxwav);            nbcode[Tvar[j]][ij]=k; 
     free_imatrix(outcome,1,maxwav+1,1,n);            /* 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; */
     free_vector(moisnais,1,n);            
     free_vector(annais,1,n);            ij++;
     /* free_matrix(mint,1,maxwav,1,n);          }
        free_matrix(anint,1,maxwav,1,n);*/          if (ij > ncodemax[j]) break; 
     free_vector(moisdc,1,n);        }  
     free_vector(andc,1,n);      } 
     }  
      
     wav=ivector(1,imx);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);   for (i=1; i<=ncovmodel-2; i++) { 
         /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     /* Concatenates waves */     ij=Tvar[i];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);     Ndum[ij]++;
    }
   
       Tcode=ivector(1,100);   ij=1;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   for (i=1; i<= maxncov; i++) {
       ncodemax[1]=1;     if((Ndum[i]!=0) && (i<=ncovcol)){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);       Tvaraff[ij]=i; /*For printing */
             ij++;
    codtab=imatrix(1,100,1,10);     }
    h=0;   }
    m=pow(2,cptcoveff);   
     cptcoveff=ij-1; /*Number of simple covariates*/
    for(k=1;k<=cptcoveff; k++){  }
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){  /*********** Health Expectancies ****************/
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;  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[] )
            if (h>m) h=1;codtab[h][k]=j;  
          }  {
        }    /* Health expectancies */
      }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
    }    double age, agelim, hf;
        double ***p3mat,***varhe;
    /* Calculates basic frequencies. Computes observed prevalence at single age    double **dnewm,**doldm;
        and prints on file fileres'p'. */    double *xp;
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint);    double **gp, **gm;
      double ***gradg, ***trgradg;
   free_matrix(mint,1,maxwav,1,n);    int theta;
   free_matrix(anint,1,maxwav,1,n);  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    xp=vector(1,npar);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    dnewm=matrix(1,nlstate*nlstate,1,npar);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficreseij,"# Local time at start: %s", strstart);
          fprintf(ficreseij,"# Health expectancies\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficreseij,"# Age");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    for(i=1; i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
     if(mle==1){    fprintf(ficreseij,"\n");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    if(estepm < stepm){
          printf ("Problem %d lower than %d\n",estepm, stepm);
     /*--------- results files --------------*/    }
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);    else  hstepm=estepm;   
    fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);    /* We compute the life expectancy from trapezoids spaced every estepm months
    fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
    jk=1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
    fprintf(ficres,"# Parameters\n");     * progression in between and thus overestimating or underestimating according
    printf("# Parameters\n");     * to the curvature of the survival function. If, for the same date, we 
    for(i=1,jk=1; i <=nlstate; i++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      for(k=1; k <=(nlstate+ndeath); k++){     * to compare the new estimate of Life expectancy with the same linear 
        if (k != i)     * hypothesis. A more precise result, taking into account a more precise
          {     * curvature will be obtained if estepm is as small as stepm. */
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    /* For example we decided to compute the life expectancy with the smallest unit */
            for(j=1; j <=ncovmodel; j++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
              printf("%f ",p[jk]);       nhstepm is the number of hstepm from age to agelim 
              fprintf(ficres,"%f ",p[jk]);       nstepm is the number of stepm from age to agelin. 
              jk++;       Look at hpijx to understand the reason of that which relies in memory size
            }       and note for a fixed period like estepm months */
            printf("\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
            fprintf(ficres,"\n");       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
      }       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.
  if(mle==1){    */
     /* Computing hessian and covariance matrix */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);    agelim=AGESUP;
  }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficres,"# Scales\n");      /* nhstepm age range expressed in number of stepm */
     printf("# Scales\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
      for(i=1,jk=1; i <=nlstate; i++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(j=1; j <=nlstate+ndeath; j++){      /* if (stepm >= YEARM) hstepm=1;*/
         if (j!=i) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           fprintf(ficres,"%1d%1d",i,j);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           printf("%1d%1d",i,j);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           for(k=1; k<=ncovmodel;k++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
             printf(" %.5e",delti[jk]);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           printf("\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           fprintf(ficres,"\n");   
         }  
       }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       }  
          /* Computing  Variances of health expectancies */
     k=1;  
     fprintf(ficres,"# Covariance\n");       for(theta=1; theta <=npar; theta++){
     printf("# Covariance\n");        for(i=1; i<=npar; i++){ 
     for(i=1;i<=npar;i++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       /*  if (k>nlstate) k=1;        }
       i1=(i-1)/(ncovmodel*nlstate)+1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    
       printf("%s%d%d",alph[k],i1,tab[i]);*/        cptj=0;
       fprintf(ficres,"%3d",i);        for(j=1; j<= nlstate; j++){
       printf("%3d",i);          for(i=1; i<=nlstate; i++){
       for(j=1; j<=i;j++){            cptj=cptj+1;
         fprintf(ficres," %.5e",matcov[i][j]);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         printf(" %.5e",matcov[i][j]);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       }            }
       fprintf(ficres,"\n");          }
       printf("\n");        }
       k++;       
     }       
            for(i=1; i<=npar; i++) 
     while((c=getc(ficpar))=='#' && c!= EOF){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fgets(line, MAXLINE, ficpar);        
       puts(line);        cptj=0;
       fputs(line,ficparo);        for(j=1; j<= nlstate; j++){
     }          for(i=1;i<=nlstate;i++){
     ungetc(c,ficpar);            cptj=cptj+1;
              for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
                  gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     if (fage <= 2) {            }
       bage = agemin;          }
       fage = agemax;        }
     }        for(j=1; j<= nlstate*nlstate; j++)
           for(h=0; h<=nhstepm-1; h++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          }
        } 
         
 /*------------ gnuplot -------------*/  /* End theta */
 chdir(pathcd);  
   if((ficgp=fopen("graph.plt","w"))==NULL) {       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     printf("Problem with file graph.gp");goto end;  
   }       for(h=0; h<=nhstepm-1; h++)
 #ifdef windows        for(j=1; j<=nlstate*nlstate;j++)
   fprintf(ficgp,"cd \"%s\" \n",pathc);          for(theta=1; theta <=npar; theta++)
 #endif            trgradg[h][j][theta]=gradg[h][theta][j];
 m=pow(2,cptcoveff);       
    
  /* 1eme*/       for(i=1;i<=nlstate*nlstate;i++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for(j=1;j<=nlstate*nlstate;j++)
    for (k1=1; k1<= m ; k1 ++) {          varhe[i][j][(int)age] =0.;
   
 #ifdef windows       printf("%d|",(int)age);fflush(stdout);
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 #endif       for(h=0;h<=nhstepm-1;h++){
 #ifdef unix        for(k=0;k<=nhstepm-1;k++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 #endif          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1;i<=nlstate*nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {            for(j=1;j<=nlstate*nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }      }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      /* Computing expectancies */
     for (i=1; i<= nlstate ; i ++) {      for(i=1; i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          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;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            
      for (i=1; i<= nlstate ; i ++) {  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      fprintf(ficreseij,"%3.0f",age );
 #ifdef unix      cptj=0;
 fprintf(ficgp,"\nset ter gif small size 400,300");      for(i=1; i<=nlstate;i++)
 #endif        for(j=1; j<=nlstate;j++){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          cptj++;
    }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   }        }
   /*2 eme*/      fprintf(ficreseij,"\n");
      
   for (k1=1; k1<= m ; k1 ++) {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
          free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     for (i=1; i<= nlstate+1 ; i ++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       k=2*i;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    }
       for (j=1; j<= nlstate+1 ; j ++) {    printf("\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficlog,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      free_vector(xp,1,npar);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       for (j=1; j<= nlstate+1 ; j ++) {  }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");  /************ 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[])
       fprintf(ficgp,"\" t\"\" w l 0,");  {
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /* Variance of health expectancies */
       for (j=1; j<= nlstate+1 ; j ++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* double **newm;*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double **dnewm,**doldm;
 }      double **dnewmp,**doldmp;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    int i, j, nhstepm, hstepm, h, nstepm ;
       else fprintf(ficgp,"\" t\"\" w l 0,");    int k, cptcode;
     }    double *xp;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
      double **gradgp, **trgradgp; /* for var p point j */
   /*3eme*/    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   for (k1=1; k1<= m ; k1 ++) {    double ***p3mat;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double age,agelim, hf;
       k=2+nlstate*(cpt-1);    double ***mobaverage;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    int theta;
       for (i=1; i< nlstate ; i ++) {    char digit[4];
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    char digitp[25];
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    char fileresprobmorprev[FILENAMELENGTH];
     }  
   }    if(popbased==1){
        if(mobilav!=0)
   /* CV preval stat */        strcpy(digitp,"-populbased-mobilav-");
   for (k1=1; k1<= m ; k1 ++) {      else strcpy(digitp,"-populbased-nomobil-");
     for (cpt=1; cpt<nlstate ; cpt ++) {    }
       k=3;    else 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      strcpy(digitp,"-stablbased-");
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);    if (mobilav!=0) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       l=3+(nlstate+ndeath)*cpt;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       for (i=1; i< nlstate ; i ++) {      }
         l=3+(nlstate+ndeath)*cpt;    }
         fprintf(ficgp,"+$%d",l+i+1);  
       }    strcpy(fileresprobmorprev,"prmorprev"); 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      sprintf(digit,"%-d",ij);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /*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 */
     strcat(fileresprobmorprev,fileres);
   /* proba elementaires */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
    for(i=1,jk=1; i <=nlstate; i++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       if (k != i) {    }
         for(j=1; j <=ncovmodel; j++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/   
           /*fprintf(ficgp,"%s",alph[1]);*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
           jk++;    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);
           fprintf(ficgp,"\n");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       }      fprintf(ficresprobmorprev," p.%-d SE",j);
     }      for(i=1; i<=nlstate;i++)
     }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
   for(jk=1; jk <=m; jk++) {    fprintf(ficresprobmorprev,"\n");
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    fprintf(ficgp,"\n# Routine varevsij");
    i=1;   fprintf(fichtm, "#Local time at start: %s", strstart);
    for(k2=1; k2<=nlstate; k2++) {    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");
      k3=i;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      for(k=1; k<=(nlstate+ndeath); k++) {  /*   } */
        if (k != k2){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);   fprintf(ficresvij, "#Local time at start: %s", strstart);
 ij=1;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
         for(j=3; j <=ncovmodel; j++) {    fprintf(ficresvij,"# Age");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for(i=1; i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for(j=1; j<=nlstate;j++)
             ij++;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
           }    fprintf(ficresvij,"\n");
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
           fprintf(ficgp,")/(1");    doldm=matrix(1,nlstate,1,nlstate);
            dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         for(k1=1; k1 <=nlstate; k1++){      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
 ij=1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           for(j=3; j <=ncovmodel; j++){    gpp=vector(nlstate+1,nlstate+ndeath);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    gmp=vector(nlstate+1,nlstate+ndeath);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             ij++;    
           }    if(estepm < stepm){
           else      printf ("Problem %d lower than %d\n",estepm, stepm);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    }
           }    else  hstepm=estepm;   
           fprintf(ficgp,")");    /* For example we decided to compute the life expectancy with the smallest unit */
         }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);       nhstepm is the number of hstepm from age to agelim 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");       nstepm is the number of stepm from age to agelin. 
         i=i+ncovmodel;       Look at hpijx to understand the reason of that which relies in memory size
        }       and note for a fixed period like k years */
      }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    }       survival function given by stepm (the optimization length). Unfortunately it
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);       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 
           results. So we changed our mind and took the option of the best precision.
   fclose(ficgp);    */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 chdir(path);    agelim = AGESUP;
        for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     free_ivector(wav,1,imx);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ivector(num,1,n);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     free_vector(agedc,1,n);      gp=matrix(0,nhstepm,1,nlstate);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      gm=matrix(0,nhstepm,1,nlstate);
     fclose(ficparo);  
     fclose(ficres);  
     /*  }*/      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
    /*________fin mle=1_________*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     /* No more information from the sample is required now */  
   /* 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);          }
          }
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        for(j=1; j<= nlstate; j++){
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          for(h=0; h<=nhstepm; h++){
 /*--------- index.htm --------*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcpy(optionfilehtm,optionfile);          }
   strcat(optionfilehtm,".htm");        }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        /* This for computing probability of death (h=1 means
     printf("Problem with %s \n",optionfilehtm);goto end;           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
         */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          for(i=1,gpp[j]=0.; i<= nlstate; i++)
 Total number of observations=%d <br>            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        }    
 <hr  size=\"2\" color=\"#EC5E5E\">        /* end probability of death */
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>   
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        if (popbased==1) {
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          if(mobilav ==0){
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            for(i=1; i<=nlstate;i++)
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>              prlim[i][i]=probs[(int)age][i][ij];
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>          }else{ /* mobilav */ 
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
  fprintf(fichtm," <li>Graphs</li><p>");          }
         }
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
  j1=0;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
  for(k1=1; k1<=m;k1++){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
    for(i1=1; i1<=ncodemax[k1];i1++){          }
        j1++;        }
        if (cptcovn > 0) {        /* This for computing probability of death (h=1 means
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");           computed over hstepm matrices product = hstepm*stepm months) 
          for (cpt=1; cpt<=cptcoveff;cpt++)           as a weighted average of prlim.
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
        }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            }    
        for(cpt=1; cpt<nlstate;cpt++){        /* end probability of death */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(j=1; j<= nlstate; j++) /* vareij */
        }          for(h=0; h<=nhstepm; h++){
     for(cpt=1; cpt<=nlstate;cpt++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          }
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
      }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
      for(cpt=1; cpt<=nlstate;cpt++) {        }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      } /* End theta */
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      for(h=0; h<=nhstepm; h++) /* veij */
 fprintf(fichtm,"\n</body>");        for(j=1; j<=nlstate;j++)
    }          for(theta=1; theta <=npar; theta++)
  }            trgradg[h][j][theta]=gradg[h][theta][j];
 fclose(fichtm);  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   /*--------------- Prevalence limit --------------*/        for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
   strcpy(filerespl,"pl");    
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      for(i=1;i<=nlstate;i++)
   }        for(j=1;j<=nlstate;j++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          vareij[i][j][(int)age] =0.;
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");      for(h=0;h<=nhstepm;h++){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(k=0;k<=nhstepm;k++){
   fprintf(ficrespl,"\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   prlim=matrix(1,nlstate,1,nlstate);          for(i=1;i<=nlstate;i++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(j=1;j<=nlstate;j++)
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   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 */    
   k=0;      /* pptj */
   agebase=agemin;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   agelim=agemax;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   ftolpl=1.e-10;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   i1=cptcoveff;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   if (cptcovn < 1){i1=1;}          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
   for(cptcov=1;cptcov<=i1;cptcov++){      /*  x centered again */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         k=k+1;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   
         fprintf(ficrespl,"\n#******");      if (popbased==1) {
         for(j=1;j<=cptcoveff;j++)        if(mobilav ==0){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(i=1; i<=nlstate;i++)
         fprintf(ficrespl,"******\n");            prlim[i][i]=probs[(int)age][i][ij];
                }else{ /* mobilav */ 
         for (age=agebase; age<=agelim; age++){          for(i=1; i<=nlstate;i++)
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            prlim[i][i]=mobaverage[(int)age][i][ij];
           fprintf(ficrespl,"%.0f",age );        }
           for(i=1; i<=nlstate;i++)      }
           fprintf(ficrespl," %.5f", prlim[i][i]);               
           fprintf(ficrespl,"\n");      /* This for computing probability of death (h=1 means
         }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       }         as a weighted average of prlim.
     }      */
   fclose(ficrespl);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   /*------------- h Pij x at various ages ------------*/          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
        }    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      /* end probability of death */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   printf("Computing pij: result on file '%s' \n", filerespij);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   /*if (stepm<=24) stepsize=2;*/        }
       } 
   agelim=AGESUP;      fprintf(ficresprobmorprev,"\n");
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   k=0;        for(j=1; j<=nlstate;j++){
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;      fprintf(ficresvij,"\n");
         fprintf(ficrespij,"\n#****** ");      free_matrix(gp,0,nhstepm,1,nlstate);
         for(j=1;j<=cptcoveff;j++)      free_matrix(gm,0,nhstepm,1,nlstate);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         fprintf(ficrespij,"******\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    } /* End age */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_vector(gpp,nlstate+1,nlstate+ndeath);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    free_vector(gmp,nlstate+1,nlstate+ndeath);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           oldm=oldms;savm=savms;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           fprintf(ficrespij,"# Age");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           for(i=1; i<=nlstate;i++)    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
             for(j=1; j<=nlstate+ndeath;j++)  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
               fprintf(ficrespij," %1d-%1d",i,j);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           fprintf(ficrespij,"\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           for (h=0; h<=nhstepm; h++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
             for(i=1; i<=nlstate;i++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
             fprintf(ficrespij,"\n");    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
           }  */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           fprintf(ficrespij,"\n");    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         }  
     }    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   fclose(ficrespij);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*---------- Forecasting ------------------*/    fclose(ficresprobmorprev);
     fflush(ficgp);
   strcpy(fileresf,"f");    fflush(fichtm); 
   strcat(fileresf,fileres);  }  /* end varevsij */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;  /************ Variance of prevlim ******************/
   }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   printf("Computing forecasting: result on file '%s' \n", fileresf);  {
     /* Variance of prevalence limit */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
  free_matrix(agev,1,maxwav,1,imx);    double **dnewm,**doldm;
   /* Mobile average */    int i, j, nhstepm, hstepm;
     int k, cptcode;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    double *xp;
     double *gp, *gm;
   if (mobilav==1) {    double **gradg, **trgradg;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double age,agelim;
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    int theta;
       for (i=1; i<=nlstate;i++)    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           mobaverage[(int)agedeb][i][cptcod]=0.;    fprintf(ficresvpl,"# Age");
        for(i=1; i<=nlstate;i++)
     for (agedeb=bage+4; agedeb<=fage; agedeb++){        fprintf(ficresvpl," %1d-%1d",i,i);
       for (i=1; i<=nlstate;i++){    fprintf(ficresvpl,"\n");
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){    xp=vector(1,npar);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    dnewm=matrix(1,nlstate,1,npar);
           }    doldm=matrix(1,nlstate,1,nlstate);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    
         }    hstepm=1*YEARM; /* Every year of age */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     }      agelim = AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   stepsize=(int) (stepm+YEARM-1)/YEARM;      if (stepm >= YEARM) hstepm=1;
   if (stepm<=12) stepsize=1;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
   agelim=AGESUP;      gp=vector(1,nlstate);
   hstepm=stepsize*YEARM; /* Every year of age */      gm=vector(1,nlstate);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  
        for(theta=1; theta <=npar; theta++){
   if (popforecast==1) {        for(i=1; i<=npar; i++){ /* Computes gradient */
     if((ficpop=fopen(popfile,"r"))==NULL)    {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       printf("Problem with population file : %s\n",popfile);goto end;        }
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     popage=ivector(0,AGESUP);        for(i=1;i<=nlstate;i++)
     popeffectif=vector(0,AGESUP);          gp[i] = prlim[i][i];
     popcount=vector(0,AGESUP);      
         for(i=1; i<=npar; i++) /* Computes gradient */
     i=1;            xp[i] = x[i] - (i==theta ?delti[theta]:0);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       {        for(i=1;i<=nlstate;i++)
         i=i+1;          gm[i] = prlim[i][i];
       }  
     imx=i;        for(i=1;i<=nlstate;i++)
            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      } /* End theta */
   }  
       trgradg =matrix(1,nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(j=1; j<=nlstate;j++)
       k=k+1;        for(theta=1; theta <=npar; theta++)
       fprintf(ficresf,"\n#****** ");          trgradg[j][theta]=gradg[theta][j];
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1;i<=nlstate;i++)
       }        varpl[i][(int)age] =0.;
       fprintf(ficresf,"******\n");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      for(i=1;i<=nlstate;i++)
       if (popforecast==1)  fprintf(ficresf," [Population]");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       for (agedeb=fage; agedeb>=bage; agedeb--){      fprintf(ficresvpl,"%.0f ",age );
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);      for(i=1; i<=nlstate;i++)
        if (mobilav==1) {        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         for(j=1; j<=nlstate;j++)      fprintf(ficresvpl,"\n");
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);      free_vector(gp,1,nlstate);
         }      free_vector(gm,1,nlstate);
         else {      free_matrix(gradg,1,npar,1,nlstate);
           for(j=1; j<=nlstate;j++)      free_matrix(trgradg,1,nlstate,1,npar);
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);    } /* End age */
         }    
     free_vector(xp,1,npar);
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");    free_matrix(doldm,1,nlstate,1,npar);
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);    free_matrix(dnewm,1,nlstate,1,nlstate);
       }  
        }
       for (cpt=1; cpt<=nforecast;cpt++) {  
         fprintf(ficresf,"\n");  /************ Variance of one-step probabilities  ******************/
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  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[])
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  {
         nhstepm = nhstepm/hstepm;    int i, j=0,  i1, k1, l1, t, tj;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int first=1, first1;
         oldm=oldms;savm=savms;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **dnewm,**doldm;
                    double *xp;
         for (h=0; h<=nhstepm; h++){    double *gp, *gm;
            double **gradg, **trgradg;
          if (h*hstepm/YEARM*stepm==cpt)    double **mu;
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);    double age,agelim, cov[NCOVMAX];
              double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
              int theta;
          for(j=1; j<=nlstate+ndeath;j++) {    char fileresprob[FILENAMELENGTH];
            kk1=0.;kk2=0;    char fileresprobcov[FILENAMELENGTH];
            for(i=1; i<=nlstate;i++) {            char fileresprobcor[FILENAMELENGTH];
              if (mobilav==1)  
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];    double ***varpij;
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];  
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    strcpy(fileresprob,"prob"); 
             }    strcat(fileresprob,fileres);
            if (h*hstepm/YEARM*stepm==cpt) {    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
              fprintf(ficresf," %.3f", kk1);      printf("Problem with resultfile: %s\n", fileresprob);
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
            }    }
           }    strcpy(fileresprobcov,"probcov"); 
         }    strcat(fileresprobcov,fileres);
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", fileresprobcov);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       }    }
     }    strcpy(fileresprobcor,"probcor"); 
   }    strcat(fileresprobcor,fileres);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if (popforecast==1) {      printf("Problem with resultfile: %s\n", fileresprobcor);
     free_ivector(popage,0,AGESUP);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     free_vector(popeffectif,0,AGESUP);    }
     free_vector(popcount,0,AGESUP);    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);
   free_imatrix(s,1,maxwav+1,1,n);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   free_vector(weight,1,n);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fclose(ficresf);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   /*---------- Health expectancies and variances ------------*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficresprob, "#Local time at start: %s", strstart);
   strcpy(filerest,"t");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   strcat(filerest,fileres);    fprintf(ficresprob,"# Age");
   if((ficrest=fopen(filerest,"w"))==NULL) {    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   }    fprintf(ficresprobcov,"# Age");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   strcpy(filerese,"e");  
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
  strcpy(fileresv,"v");      }  
   strcat(fileresv,fileres);   /* fprintf(ficresprob,"\n");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fprintf(ficresprobcov,"\n");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fprintf(ficresprobcor,"\n");
   }   */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   k=0;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   for(cptcov=1;cptcov<=i1;cptcov++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       k=k+1;    first=1;
       fprintf(ficrest,"\n#****** ");    fprintf(ficgp,"\n# Routine varprob");
       for(j=1;j<=cptcoveff;j++)    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(fichtm,"\n");
       fprintf(ficrest,"******\n");  
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       fprintf(ficreseij,"\n#****** ");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
       for(j=1;j<=cptcoveff;j++)    file %s<br>\n",optionfilehtmcov);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       fprintf(ficreseij,"******\n");  and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(ficresvij,"\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. \
       for(j=1;j<=cptcoveff;j++)  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       fprintf(ficresvij,"******\n");  standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       oldm=oldms;savm=savms;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    cov[1]=1;
       oldm=oldms;savm=savms;    tj=cptcoveff;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
          j1=0;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    for(t=1; t<=tj;t++){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      for(i1=1; i1<=ncodemax[t];i1++){ 
       fprintf(ficrest,"\n");        j1++;
                if  (cptcovn>0) {
       hf=1;          fprintf(ficresprob, "\n#********** Variable "); 
       if (stepm >= YEARM) hf=stepm/YEARM;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       epj=vector(1,nlstate+1);          fprintf(ficresprob, "**********\n#\n");
       for(age=bage; age <=fage ;age++){          fprintf(ficresprobcov, "\n#********** Variable "); 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         if (popbased==1) {          fprintf(ficresprobcov, "**********\n#\n");
           for(i=1; i<=nlstate;i++)          
             prlim[i][i]=probs[(int)age][i][k];          fprintf(ficgp, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficgp, "**********\n#\n");
         fprintf(ficrest," %.0f",age);          
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           epj[nlstate+1] +=epj[j];          
         }          fprintf(ficresprobcor, "\n#********** Variable ");    
         for(i=1, vepp=0.;i <=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(j=1;j <=nlstate;j++)          fprintf(ficresprobcor, "**********\n#");    
             vepp += vareij[i][j][(int)age];        }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        
         for(j=1;j <=nlstate;j++){        for (age=bage; age<=fage; age ++){ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          cov[2]=age;
         }          for (k=1; k<=cptcovn;k++) {
         fprintf(ficrest,"\n");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       }          }
     }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }          for (k=1; k<=cptcovprod;k++)
                    cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                  
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
  fclose(ficreseij);          gp=vector(1,(nlstate)*(nlstate+ndeath));
  fclose(ficresvij);          gm=vector(1,(nlstate)*(nlstate+ndeath));
   fclose(ficrest);      
   fclose(ficpar);          for(theta=1; theta <=npar; theta++){
   free_vector(epj,1,nlstate+1);            for(i=1; i<=npar; i++)
   /*  scanf("%d ",i); */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   /*------- Variance limit prevalence------*/              pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
 strcpy(fileresvpl,"vpl");            k=0;
   strcat(fileresvpl,fileres);            for(i=1; i<= (nlstate); i++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {              for(j=1; j<=(nlstate+ndeath);j++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                k=k+1;
     exit(0);                gp[k]=pmmij[i][j];
   }              }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            }
             
  k=0;            for(i=1; i<=npar; i++)
  for(cptcov=1;cptcov<=i1;cptcov++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      
      k=k+1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
      fprintf(ficresvpl,"\n#****** ");            k=0;
      for(j=1;j<=cptcoveff;j++)            for(i=1; i<=(nlstate); i++){
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              for(j=1; j<=(nlstate+ndeath);j++){
      fprintf(ficresvpl,"******\n");                k=k+1;
                      gm[k]=pmmij[i][j];
      varpl=matrix(1,nlstate,(int) bage, (int) fage);              }
      oldm=oldms;savm=savms;            }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       
    }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
  }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   fclose(ficresvpl);  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   /*---------- End : free ----------------*/            for(theta=1; theta <=npar; theta++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              trgradg[j][theta]=gradg[theta][j];
            
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
            free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   free_matrix(matcov,1,npar,1,npar);          k=0;
   free_vector(delti,1,npar);          for(i=1; i<=(nlstate); i++){
              for(j=1; j<=(nlstate+ndeath);j++){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
   printf("End of Imach\n");            }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          }
            for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/              varpij[i][j][(int)age] = doldm[i][j];
   /*------ End -----------*/  
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
  end:            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
 #ifdef windows            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  chdir(pathcd);            }*/
 #endif  
            fprintf(ficresprob,"\n%d ",(int)age);
  system("..\\gp37mgw\\wgnuplot graph.plt");          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
 #ifdef windows  
   while (z[0] != 'q') {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     chdir(pathcd);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     scanf("%s",z);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     if (z[0] == 'c') system("./imach");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     else if (z[0] == 'e') {          }
       chdir(path);          i=0;
       system(optionfilehtm);          for (k=1; k<=(nlstate);k++){
     }            for (l=1; l<=(nlstate+ndeath);l++){ 
     else if (z[0] == 'q') exit(0);              i=i++;
   }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
 #endif              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]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         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;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> Result files (second order: variances)</h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           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   lx     qx    dx    Lx     Tx     e(x)<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 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 */
     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],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,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;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); 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;
       }
     }
     /* 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 parameter 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 (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    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;
           
           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[2]=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);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" 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);
     }
   }
   
   
   

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  Added in v.1.105


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