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version 1.7, 2001/05/02 17:50:24 version 1.107, 2006/01/19 16:20:37
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.107  2006/01/19 16:20:37  brouard
   individuals from different ages are interviewed on their health status    Test existence of gnuplot in imach path
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.106  2006/01/19 13:24:36  brouard
   Health expectancies are computed from the transistions observed between    Some cleaning and links added in html output
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.105  2006/01/05 20:23:19  lievre
   reach the Maximum Likelihood of the parameters involved in the model.    *** empty log message ***
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.104  2005/09/30 16:11:43  lievre
   to be observed in state i at the first wave. Therefore the model is:    (Module): sump fixed, loop imx fixed, and simplifications.
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    (Module): If the status is missing at the last wave but we know
   is a covariate. If you want to have a more complex model than "constant and    that the person is alive, then we can code his/her status as -2
   age", you should modify the program where the markup    (instead of missing=-1 in earlier versions) and his/her
     *Covariates have to be included here again* invites you to do it.    contributions to the likelihood is 1 - Prob of dying from last
   More covariates you add, less is the speed of the convergence.    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
   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 1.103  2005/09/30 15:54:49  lievre
   individual missed an interview, the information is not rounded or lost, but    (Module): sump fixed, loop imx fixed, and simplifications.
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.102  2004/09/15 17:31:30  brouard
   observed in state i at age x+h conditional to the observed state i at age    Add the possibility to read data file including tab characters.
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.101  2004/09/15 10:38:38  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    Fix on curr_time
   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 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.99  2004/06/05 08:57:40  brouard
      *** empty log message ***
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.98  2004/05/16 15:05:56  brouard
   This software have been partly granted by Euro-REVES, a concerted action    New version 0.97 . First attempt to estimate force of mortality
   from the European Union.    directly from the data i.e. without the need of knowing the health
   It is copyrighted identically to a GNU software product, ie programme and    state at each age, but using a Gompertz model: log u =a + b*age .
   software can be distributed freely for non commercial use. Latest version    This is the basic analysis of mortality and should be done before any
   can be accessed at http://euroreves.ined.fr/imach .    other analysis, in order to test if the mortality estimated from the
   **********************************************************************/    cross-longitudinal survey is different from the mortality estimated
      from other sources like vital statistic data.
 #include <math.h>  
 #include <stdio.h>    The same imach parameter file can be used but the option for mle should be -3.
 #include <stdlib.h>  
 #include <unistd.h>    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.
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    The output is very simple: only an estimate of the intercept and of
 /*#define DEBUG*/    the slope with 95% confident intervals.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Current limitations:
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    B) There is no computation of Life Expectancy nor Life Table.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.97  2004/02/20 13:25:42  lievre
 #define NINTERVMAX 8    Version 0.96d. Population forecasting command line is (temporarily)
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    suppressed.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.96  2003/07/15 15:38:55  brouard
 #define MAXN 20000    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define YEARM 12. /* Number of months per year */    rewritten within the same printf. Workaround: many printfs.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 int nvar;    matrix (cov(a12,c31) instead of numbers.
 static int cptcov;  
 int cptcovn, cptcovage=0, cptcoveff=0;    Revision 1.94  2003/06/27 13:00:02  brouard
 int npar=NPARMAX;    Just cleaning
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.93  2003/06/25 16:33:55  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Version 0.96b
 int maxwav; /* Maxim number of waves */  
 int mle, weightopt;    Revision 1.92  2003/06/25 16:30:45  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): On windows (cygwin) function asctime_r doesn't
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    exist so I changed back to asctime which exists.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.91  2003/06/25 15:30:29  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    * imach.c (Repository): Duplicated warning errors corrected.
 FILE *ficgp, *fichtm;    (Repository): Elapsed time after each iteration is now output. It
 FILE *ficreseij;    helps to forecast when convergence will be reached. Elapsed time
   char filerese[FILENAMELENGTH];    is stamped in powell.  We created a new html file for the graphs
  FILE  *ficresvij;    concerning matrix of covariance. It has extension -cov.htm.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.90  2003/06/24 12:34:15  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define NR_END 1    of the covariance matrix to be input.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 #define NRANSI    mle=-1 a template is output in file "or"mypar.txt with the design
 #define ITMAX 200    of the covariance matrix to be input.
   
 #define TOL 2.0e-4    Revision 1.88  2003/06/23 17:54:56  brouard
     * 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 CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.87  2003/06/18 12:26:01  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Version 0.96
   
 #define GOLD 1.618034    Revision 1.86  2003/06/17 20:04:08  brouard
 #define GLIMIT 100.0    (Module): Change position of html and gnuplot routines and added
 #define TINY 1.0e-20    routine fileappend.
   
 static double maxarg1,maxarg2;    Revision 1.85  2003/06/17 13:12:43  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Repository): Check when date of death was earlier that
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    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 SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    was wrong (infinity). We still send an "Error" but patch by
 #define rint(a) floor(a+0.5)    assuming that the date of death was just one stepm after the
     interview.
 static double sqrarg;    (Repository): Because some people have very long ID (first column)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    we changed int to long in num[] and we added a new lvector for
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    memory allocation. But we also truncated to 8 characters (left
     truncation)
 int imx;    (Repository): No more line truncation errors.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 int m,nb;    place. It differs from routine "prevalence" which may be called
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    many times. Probs is memory consuming and must be used with
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    parcimony.
 double **pmmij;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 double *weight;    Revision 1.83  2003/06/10 13:39:11  lievre
 int **s; /* Status */    *** empty log message ***
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  */
   /*
 /**************** split *************************/     Interpolated Markov Chain
 static  int split( char *path, char *dirc, char *name )  
 {    Short summary of the programme:
    char *s;                             /* pointer */    
    int  l1, l2;                         /* length counters */    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    l1 = strlen( path );                 /* length of path */    first survey ("cross") where individuals from different ages are
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    interviewed on their health status or degree of disability (in the
    s = strrchr( path, '\\' );           /* find last / */    case of a health survey which is our main interest) -2- at least a
    if ( s == NULL ) {                   /* no directory, so use current */    second wave of interviews ("longitudinal") which measure each change
 #if     defined(__bsd__)                /* get current working directory */    (if any) in individual health status.  Health expectancies are
       extern char       *getwd( );    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
       if ( getwd( dirc ) == NULL ) {    Maximum Likelihood of the parameters involved in the model.  The
 #else    simplest model is the multinomial logistic model where pij is the
       extern char       *getcwd( );    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #endif    'age' is age and 'sex' is a covariate. If you want to have a more
          return( GLOCK_ERROR_GETCWD );    complex model than "constant and age", you should modify the program
       }    where the markup *Covariates have to be included here again* invites
       strcpy( name, path );             /* we've got it */    you to do it.  More covariates you add, slower the
    } else {                             /* strip direcotry from path */    convergence.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    The advantage of this computer programme, compared to a simple
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    multinomial logistic model, is clear when the delay between waves is not
       strcpy( name, s );                /* save file name */    identical for each individual. Also, if a individual missed an
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    intermediate interview, the information is lost, but taken into
       dirc[l1-l2] = 0;                  /* add zero */    account using an interpolation or extrapolation.  
    }  
    l1 = strlen( dirc );                 /* length of directory */    hPijx is the probability to be observed in state i at age x+h
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    conditional to the observed state i at age x. The delay 'h' can be
    return( 0 );                         /* we're done */    split into an exact number (nh*stepm) of unobserved intermediate
 }    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 /******************************************/    and the contribution of each individual to the likelihood is simply
     hPijx.
 void replace(char *s, char*t)  
 {    Also this programme outputs the covariance matrix of the parameters but also
   int i;    of the life expectancies. It also computes the stable prevalence. 
   int lg=20;    
   i=0;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   lg=strlen(t);             Institut national d'études démographiques, Paris.
   for(i=0; i<= lg; i++) {    This software have been partly granted by Euro-REVES, a concerted action
     (s[i] = t[i]);    from the European Union.
     if (t[i]== '\\') s[i]='/';    It is copyrighted identically to a GNU software product, ie programme and
   }    software can be distributed freely for non commercial use. Latest version
 }    can be accessed at http://euroreves.ined.fr/imach .
   
 int nbocc(char *s, char occ)    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   int i,j=0;    
   int lg=20;    **********************************************************************/
   i=0;  /*
   lg=strlen(s);    main
   for(i=0; i<= lg; i++) {    read parameterfile
   if  (s[i] == occ ) j++;    read datafile
   }    concatwav
   return j;    freqsummary
 }    if (mle >= 1)
       mlikeli
 void cutv(char *u,char *v, char*t, char occ)    print results files
 {    if mle==1 
   int i,lg,j,p=0;       computes hessian
   i=0;    read end of parameter file: agemin, agemax, bage, fage, estepm
   for(j=0; j<=strlen(t)-1; j++) {        begin-prev-date,...
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    open gnuplot file
   }    open html file
     stable prevalence
   lg=strlen(t);     for age prevalim()
   for(j=0; j<p; j++) {    h Pij x
     (u[j] = t[j]);    variance of p varprob
   }    forecasting if prevfcast==1 prevforecast call prevalence()
      u[p]='\0';    health expectancies
     Variance-covariance of DFLE
    for(j=0; j<= lg; j++) {    prevalence()
     if (j>=(p+1))(v[j-p-1] = t[j]);     movingaverage()
   }    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
 /********************** nrerror ********************/    Variance of stable prevalence
    end
 void nrerror(char error_text[])  */
 {  
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  
   exit(1);   
 }  #include <math.h>
 /*********************** vector *******************/  #include <stdio.h>
 double *vector(int nl, int nh)  #include <stdlib.h>
 {  #include <string.h>
   double *v;  #include <unistd.h>
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #include <sys/types.h>
   return v-nl+NR_END;  #include <sys/stat.h>
 }  #include <errno.h>
   extern int errno;
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  /* #include <sys/time.h> */
 {  #include <time.h>
   free((FREE_ARG)(v+nl-NR_END));  #include "timeval.h"
 }  
   /* #include <libintl.h> */
 /************************ivector *******************************/  /* #define _(String) gettext (String) */
 int *ivector(long nl,long nh)  
 {  #define MAXLINE 256
   int *v;  #define GNUPLOTPROGRAM "gnuplot"
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   if (!v) nrerror("allocation failure in ivector");  #define FILENAMELENGTH 132
   return v-nl+NR_END;  /*#define DEBUG*/
 }  /*#define windows*/
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /******************free ivector **************************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 void free_ivector(int *v, long nl, long nh)  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   free((FREE_ARG)(v+nl-NR_END));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /******************* imatrix *******************************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define NCOVMAX 8 /* Maximum number of covariates */
 {  #define MAXN 20000
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define YEARM 12. /* Number of months per year */
   int **m;  #define AGESUP 130
    #define AGEBASE 40
   /* allocate pointers to rows */  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #ifdef UNIX
   if (!m) nrerror("allocation failure 1 in matrix()");  #define DIRSEPARATOR '/'
   m += NR_END;  #define CHARSEPARATOR "/"
   m -= nrl;  #define ODIRSEPARATOR '\\'
    #else
    #define DIRSEPARATOR '\\'
   /* allocate rows and set pointers to them */  #define CHARSEPARATOR "\\"
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define ODIRSEPARATOR '/'
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #endif
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /* $Id$ */
    /* $State$ */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
   /* return pointer to array of pointers to rows */  char fullversion[]="$Revision$ $Date$"; 
   return m;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 }  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 /****************** free_imatrix *************************/  int npar=NPARMAX;
 void free_imatrix(m,nrl,nrh,ncl,nch)  int nlstate=2; /* Number of live states */
       int **m;  int ndeath=1; /* Number of dead states */
       long nch,ncl,nrh,nrl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
      /* free an int matrix allocated by imatrix() */  int popbased=0;
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int *wav; /* Number of waves for this individuual 0 is possible */
   free((FREE_ARG) (m+nrl-NR_END));  int maxwav; /* Maxim number of waves */
 }  int jmin, jmax; /* min, max spacing between 2 waves */
   int gipmx, gsw; /* Global variables on the number of contributions 
 /******************* matrix *******************************/                     to the likelihood and the sum of weights (done by funcone)*/
 double **matrix(long nrl, long nrh, long ncl, long nch)  int mle, weightopt;
 {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double **m;  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. */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double jmean; /* Mean space between 2 waves */
   if (!m) nrerror("allocation failure 1 in matrix()");  double **oldm, **newm, **savm; /* Working pointers to matrices */
   m += NR_END;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m -= nrl;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int globpr; /* Global variable for printing or not */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double fretone; /* Only one call to likelihood */
   m[nrl] += NR_END;  long ipmx; /* Number of contributions */
   m[nrl] -= ncl;  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   return m;  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /*************************free matrix ************************/  FILE *fichtm, *fichtmcov; /* Html File */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE  *ficresvij;
   free((FREE_ARG)(m+nrl-NR_END));  char fileresv[FILENAMELENGTH];
 }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 /******************* ma3x *******************************/  char title[MAXLINE];
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double ***m;  char command[FILENAMELENGTH];
   int  outcmd=0;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   m += NR_END;  
   m -= nrl;  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fileregp[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char popfile[FILENAMELENGTH];
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  extern int gettimeofday();
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   m[nrl][ncl] += NR_END;  long time_value;
   m[nrl][ncl] -= nll;  extern long time();
   for (j=ncl+1; j<=nch; j++)  char strcurr[80], strfor[80];
     m[nrl][j]=m[nrl][j-1]+nlay;  
    #define NR_END 1
   for (i=nrl+1; i<=nrh; i++) {  #define FREE_ARG char*
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define FTOL 1.0e-10
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define NRANSI 
   }  #define ITMAX 200 
   return m;  
 }  #define TOL 2.0e-4 
   
 /*************************free ma3x ************************/  #define CGOLD 0.3819660 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define GOLD 1.618034 
   free((FREE_ARG)(m+nrl-NR_END));  #define GLIMIT 100.0 
 }  #define TINY 1.0e-20 
   
 /***************** f1dim *************************/  static double maxarg1,maxarg2;
 extern int ncom;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 extern double *pcom,*xicom;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 extern double (*nrfunc)(double []);    
    #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double f1dim(double x)  #define rint(a) floor(a+0.5)
 {  
   int j;  static double sqrarg;
   double f;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double *xt;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    int agegomp= AGEGOMP;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int imx; 
   f=(*nrfunc)(xt);  int stepm=1;
   free_vector(xt,1,ncom);  /* Stepm, step in month: minimum step interpolation*/
   return f;  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int m,nb;
 {  long *num;
   int iter;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double a,b,d,etemp;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double fu,fv,fw,fx;  double **pmmij, ***probs;
   double ftemp;  double *ageexmed,*agecens;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double dateintmean=0;
   double e=0.0;  
    double *weight;
   a=(ax < cx ? ax : cx);  int **s; /* Status */
   b=(ax > cx ? ax : cx);  double *agedc, **covar, idx;
   x=w=v=bx;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   fw=fv=fx=(*f)(x);  double *lsurv, *lpop, *tpop;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double ftolhess; /* Tolerance for computing hessian */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /**************** split *************************/
 #ifdef DEBUG  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 #endif       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    */ 
       *xmin=x;    char  *ss;                            /* pointer */
       return fx;    int   l1, l2;                         /* length counters */
     }  
     ftemp=fu;    l1 = strlen(path );                   /* length of path */
     if (fabs(e) > tol1) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       r=(x-w)*(fx-fv);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       q=(x-v)*(fx-fw);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       p=(x-v)*q-(x-w)*r;      strcpy( name, path );               /* we got the fullname name because no directory */
       q=2.0*(q-r);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       if (q > 0.0) p = -p;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       q=fabs(q);      /* get current working directory */
       etemp=e;      /*    extern  char* getcwd ( char *buf , int len);*/
       e=d;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))        return( GLOCK_ERROR_GETCWD );
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      }
       else {      /* got dirc from getcwd*/
         d=p/q;      printf(" DIRC = %s \n",dirc);
         u=x+d;    } else {                              /* strip direcotry from path */
         if (u-a < tol2 || b-u < tol2)      ss++;                               /* after this, the filename */
           d=SIGN(tol1,xm-x);      l2 = strlen( ss );                  /* length of filename */
       }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     } else {      strcpy( name, ss );         /* save file name */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     }      dirc[l1-l2] = 0;                    /* add zero */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      printf(" DIRC2 = %s \n",dirc);
     fu=(*f)(u);    }
     if (fu <= fx) {    /* We add a separator at the end of dirc if not exists */
       if (u >= x) a=x; else b=x;    l1 = strlen( dirc );                  /* length of directory */
       SHFT(v,w,x,u)    if( dirc[l1-1] != DIRSEPARATOR ){
         SHFT(fv,fw,fx,fu)      dirc[l1] =  DIRSEPARATOR;
         } else {      dirc[l1+1] = 0; 
           if (u < x) a=u; else b=u;      printf(" DIRC3 = %s \n",dirc);
           if (fu <= fw || w == x) {    }
             v=w;    ss = strrchr( name, '.' );            /* find last / */
             w=u;    if (ss >0){
             fv=fw;      ss++;
             fw=fu;      strcpy(ext,ss);                     /* save extension */
           } else if (fu <= fv || v == x || v == w) {      l1= strlen( name);
             v=u;      l2= strlen(ss)+1;
             fv=fu;      strncpy( finame, name, l1-l2);
           }      finame[l1-l2]= 0;
         }    }
   }  
   nrerror("Too many iterations in brent");    return( 0 );                          /* we're done */
   *xmin=x;  }
   return fx;  
 }  
   /******************************************/
 /****************** mnbrak ***********************/  
   void replace_back_to_slash(char *s, char*t)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  {
             double (*func)(double))    int i;
 {    int lg=0;
   double ulim,u,r,q, dum;    i=0;
   double fu;    lg=strlen(t);
      for(i=0; i<= lg; i++) {
   *fa=(*func)(*ax);      (s[i] = t[i]);
   *fb=(*func)(*bx);      if (t[i]== '\\') s[i]='/';
   if (*fb > *fa) {    }
     SHFT(dum,*ax,*bx,dum)  }
       SHFT(dum,*fb,*fa,dum)  
       }  int nbocc(char *s, char occ)
   *cx=(*bx)+GOLD*(*bx-*ax);  {
   *fc=(*func)(*cx);    int i,j=0;
   while (*fb > *fc) {    int lg=20;
     r=(*bx-*ax)*(*fb-*fc);    i=0;
     q=(*bx-*cx)*(*fb-*fa);    lg=strlen(s);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    for(i=0; i<= lg; i++) {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    if  (s[i] == occ ) j++;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    }
     if ((*bx-u)*(u-*cx) > 0.0) {    return j;
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  void cutv(char *u,char *v, char*t, char occ)
       if (fu < *fc) {  {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
           SHFT(*fb,*fc,fu,(*func)(u))       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
           }       gives u="abcedf" and v="ghi2j" */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    int i,lg,j,p=0;
       u=ulim;    i=0;
       fu=(*func)(u);    for(j=0; j<=strlen(t)-1; j++) {
     } else {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       u=(*cx)+GOLD*(*cx-*bx);    }
       fu=(*func)(u);  
     }    lg=strlen(t);
     SHFT(*ax,*bx,*cx,u)    for(j=0; j<p; j++) {
       SHFT(*fa,*fb,*fc,fu)      (u[j] = t[j]);
       }    }
 }       u[p]='\0';
   
 /*************** linmin ************************/     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 int ncom;    }
 double *pcom,*xicom;  }
 double (*nrfunc)(double []);  
    /********************** nrerror ********************/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  void nrerror(char error_text[])
   double brent(double ax, double bx, double cx,  {
                double (*f)(double), double tol, double *xmin);    fprintf(stderr,"ERREUR ...\n");
   double f1dim(double x);    fprintf(stderr,"%s\n",error_text);
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    exit(EXIT_FAILURE);
               double *fc, double (*func)(double));  }
   int j;  /*********************** vector *******************/
   double xx,xmin,bx,ax;  double *vector(int nl, int nh)
   double fx,fb,fa;  {
      double *v;
   ncom=n;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   pcom=vector(1,n);    if (!v) nrerror("allocation failure in vector");
   xicom=vector(1,n);    return v-nl+NR_END;
   nrfunc=func;  }
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /************************ free vector ******************/
     xicom[j]=xi[j];  void free_vector(double*v, int nl, int nh)
   }  {
   ax=0.0;    free((FREE_ARG)(v+nl-NR_END));
   xx=1.0;  }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /************************ivector *******************************/
 #ifdef DEBUG  int *ivector(long nl,long nh)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  {
 #endif    int *v;
   for (j=1;j<=n;j++) {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     xi[j] *= xmin;    if (!v) nrerror("allocation failure in ivector");
     p[j] += xi[j];    return v-nl+NR_END;
   }  }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 /*************** powell ************************/    free((FREE_ARG)(v+nl-NR_END));
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  
 {  /************************lvector *******************************/
   void linmin(double p[], double xi[], int n, double *fret,  long *lvector(long nl,long nh)
               double (*func)(double []));  {
   int i,ibig,j;    long *v;
   double del,t,*pt,*ptt,*xit;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double fp,fptt;    if (!v) nrerror("allocation failure in ivector");
   double *xits;    return v-nl+NR_END;
   pt=vector(1,n);  }
   ptt=vector(1,n);  
   xit=vector(1,n);  /******************free lvector **************************/
   xits=vector(1,n);  void free_lvector(long *v, long nl, long nh)
   *fret=(*func)(p);  {
   for (j=1;j<=n;j++) pt[j]=p[j];    free((FREE_ARG)(v+nl-NR_END));
   for (*iter=1;;++(*iter)) {  }
     fp=(*fret);  
     ibig=0;  /******************* imatrix *******************************/
     del=0.0;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for (i=1;i<=n;i++)  { 
       printf(" %d %.12f",i, p[i]);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     printf("\n");    int **m; 
     for (i=1;i<=n;i++) {    
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    /* allocate pointers to rows */ 
       fptt=(*fret);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()"); 
       printf("fret=%lf \n",*fret);    m += NR_END; 
 #endif    m -= nrl; 
       printf("%d",i);fflush(stdout);    
       linmin(p,xit,n,fret,func);    
       if (fabs(fptt-(*fret)) > del) {    /* allocate rows and set pointers to them */ 
         del=fabs(fptt-(*fret));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         ibig=i;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       }    m[nrl] += NR_END; 
 #ifdef DEBUG    m[nrl] -= ncl; 
       printf("%d %.12e",i,(*fret));    
       for (j=1;j<=n;j++) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    
         printf(" x(%d)=%.12e",j,xit[j]);    /* return pointer to array of pointers to rows */ 
       }    return m; 
       for(j=1;j<=n;j++)  } 
         printf(" p=%.12e",p[j]);  
       printf("\n");  /****************** free_imatrix *************************/
 #endif  void free_imatrix(m,nrl,nrh,ncl,nch)
     }        int **m;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        long nch,ncl,nrh,nrl; 
 #ifdef DEBUG       /* free an int matrix allocated by imatrix() */ 
       int k[2],l;  { 
       k[0]=1;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       k[1]=-1;    free((FREE_ARG) (m+nrl-NR_END)); 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /******************* matrix *******************************/
       printf("\n");  double **matrix(long nrl, long nrh, long ncl, long nch)
       for(l=0;l<=1;l++) {  {
         for (j=1;j<=n;j++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double **m;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
 #endif    m -= nrl;
   
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       free_vector(xit,1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       free_vector(xits,1,n);    m[nrl] += NR_END;
       free_vector(ptt,1,n);    m[nrl] -= ncl;
       free_vector(pt,1,n);  
       return;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     for (j=1;j<=n;j++) {     */
       ptt[j]=2.0*p[j]-pt[j];  }
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     fptt=(*func)(ptt);  {
     if (fptt < fp) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    free((FREE_ARG)(m+nrl-NR_END));
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /******************* ma3x *******************************/
           xi[j][ibig]=xi[j][n];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           xi[j][n]=xit[j];  {
         }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 #ifdef DEBUG    double ***m;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           printf(" %.12e",xit[j]);    if (!m) nrerror("allocation failure 1 in matrix()");
         printf("\n");    m += NR_END;
 #endif    m -= nrl;
       }  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /**** Prevalence limit ****************/  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      matrix by transitions matrix until convergence is reached */    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   int i, ii,j,k;    for (j=ncl+1; j<=nch; j++) 
   double min, max, maxmin, maxmax,sumnew=0.;      m[nrl][j]=m[nrl][j-1]+nlay;
   double **matprod2();    
   double **out, cov[NCOVMAX], **pmij();    for (i=nrl+1; i<=nrh; i++) {
   double **newm;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   double agefin, delaymax=50 ; /* Max number of years to converge */      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
   for (ii=1;ii<=nlstate+ndeath;ii++)    }
     for (j=1;j<=nlstate+ndeath;j++){    return m; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    /*  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)
     */
    cov[1]=1.;  }
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*************************free ma3x ************************/
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     newm=savm;  {
     /* Covariates have to be included here again */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
      cov[2]=agefin;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
       for (k=1; k<=cptcovn;k++) {  }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  /*************** function subdirf ***********/
       }  char *subdirf(char fileres[])
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovprod;k++)    strcpy(tmpout,optionfilefiname);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    return tmpout;
   }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   /*************** function subdirf2 ***********/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  char *subdirf2(char fileres[], char *preop)
   {
     savm=oldm;    
     oldm=newm;    /* Caution optionfilefiname is hidden */
     maxmax=0.;    strcpy(tmpout,optionfilefiname);
     for(j=1;j<=nlstate;j++){    strcat(tmpout,"/");
       min=1.;    strcat(tmpout,preop);
       max=0.;    strcat(tmpout,fileres);
       for(i=1; i<=nlstate; i++) {    return tmpout;
         sumnew=0;  }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  /*************** function subdirf3 ***********/
         max=FMAX(max,prlim[i][j]);  char *subdirf3(char fileres[], char *preop, char *preop2)
         min=FMIN(min,prlim[i][j]);  {
       }    
       maxmin=max-min;    /* Caution optionfilefiname is hidden */
       maxmax=FMAX(maxmax,maxmin);    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     if(maxmax < ftolpl){    strcat(tmpout,preop);
       return prlim;    strcat(tmpout,preop2);
     }    strcat(tmpout,fileres);
   }    return tmpout;
 }  }
   
 /*************** transition probabilities **********/  /***************** f1dim *************************/
   extern int ncom; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  extern double *pcom,*xicom;
 {  extern double (*nrfunc)(double []); 
   double s1, s2;   
   /*double t34;*/  double f1dim(double x) 
   int i,j,j1, nc, ii, jj;  { 
     int j; 
     for(i=1; i<= nlstate; i++){    double f;
     for(j=1; j<i;j++){    double *xt; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){   
         /*s2 += param[i][j][nc]*cov[nc];*/    xt=vector(1,ncom); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
       ps[i][j]=s2;    return f; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  } 
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  /*****************brent *************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    int iter; 
       }    double a,b,d,etemp;
       ps[i][j]=s2;    double fu,fv,fw,fx;
     }    double ftemp;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   for(i=1; i<= nlstate; i++){    double e=0.0; 
      s1=0;   
     for(j=1; j<i; j++)    a=(ax < cx ? ax : cx); 
       s1+=exp(ps[i][j]);    b=(ax > cx ? ax : cx); 
     for(j=i+1; j<=nlstate+ndeath; j++)    x=w=v=bx; 
       s1+=exp(ps[i][j]);    fw=fv=fx=(*f)(x); 
     ps[i][i]=1./(s1+1.);    for (iter=1;iter<=ITMAX;iter++) { 
     for(j=1; j<i; j++)      xm=0.5*(a+b); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for(j=i+1; j<=nlstate+ndeath; j++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       ps[i][j]= exp(ps[i][j])*ps[i][i];      printf(".");fflush(stdout);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      fprintf(ficlog,".");fflush(ficlog);
   } /* end i */  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(jj=1; jj<= nlstate+ndeath; jj++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       ps[ii][jj]=0;  #endif
       ps[ii][ii]=1;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     }        *xmin=x; 
   }        return fx; 
       } 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      ftemp=fu;
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (fabs(e) > tol1) { 
      printf("%lf ",ps[ii][jj]);        r=(x-w)*(fx-fv); 
    }        q=(x-v)*(fx-fw); 
     printf("\n ");        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     printf("\n ");printf("%lf ",cov[2]);*/        if (q > 0.0) p = -p; 
 /*        q=fabs(q); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        etemp=e; 
   goto end;*/        e=d; 
     return ps;        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)); 
         else { 
 /**************** Product of 2 matrices ******************/          d=p/q; 
           u=x+d; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          if (u-a < tol2 || b-u < tol2) 
 {            d=SIGN(tol1,xm-x); 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      } else { 
   /* in, b, out are matrice of pointers which should have been initialized        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      before: only the contents of out is modified. The function returns      } 
      a pointer to pointers identical to out */      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   long i, j, k;      fu=(*f)(u); 
   for(i=nrl; i<= nrh; i++)      if (fu <= fx) { 
     for(k=ncolol; k<=ncoloh; k++)        if (u >= x) a=x; else b=x; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        SHFT(v,w,x,u) 
         out[i][k] +=in[i][j]*b[j][k];          SHFT(fv,fw,fx,fu) 
           } else { 
   return out;            if (u < x) a=u; else b=u; 
 }            if (fu <= fw || w == x) { 
               v=w; 
               w=u; 
 /************* Higher Matrix Product ***************/              fv=fw; 
               fw=fu; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            } else if (fu <= fv || v == x || v == w) { 
 {              v=u; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month              fv=fu; 
      duration (i.e. until            } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          } 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    } 
      (typically every 2 years instead of every month which is too big).    nrerror("Too many iterations in brent"); 
      Model is determined by parameters x and covariates have to be    *xmin=x; 
      included manually here.    return fx; 
   } 
      */  
   /****************** mnbrak ***********************/
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double **newm;              double (*func)(double)) 
   { 
   /* Hstepm could be zero and should return the unit matrix */    double ulim,u,r,q, dum;
   for (i=1;i<=nlstate+ndeath;i++)    double fu; 
     for (j=1;j<=nlstate+ndeath;j++){   
       oldm[i][j]=(i==j ? 1.0 : 0.0);    *fa=(*func)(*ax); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    *fb=(*func)(*bx); 
     }    if (*fb > *fa) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      SHFT(dum,*ax,*bx,dum) 
   for(h=1; h <=nhstepm; h++){        SHFT(dum,*fb,*fa,dum) 
     for(d=1; d <=hstepm; d++){        } 
       newm=savm;    *cx=(*bx)+GOLD*(*bx-*ax); 
       /* Covariates have to be included here again */    *fc=(*func)(*cx); 
       cov[1]=1.;    while (*fb > *fc) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      r=(*bx-*ax)*(*fb-*fc); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      q=(*bx-*cx)*(*fb-*fa); 
 for (k=1; k<=cptcovage;k++)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
    for (k=1; k<=cptcovprod;k++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        fu=(*func)(u); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        if (fu < *fc) { 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));            SHFT(*fb,*fc,fu,(*func)(u)) 
       savm=oldm;            } 
       oldm=newm;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     }        u=ulim; 
     for(i=1; i<=nlstate+ndeath; i++)        fu=(*func)(u); 
       for(j=1;j<=nlstate+ndeath;j++) {      } else { 
         po[i][j][h]=newm[i][j];        u=(*cx)+GOLD*(*cx-*bx); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        fu=(*func)(u); 
          */      } 
       }      SHFT(*ax,*bx,*cx,u) 
   } /* end h */        SHFT(*fa,*fb,*fc,fu) 
   return po;        } 
 }  } 
   
   /*************** linmin ************************/
 /*************** log-likelihood *************/  
 double func( double *x)  int ncom; 
 {  double *pcom,*xicom;
   int i, ii, j, k, mi, d, kk;  double (*nrfunc)(double []); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];   
   double **out;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double sw; /* Sum of weights */  { 
   double lli; /* Individual log likelihood */    double brent(double ax, double bx, double cx, 
   long ipmx;                 double (*f)(double), double tol, double *xmin); 
   /*extern weight */    double f1dim(double x); 
   /* We are differentiating ll according to initial status */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/                double *fc, double (*func)(double)); 
   /*for(i=1;i<imx;i++)    int j; 
 printf(" %d\n",s[4][i]);    double xx,xmin,bx,ax; 
   */    double fx,fb,fa;
   cov[1]=1.;   
     ncom=n; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    pcom=vector(1,n); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    xicom=vector(1,n); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    nrfunc=func; 
        for(mi=1; mi<= wav[i]-1; mi++){    for (j=1;j<=n;j++) { 
       for (ii=1;ii<=nlstate+ndeath;ii++)      pcom[j]=p[j]; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      xicom[j]=xi[j]; 
             for(d=0; d<dh[mi][i]; d++){    } 
               newm=savm;    ax=0.0; 
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    xx=1.0; 
               for (kk=1; kk<=cptcovage;kk++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
                  /*printf("%d %d",kk,Tage[kk]);*/  #ifdef DEBUG
               }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               /*cov[3]=pow(cov[2],2)/1000.;*/  #endif
     for (j=1;j<=n;j++) { 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      xi[j] *= xmin; 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      p[j] += xi[j]; 
           savm=oldm;    } 
           oldm=newm;    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   } 
       } /* end mult */  
      char *asc_diff_time(long time_sec, char ascdiff[])
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    long sec_left, days, hours, minutes;
       ipmx +=1;    days = (time_sec) / (60*60*24);
       sw += weight[i];    sec_left = (time_sec) % (60*60*24);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    hours = (sec_left) / (60*60) ;
     } /* end of wave */    sec_left = (sec_left) %(60*60);
   } /* end of individual */    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    return ascdiff;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  }
   return -l;  
 }  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
 /*********** Maximum Likelihood Estimation ***************/  { 
     void linmin(double p[], double xi[], int n, double *fret, 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))                double (*func)(double [])); 
 {    int i,ibig,j; 
   int i,j, iter;    double del,t,*pt,*ptt,*xit;
   double **xi,*delti;    double fp,fptt;
   double fret;    double *xits;
   xi=matrix(1,npar,1,npar);    int niterf, itmp;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)    pt=vector(1,n); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    ptt=vector(1,n); 
   printf("Powell\n");    xit=vector(1,n); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    xits=vector(1,n); 
     *fret=(*func)(p); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    for (j=1;j<=n;j++) pt[j]=p[j]; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 }      ibig=0; 
       del=0.0; 
 /**** Computes Hessian and covariance matrix ***/      last_time=curr_time;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      (void) gettimeofday(&curr_time,&tzp);
 {      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   double  **a,**y,*x,pd;      /*    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);
   double **hess;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   int i, j,jk;      */
   int *indx;     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
   double hessii(double p[], double delta, int theta, double delti[]);        fprintf(ficlog," %d %.12lf",i, p[i]);
   double hessij(double p[], double delti[], int i, int j);        fprintf(ficrespow," %.12lf", p[i]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      }
   void ludcmp(double **a, int npar, int *indx, double *d) ;      printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
   hess=matrix(1,npar,1,npar);      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
   printf("\nCalculation of the hessian matrix. Wait...\n");        strcpy(strcurr,asctime(&tm));
   for (i=1;i<=npar;i++){  /*       asctime_r(&tm,strcurr); */
     printf("%d",i);fflush(stdout);        forecast_time=curr_time; 
     hess[i][i]=hessii(p,ftolhess,i,delti);        itmp = strlen(strcurr);
     /*printf(" %f ",p[i]);*/        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   }          strcurr[itmp-1]='\0';
         printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   for (i=1;i<=npar;i++) {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (j=1;j<=npar;j++)  {        for(niterf=10;niterf<=30;niterf+=10){
       if (j>i) {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         printf(".%d%d",i,j);fflush(stdout);          tmf = *localtime(&forecast_time.tv_sec);
         hess[i][j]=hessij(p,delti,i,j);  /*      asctime_r(&tmf,strfor); */
         hess[j][i]=hess[i][j];          strcpy(strfor,asctime(&tmf));
       }          itmp = strlen(strfor);
     }          if(strfor[itmp-1]=='\n')
   }          strfor[itmp-1]='\0';
   printf("\n");          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("\nInverting the hessian to get the covariance matrix. Wait...\n");        }
        }
   a=matrix(1,npar,1,npar);      for (i=1;i<=n;i++) { 
   y=matrix(1,npar,1,npar);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   x=vector(1,npar);        fptt=(*fret); 
   indx=ivector(1,npar);  #ifdef DEBUG
   for (i=1;i<=npar;i++)        printf("fret=%lf \n",*fret);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fprintf(ficlog,"fret=%lf \n",*fret);
   ludcmp(a,npar,indx,&pd);  #endif
         printf("%d",i);fflush(stdout);
   for (j=1;j<=npar;j++) {        fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=1;i<=npar;i++) x[i]=0;        linmin(p,xit,n,fret,func); 
     x[j]=1;        if (fabs(fptt-(*fret)) > del) { 
     lubksb(a,npar,indx,x);          del=fabs(fptt-(*fret)); 
     for (i=1;i<=npar;i++){          ibig=i; 
       matcov[i][j]=x[i];        } 
     }  #ifdef DEBUG
   }        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   printf("\n#Hessian matrix#\n");        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (j=1;j<=npar;j++) {          printf(" x(%d)=%.12e",j,xit[j]);
       printf("%.3e ",hess[i][j]);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
     printf("\n");        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
   /* Recompute Inverse */        }
   for (i=1;i<=npar;i++)        printf("\n");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        fprintf(ficlog,"\n");
   ludcmp(a,npar,indx,&pd);  #endif
       } 
   /*  printf("\n#Hessian matrix recomputed#\n");      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
   for (j=1;j<=npar;j++) {        int k[2],l;
     for (i=1;i<=npar;i++) x[i]=0;        k[0]=1;
     x[j]=1;        k[1]=-1;
     lubksb(a,npar,indx,x);        printf("Max: %.12e",(*func)(p));
     for (i=1;i<=npar;i++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
       y[i][j]=x[i];        for (j=1;j<=n;j++) {
       printf("%.3e ",y[i][j]);          printf(" %.12e",p[j]);
     }          fprintf(ficlog," %.12e",p[j]);
     printf("\n");        }
   }        printf("\n");
   */        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
   free_matrix(a,1,npar,1,npar);          for (j=1;j<=n;j++) {
   free_matrix(y,1,npar,1,npar);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   free_vector(x,1,npar);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   free_ivector(indx,1,npar);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   free_matrix(hess,1,npar,1,npar);          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 }        }
   #endif
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  
 {        free_vector(xit,1,n); 
   int i;        free_vector(xits,1,n); 
   int l=1, lmax=20;        free_vector(ptt,1,n); 
   double k1,k2;        free_vector(pt,1,n); 
   double p2[NPARMAX+1];        return; 
   double res;      } 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double fx;      for (j=1;j<=n;j++) { 
   int k=0,kmax=10;        ptt[j]=2.0*p[j]-pt[j]; 
   double l1;        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   fx=func(x);      } 
   for (i=1;i<=npar;i++) p2[i]=x[i];      fptt=(*func)(ptt); 
   for(l=0 ; l <=lmax; l++){      if (fptt < fp) { 
     l1=pow(10,l);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     delts=delt;        if (t < 0.0) { 
     for(k=1 ; k <kmax; k=k+1){          linmin(p,xit,n,fret,func); 
       delt = delta*(l1*k);          for (j=1;j<=n;j++) { 
       p2[theta]=x[theta] +delt;            xi[j][ibig]=xi[j][n]; 
       k1=func(p2)-fx;            xi[j][n]=xit[j]; 
       p2[theta]=x[theta]-delt;          }
       k2=func(p2)-fx;  #ifdef DEBUG
       /*res= (k1-2.0*fx+k2)/delt/delt; */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                for(j=1;j<=n;j++){
 #ifdef DEBUG            printf(" %.12e",xit[j]);
       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);            fprintf(ficlog," %.12e",xit[j]);
 #endif          }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          printf("\n");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          fprintf(ficlog,"\n");
         k=kmax;  #endif
       }        }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      } 
         k=kmax; l=lmax*10.;    } 
       }  } 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /**** Prevalence limit (stable prevalence)  ****************/
       }  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
   delti[theta]=delts;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   return res;       matrix by transitions matrix until convergence is reached */
    
 }    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
 double hessij( double x[], double delti[], int thetai,int thetaj)    double **matprod2();
 {    double **out, cov[NCOVMAX], **pmij();
   int i;    double **newm;
   int l=1, l1, lmax=20;    double agefin, delaymax=50 ; /* Max number of years to converge */
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    for (ii=1;ii<=nlstate+ndeath;ii++)
   int k;      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fx=func(x);      }
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];     cov[1]=1.;
     p2[thetai]=x[thetai]+delti[thetai]/k;   
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     k1=func(p2)-fx;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
        newm=savm;
     p2[thetai]=x[thetai]+delti[thetai]/k;      /* Covariates have to be included here again */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       cov[2]=agefin;
     k2=func(p2)-fx;    
          for (k=1; k<=cptcovn;k++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     k3=func(p2)-fx;        }
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for (k=1; k<=cptcovprod;k++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 #ifdef DEBUG        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     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);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 #endif      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
   return res;      savm=oldm;
 }      oldm=newm;
       maxmax=0.;
 /************** Inverse of matrix **************/      for(j=1;j<=nlstate;j++){
 void ludcmp(double **a, int n, int *indx, double *d)        min=1.;
 {        max=0.;
   int i,imax,j,k;        for(i=1; i<=nlstate; i++) {
   double big,dum,sum,temp;          sumnew=0;
   double *vv;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            prlim[i][j]= newm[i][j]/(1-sumnew);
   vv=vector(1,n);          max=FMAX(max,prlim[i][j]);
   *d=1.0;          min=FMIN(min,prlim[i][j]);
   for (i=1;i<=n;i++) {        }
     big=0.0;        maxmin=max-min;
     for (j=1;j<=n;j++)        maxmax=FMAX(maxmax,maxmin);
       if ((temp=fabs(a[i][j])) > big) big=temp;      }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      if(maxmax < ftolpl){
     vv[i]=1.0/big;        return prlim;
   }      }
   for (j=1;j<=n;j++) {    }
     for (i=1;i<j;i++) {  }
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*************** transition probabilities ***************/ 
       a[i][j]=sum;  
     }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     big=0.0;  {
     for (i=j;i<=n;i++) {    double s1, s2;
       sum=a[i][j];    /*double t34;*/
       for (k=1;k<j;k++)    int i,j,j1, nc, ii, jj;
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;      for(i=1; i<= nlstate; i++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for(j=1; j<i;j++){
         big=dum;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         imax=i;            /*s2 += param[i][j][nc]*cov[nc];*/
       }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     if (j != imax) {          }
       for (k=1;k<=n;k++) {          ps[i][j]=s2;
         dum=a[imax][k];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;        for(j=i+1; j<=nlstate+ndeath;j++){
       }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       *d = -(*d);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       vv[imax]=vv[j];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     }          }
     indx[j]=imax;          ps[i][j]=s2;
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {      }
       dum=1.0/(a[j][j]);      /*ps[3][2]=1;*/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      
     }      for(i=1; i<= nlstate; i++){
   }        s1=0;
   free_vector(vv,1,n);  /* Doesn't work */        for(j=1; j<i; j++)
 ;          s1+=exp(ps[i][j]);
 }        for(j=i+1; j<=nlstate+ndeath; j++)
           s1+=exp(ps[i][j]);
 void lubksb(double **a, int n, int *indx, double b[])        ps[i][i]=1./(s1+1.);
 {        for(j=1; j<i; j++)
   int i,ii=0,ip,j;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   double sum;        for(j=i+1; j<=nlstate+ndeath; j++)
            ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (i=1;i<=n;i++) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     ip=indx[i];      } /* end i */
     sum=b[ip];      
     b[ip]=b[i];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     if (ii)        for(jj=1; jj<= nlstate+ndeath; jj++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          ps[ii][jj]=0;
     else if (sum) ii=i;          ps[ii][ii]=1;
     b[i]=sum;        }
   }      }
   for (i=n;i>=1;i--) {      
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     b[i]=sum/a[i][i];  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   }  /*         printf("ddd %lf ",ps[ii][jj]); */
 }  /*       } */
   /*       printf("\n "); */
 /************ Frequencies ********************/  /*        } */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  /*        printf("\n ");printf("%lf ",cov[2]); */
 {  /* Some frequencies */         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        goto end;*/
   double ***freq; /* Frequencies */      return ps;
   double *pp;  }
   double pos;  
   FILE *ficresp;  /**************** Product of 2 matrices ******************/
   char fileresp[FILENAMELENGTH];  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   pp=vector(1,nlstate);  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   strcpy(fileresp,"p");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   strcat(fileresp,fileres);    /* in, b, out are matrice of pointers which should have been initialized 
   if((ficresp=fopen(fileresp,"w"))==NULL) {       before: only the contents of out is modified. The function returns
     printf("Problem with prevalence resultfile: %s\n", fileresp);       a pointer to pointers identical to out */
     exit(0);    long i, j, k;
   }    for(i=nrl; i<= nrh; i++)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for(k=ncolol; k<=ncoloh; k++)
   j1=0;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    return out;
   }
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;  /************* Higher Matrix Product ***************/
   
         for (i=-1; i<=nlstate+ndeath; i++)    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
          for (jk=-1; jk<=nlstate+ndeath; jk++)    {
            for(m=agemin; m <= agemax+3; m++)    /* Computes the transition matrix starting at age 'age' over 
              freq[i][jk][m]=0;       'nhstepm*hstepm*stepm' months (i.e. until
               age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        for (i=1; i<=imx; i++) {       nhstepm*hstepm matrices. 
          bool=1;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
          if  (cptcovn>0) {       (typically every 2 years instead of every month which is too big 
            for (z1=1; z1<=cptcoveff; z1++)       for the memory).
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;       Model is determined by parameters x and covariates have to be 
          }       included manually here. 
           if (bool==1) {  
            for(m=firstpass; m<=lastpass-1; m++){       */
              if(agev[m][i]==0) agev[m][i]=agemax+1;  
              if(agev[m][i]==1) agev[m][i]=agemax+2;    int i, j, d, h, k;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double **out, cov[NCOVMAX];
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double **newm;
            }  
          }    /* Hstepm could be zero and should return the unit matrix */
        }    for (i=1;i<=nlstate+ndeath;i++)
         if  (cptcovn>0) {      for (j=1;j<=nlstate+ndeath;j++){
          fprintf(ficresp, "\n#********** Variable ");        oldm[i][j]=(i==j ? 1.0 : 0.0);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        po[i][j][0]=(i==j ? 1.0 : 0.0);
        }      }
        fprintf(ficresp, "**********\n#");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        for(i=1; i<=nlstate;i++)    for(h=1; h <=nhstepm; h++){
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for(d=1; d <=hstepm; d++){
        fprintf(ficresp, "\n");        newm=savm;
                /* Covariates have to be included here again */
   for(i=(int)agemin; i <= (int)agemax+3; i++){        cov[1]=1.;
     if(i==(int)agemax+3)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       printf("Total");        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     else        for (k=1; k<=cptcovage;k++)
       printf("Age %d", i);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovprod;k++)
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         pp[jk] += freq[jk][m][i];  
     }  
     for(jk=1; jk <=nlstate ; jk++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for(m=-1, pos=0; m <=0 ; m++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         pos += freq[jk][m][i];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       if(pp[jk]>=1.e-10)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        savm=oldm;
       else        oldm=newm;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      }
     }      for(i=1; i<=nlstate+ndeath; i++)
     for(jk=1; jk <=nlstate ; jk++){        for(j=1;j<=nlstate+ndeath;j++) {
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)          po[i][j][h]=newm[i][j];
         pp[jk] += freq[jk][m][i];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     }           */
     for(jk=1,pos=0; jk <=nlstate ; jk++)        }
       pos += pp[jk];    } /* end h */
     for(jk=1; jk <=nlstate ; jk++){    return po;
       if(pos>=1.e-5)  }
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
       else  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*************** log-likelihood *************/
       if( i <= (int) agemax){  double func( double *x)
         if(pos>=1.e-5)  {
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    int i, ii, j, k, mi, d, kk;
       else    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    double **out;
       }    double sw; /* Sum of weights */
     }    double lli; /* Individual log likelihood */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    int s1, s2;
       for(m=-1; m <=nlstate+ndeath; m++)    double bbh, survp;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    long ipmx;
     if(i <= (int) agemax)    /*extern weight */
       fprintf(ficresp,"\n");    /* We are differentiating ll according to initial status */
     printf("\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
     }      printf(" %d\n",s[4][i]);
  }    */
      cov[1]=1.;
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   free_vector(pp,1,nlstate);  
     if(mle==1){
 }  /* End of Freq */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************* Waves Concatenation ***************/        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            for (j=1;j<=nlstate+ndeath;j++){
 {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      Death is a valid wave (if date is known).            }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          for(d=0; d<dh[mi][i]; d++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            newm=savm;
      and mw[mi+1][i]. dh depends on stepm.            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, mi, m;            }
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 float sum=0.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for(i=1; i<=imx; i++){            oldm=newm;
     mi=0;          } /* end mult */
     m=firstpass;        
     while(s[m][i] <= nlstate){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       if(s[m][i]>=1)          /* But now since version 0.9 we anticipate for bias at large stepm.
         mw[++mi][i]=m;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       if(m >=lastpass)           * (in months) between two waves is not a multiple of stepm, we rounded to 
         break;           * the nearest (and in case of equal distance, to the lowest) interval but now
       else           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         m++;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     }/* end while */           * probability in order to take into account the bias as a fraction of the way
     if (s[m][i] > nlstate){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       mi++;     /* Death is another wave */           * -stepm/2 to stepm/2 .
       /* if(mi==0)  never been interviewed correctly before death */           * For stepm=1 the results are the same as for previous versions of Imach.
          /* Only death is a correct wave */           * For stepm > 1 the results are less biased than in previous versions. 
       mw[mi][i]=m;           */
     }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     wav[i]=mi;          bbh=(double)bh[mi][i]/(double)stepm; 
     if(mi==0)          /* bias bh is positive if real duration
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);           * is higher than the multiple of stepm and negative otherwise.
   }           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for(i=1; i<=imx; i++){          if( s2 > nlstate){ 
     for(mi=1; mi<wav[i];mi++){            /* i.e. if s2 is a death state and if the date of death is known 
       if (stepm <=0)               then the contribution to the likelihood is the probability to 
         dh[mi][i]=1;               die between last step unit time and current  step unit time, 
       else{               which is also equal to probability to die before dh 
         if (s[mw[mi+1][i]][i] > nlstate) {               minus probability to die before dh-stepm . 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               In version up to 0.92 likelihood was computed
           if(j=0) j=1;  /* Survives at least one month after exam */          as if date of death was unknown. Death was treated as any other
         }          health state: the date of the interview describes the actual state
         else{          and not the date of a change in health state. The former idea was
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          to consider that at each interview the state was recorded
           k=k+1;          (healthy, disable or death) and IMaCh was corrected; but when we
           if (j >= jmax) jmax=j;          introduced the exact date of death then we should have modified
           else if (j <= jmin)jmin=j;          the contribution of an exact death to the likelihood. This new
           sum=sum+j;          contribution is smaller and very dependent of the step unit
         }          stepm. It is no more the probability to die between last interview
         jk= j/stepm;          and month of death but the probability to survive from last
         jl= j -jk*stepm;          interview up to one month before death multiplied by the
         ju= j -(jk+1)*stepm;          probability to die within a month. Thanks to Chris
         if(jl <= -ju)          Jackson for correcting this bug.  Former versions increased
           dh[mi][i]=jk;          mortality artificially. The bad side is that we add another loop
         else          which slows down the processing. The difference can be up to 10%
           dh[mi][i]=jk+1;          lower mortality.
         if(dh[mi][i]==0)            */
           dh[mi][i]=1; /* At least one step */            lli=log(out[s1][s2] - savm[s1][s2]);
       }  
     }  
   }          } else if  (s2==-2) {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);            for (j=1,survp=0. ; j<=nlstate; j++) 
 }              survp += out[s1][j];
 /*********** Tricode ****************************/            lli= survp;
 void tricode(int *Tvar, int **nbcode, int imx)          }
 {          
   int Ndum[20],ij=1, k, j, i;          else if  (s2==-4) {
   int cptcode=0;            for (j=3,survp=0. ; j<=nlstate; j++) 
   cptcoveff=0;              survp += out[s1][j];
              lli= survp;
   for (k=0; k<19; k++) Ndum[k]=0;          }
   for (k=1; k<=7; k++) ncodemax[k]=0;          
           else if  (s2==-5) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for (j=1,survp=0. ; j<=2; j++) 
     for (i=1; i<=imx; i++) {              survp += out[s1][j];
       ij=(int)(covar[Tvar[j]][i]);            lli= survp;
       Ndum[ij]++;          }
       if (ij > cptcode) cptcode=ij;  
     }  
           else{
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for (i=0; i<=cptcode; i++) {            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       if(Ndum[i]!=0) ncodemax[j]++;          } 
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     ij=1;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     for (i=1; i<=ncodemax[j]; i++) {          ipmx +=1;
       for (k=0; k<=19; k++) {          sw += weight[i];
         if (Ndum[k] != 0) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           nbcode[Tvar[j]][ij]=k;        } /* end of wave */
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/      } /* end of individual */
           ij++;    }  else if(mle==2){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if (ij > ncodemax[j]) break;        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++){
  for (i=1; i<=10; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=Tvar[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       Ndum[ij]++;            }
     }          for(d=0; d<=dh[mi][i]; d++){
  ij=1;            newm=savm;
  for (i=1; i<=cptcovn; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    if((Ndum[i]!=0) && (i<=ncov)){            for (kk=1; kk<=cptcovage;kk++) {
      Tvaraff[i]=ij;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    ij++;            }
    }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            oldm=newm;
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];          } /* end mult */
    /*printf("j=%d %d\n",j,Tvar[j]);*/        
  }          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);          bbh=(double)bh[mi][i]/(double)stepm; 
     scanf("%d",i);*/          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 }          ipmx +=1;
           sw += weight[i];
 /*********** Health Expectancies ****************/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      } /* end of individual */
 {    }  else if(mle==3){  /* exponential inter-extrapolation */
   /* Health expectancies */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j, nhstepm, hstepm, h;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double age, agelim,hf;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***p3mat;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficreseij,"# Health expectancies\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"# Age");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=nlstate;j++)          for(d=0; d<dh[mi][i]; d++){
       fprintf(ficreseij," %1d-%1d",i,j);            newm=savm;
   fprintf(ficreseij,"\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   hstepm=1*YEARM; /*  Every j years of age (in month) */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   agelim=AGESUP;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            savm=oldm;
     /* nhstepm age range expressed in number of stepm */            oldm=newm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          } /* end mult */
     /* Typically if 20 years = 20*12/6=40 stepm */        
     if (stepm >= YEARM) hstepm=1;          s1=s[mw[mi][i]][i];
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          s2=s[mw[mi+1][i]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          bbh=(double)bh[mi][i]/(double)stepm; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          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 */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          ipmx +=1;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     for(i=1; i<=nlstate;i++)      } /* end of individual */
       for(j=1; j<=nlstate;j++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           eij[i][j][(int)age] +=p3mat[i][j][h];        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++)
     hf=1;            for (j=1;j<=nlstate+ndeath;j++){
     if (stepm >= YEARM) hf=stepm/YEARM;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficreseij,"%.0f",age );              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          for(d=0; d<dh[mi][i]; d++){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficreseij,"\n");            for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************ Variance ******************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 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)            savm=oldm;
 {            oldm=newm;
   /* Variance of health expectancies */          } /* end mult */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        
   double **newm;          s1=s[mw[mi][i]][i];
   double **dnewm,**doldm;          s2=s[mw[mi+1][i]][i];
   int i, j, nhstepm, hstepm, h;          if( s2 > nlstate){ 
   int k, cptcode;            lli=log(out[s1][s2] - savm[s1][s2]);
    double *xp;          }else{
   double **gp, **gm;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double ***gradg, ***trgradg;          }
   double ***p3mat;          ipmx +=1;
   double age,agelim;          sw += weight[i];
   int theta;          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]); */
    fprintf(ficresvij,"# Covariances of life expectancies\n");        } /* end of wave */
   fprintf(ficresvij,"# Age");      } /* end of individual */
   for(i=1; i<=nlstate;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(j=1; j<=nlstate;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficresvij,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   xp=vector(1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   dnewm=matrix(1,nlstate,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   doldm=matrix(1,nlstate,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   hstepm=1*YEARM; /* Every year of age */          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;
   agelim = AGESUP;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for (kk=1; kk<=cptcovage;kk++) {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (stepm >= YEARM) hstepm=1;            }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gp=matrix(0,nhstepm,1,nlstate);            savm=oldm;
     gm=matrix(0,nhstepm,1,nlstate);            oldm=newm;
           } /* end mult */
     for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++){ /* Computes gradient */          s1=s[mw[mi][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s2=s[mw[mi+1][i]][i];
       }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ipmx +=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          sw += weight[i];
       for(j=1; j<= nlstate; j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(h=0; h<=nhstepm; h++){          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        } /* end of wave */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      } /* end of individual */
         }    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(i=1; i<=npar; i++) /* Computes gradient */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return -l;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(j=1; j<= nlstate; j++){  /*************** log-likelihood *************/
         for(h=0; h<=nhstepm; h++){  double funcone( double *x)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  {
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    /* Same as likeli but slower because of a lot of printf and if */
         }    int i, ii, j, k, mi, d, kk;
       }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       for(j=1; j<= nlstate; j++)    double **out;
         for(h=0; h<=nhstepm; h++){    double lli; /* Individual log likelihood */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double llt;
         }    int s1, s2;
     } /* End theta */    double bbh, survp;
     /*extern weight */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(h=0; h<=nhstepm; h++)    /*for(i=1;i<imx;i++) 
       for(j=1; j<=nlstate;j++)      printf(" %d\n",s[4][i]);
         for(theta=1; theta <=npar; theta++)    */
           trgradg[h][j][theta]=gradg[h][theta][j];    cov[1]=1.;
   
     for(i=1;i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(h=0;h<=nhstepm;h++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(k=0;k<=nhstepm;k++){      for(mi=1; mi<= wav[i]-1; mi++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        for (ii=1;ii<=nlstate+ndeath;ii++)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          for (j=1;j<=nlstate+ndeath;j++){
         for(i=1;i<=nlstate;i++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(j=1;j<=nlstate;j++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
             vareij[i][j][(int)age] += doldm[i][j];          }
       }        for(d=0; d<dh[mi][i]; d++){
     }          newm=savm;
     h=1;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (stepm >= YEARM) h=stepm/YEARM;          for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficresvij,"%.0f ",age );            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }          savm=oldm;
     fprintf(ficresvij,"\n");          oldm=newm;
     free_matrix(gp,0,nhstepm,1,nlstate);        } /* end mult */
     free_matrix(gm,0,nhstepm,1,nlstate);        
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        s1=s[mw[mi][i]][i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        s2=s[mw[mi+1][i]][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        bbh=(double)bh[mi][i]/(double)stepm; 
   } /* End age */        /* bias is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
   free_vector(xp,1,npar);         */
   free_matrix(doldm,1,nlstate,1,npar);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   free_matrix(dnewm,1,nlstate,1,nlstate);          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 */
         } else if(mle==2){
 /************ Variance of prevlim ******************/          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 */
 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)        } else if(mle==3){  /* exponential inter-extrapolation */
 {          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   /* Variance of prevalence limit */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          lli=log(out[s1][s2]); /* Original formula */
   double **newm;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   double **dnewm,**doldm;          lli=log(out[s1][s2]); /* Original formula */
   int i, j, nhstepm, hstepm;        } /* End of if */
   int k, cptcode;        ipmx +=1;
   double *xp;        sw += weight[i];
   double *gp, *gm;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **gradg, **trgradg;  /*       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]); */
   double age,agelim;        if(globpr){
   int theta;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       %10.6f %10.6f %10.6f ", \
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   fprintf(ficresvpl,"# Age");                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   for(i=1; i<=nlstate;i++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       fprintf(ficresvpl," %1d-%1d",i,i);            llt +=ll[k]*gipmx/gsw;
   fprintf(ficresvpl,"\n");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
   xp=vector(1,npar);          fprintf(ficresilk," %10.6f\n", -llt);
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);      } /* end of wave */
      } /* end of individual */
   hstepm=1*YEARM; /* Every year of age */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   agelim = AGESUP;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    if(globpr==0){ /* First time we count the contributions and weights */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      gipmx=ipmx;
     if (stepm >= YEARM) hstepm=1;      gsw=sw;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     gradg=matrix(1,npar,1,nlstate);    return -l;
     gp=vector(1,nlstate);  }
     gm=vector(1,nlstate);  
   
     for(theta=1; theta <=npar; theta++){  /*************** function likelione ***********/
       for(i=1; i<=npar; i++){ /* Computes gradient */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    /* This routine should help understanding what is done with 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       the selection of individuals/waves and
       for(i=1;i<=nlstate;i++)       to check the exact contribution to the likelihood.
         gp[i] = prlim[i][i];       Plotting could be done.
         */
       for(i=1; i<=npar; i++) /* Computes gradient */    int k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if(*globpri !=0){ /* Just counts and sums, no printings */
       for(i=1;i<=nlstate;i++)      strcpy(fileresilk,"ilk"); 
         gm[i] = prlim[i][i];      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(i=1;i<=nlstate;i++)        printf("Problem with resultfile: %s\n", fileresilk);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     } /* End theta */      }
       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");
     trgradg =matrix(1,nlstate,1,npar);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(j=1; j<=nlstate;j++)      for(k=1; k<=nlstate; k++) 
       for(theta=1; theta <=npar; theta++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         trgradg[j][theta]=gradg[theta][j];      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;    *fretone=(*funcone)(p);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    if(*globpri !=0){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      fclose(ficresilk);
     for(i=1;i<=nlstate;i++)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      fflush(fichtm); 
     } 
     fprintf(ficresvpl,"%.0f ",age );    return;
     for(i=1; i<=nlstate;i++)  }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);  /*********** Maximum Likelihood Estimation ***************/
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     free_matrix(trgradg,1,nlstate,1,npar);  {
   } /* End age */    int i,j, iter;
     double **xi;
   free_vector(xp,1,npar);    double fret;
   free_matrix(doldm,1,nlstate,1,npar);    double fretone; /* Only one call to likelihood */
   free_matrix(dnewm,1,nlstate,1,nlstate);    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
 }    for (i=1;i<=npar;i++)
       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"); 
 /**************** Main Program *****************/    strcat(filerespow,fileres);
 /***********************************************/    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
 /*int main(int argc, char *argv[])*/      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 int main()    }
 {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;      for(j=1;j<=nlstate+ndeath;j++)
   double agedeb, agefin,hf;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double agemin=1.e20, agemax=-1.e20;    fprintf(ficrespow,"\n");
   
   double fret;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double **xi,tmp,delta;  
     fclose(ficrespow);
   double dum; /* Dummy variable */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double ***p3mat;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int *indx;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];  }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];  /**** Computes Hessian and covariance matrix ***/
   char filerest[FILENAMELENGTH];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   char fileregp[FILENAMELENGTH];  {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    double  **a,**y,*x,pd;
   int firstobs=1, lastobs=10;    double **hess;
   int sdeb, sfin; /* Status at beginning and end */    int i, j,jk;
   int c,  h , cpt,l;    int *indx;
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      void lubksb(double **a, int npar, int *indx, double b[]) ;
   int hstepm, nhstepm;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double bage, fage, age, agelim, agebase;    double gompertz(double p[]);
   double ftolpl=FTOL;    hess=matrix(1,npar,1,npar);
   double **prlim;  
   double *severity;    printf("\nCalculation of the hessian matrix. Wait...\n");
   double ***param; /* Matrix of parameters */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double  *p;    for (i=1;i<=npar;i++){
   double **matcov; /* Matrix of covariance */      printf("%d",i);fflush(stdout);
   double ***delti3; /* Scale */      fprintf(ficlog,"%d",i);fflush(ficlog);
   double *delti; /* Scale */     
   double ***eij, ***vareij;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   double **varpl; /* Variances of prevalence limits by age */      
   double *epj, vepp;      /*  printf(" %f ",p[i]);
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   char *alph[]={"a","a","b","c","d","e"}, str[4];    }
     
   char z[1]="c", occ;    for (i=1;i<=npar;i++) {
 #include <sys/time.h>      for (j=1;j<=npar;j++)  {
 #include <time.h>        if (j>i) { 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          printf(".%d%d",i,j);fflush(stdout);
   /* long total_usecs;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   struct timeval start_time, end_time;          hess[i][j]=hessij(p,delti,i,j,func,npar);
            
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
         }
   printf("\nIMACH, Version 0.64a");      }
   printf("\nEnter the parameter file name: ");    }
     printf("\n");
 #ifdef windows    fprintf(ficlog,"\n");
   scanf("%s",pathtot);  
   getcwd(pathcd, size);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    
   /* cutv(path,optionfile,pathtot,'\\');*/    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
 split(pathtot, path,optionfile);    x=vector(1,npar);
   chdir(path);    indx=ivector(1,npar);
   replace(pathc,path);    for (i=1;i<=npar;i++)
 #endif      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 #ifdef unix    ludcmp(a,npar,indx,&pd);
   scanf("%s",optionfile);  
 #endif    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
 /*-------- arguments in the command line --------*/      x[j]=1;
       lubksb(a,npar,indx,x);
   strcpy(fileres,"r");      for (i=1;i<=npar;i++){ 
   strcat(fileres, optionfile);        matcov[i][j]=x[i];
       }
   /*---------arguments file --------*/    }
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    printf("\n#Hessian matrix#\n");
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficlog,"\n#Hessian matrix#\n");
     goto end;    for (i=1;i<=npar;i++) { 
   }      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
   strcpy(filereso,"o");        fprintf(ficlog,"%.3e ",hess[i][j]);
   strcat(filereso,fileres);      }
   if((ficparo=fopen(filereso,"w"))==NULL) {      printf("\n");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(ficlog,"\n");
   }    }
   
   /* Reads comments: lines beginning with '#' */    /* Recompute Inverse */
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=npar;i++)
     ungetc(c,ficpar);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fgets(line, MAXLINE, ficpar);    ludcmp(a,npar,indx,&pd);
     puts(line);  
     fputs(line,ficparo);    /*  printf("\n#Hessian matrix recomputed#\n");
   }  
   ungetc(c,ficpar);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      x[j]=1;
   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);      lubksb(a,npar,indx,x);
   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);      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
   covar=matrix(0,NCOVMAX,1,n);            printf("%.3e ",y[i][j]);
   if (strlen(model)<=1) cptcovn=0;        fprintf(ficlog,"%.3e ",y[i][j]);
   else {      }
     j=0;      printf("\n");
     j=nbocc(model,'+');      fprintf(ficlog,"\n");
     cptcovn=j+1;    }
   }    */
   
   ncovmodel=2+cptcovn;    free_matrix(a,1,npar,1,npar);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    free_matrix(y,1,npar,1,npar);
      free_vector(x,1,npar);
   /* Read guess parameters */    free_ivector(indx,1,npar);
   /* Reads comments: lines beginning with '#' */    free_matrix(hess,1,npar,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /*************** hessian matrix ****************/
   }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   ungetc(c,ficpar);  {
      int i;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    int l=1, lmax=20;
     for(i=1; i <=nlstate; i++)    double k1,k2;
     for(j=1; j <=nlstate+ndeath-1; j++){    double p2[NPARMAX+1];
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double res;
       fprintf(ficparo,"%1d%1d",i1,j1);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       printf("%1d%1d",i,j);    double fx;
       for(k=1; k<=ncovmodel;k++){    int k=0,kmax=10;
         fscanf(ficpar," %lf",&param[i][j][k]);    double l1;
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
       fscanf(ficpar,"\n");    for(l=0 ; l <=lmax; l++){
       printf("\n");      l1=pow(10,l);
       fprintf(ficparo,"\n");      delts=delt;
     }      for(k=1 ; k <kmax; k=k+1){
          delt = delta*(l1*k);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        p2[theta]=x[theta] +delt;
   p=param[1][1];        k1=func(p2)-fx;
          p2[theta]=x[theta]-delt;
   /* Reads comments: lines beginning with '#' */        k2=func(p2)-fx;
   while((c=getc(ficpar))=='#' && c!= EOF){        /*res= (k1-2.0*fx+k2)/delt/delt; */
     ungetc(c,ficpar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     fgets(line, MAXLINE, ficpar);        
     puts(line);  #ifdef DEBUG
     fputs(line,ficparo);        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);
   }        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);
   ungetc(c,ficpar);  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          k=kmax;
   for(i=1; i <=nlstate; i++){        }
     for(j=1; j <=nlstate+ndeath-1; j++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       fscanf(ficpar,"%1d%1d",&i1,&j1);          k=kmax; l=lmax*10.;
       printf("%1d%1d",i,j);        }
       fprintf(ficparo,"%1d%1d",i1,j1);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(k=1; k<=ncovmodel;k++){          delts=delt;
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);      }
         fprintf(ficparo," %le",delti3[i][j][k]);    }
       }    delti[theta]=delts;
       fscanf(ficpar,"\n");    return res; 
       printf("\n");    
       fprintf(ficparo,"\n");  }
     }  
   }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   delti=delti3[1][1];  {
      int i;
   /* Reads comments: lines beginning with '#' */    int l=1, l1, lmax=20;
   while((c=getc(ficpar))=='#' && c!= EOF){    double k1,k2,k3,k4,res,fx;
     ungetc(c,ficpar);    double p2[NPARMAX+1];
     fgets(line, MAXLINE, ficpar);    int k;
     puts(line);  
     fputs(line,ficparo);    fx=func(x);
   }    for (k=1; k<=2; k++) {
   ungetc(c,ficpar);      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
   matcov=matrix(1,npar,1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for(i=1; i <=npar; i++){      k1=func(p2)-fx;
     fscanf(ficpar,"%s",&str);    
     printf("%s",str);      p2[thetai]=x[thetai]+delti[thetai]/k;
     fprintf(ficparo,"%s",str);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(j=1; j <=i; j++){      k2=func(p2)-fx;
       fscanf(ficpar," %le",&matcov[i][j]);    
       printf(" %.5le",matcov[i][j]);      p2[thetai]=x[thetai]-delti[thetai]/k;
       fprintf(ficparo," %.5le",matcov[i][j]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }      k3=func(p2)-fx;
     fscanf(ficpar,"\n");    
     printf("\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
     fprintf(ficparo,"\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k4=func(p2)-fx;
   for(i=1; i <=npar; i++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     for(j=i+1;j<=npar;j++)  #ifdef DEBUG
       matcov[i][j]=matcov[j][i];      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);
          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);
   printf("\n");  #endif
     }
     return res;
     /*-------- data file ----------*/  }
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;  /************** Inverse of matrix **************/
     }  void ludcmp(double **a, int n, int *indx, double *d) 
     fprintf(ficres,"#%s\n",version);  { 
        int i,imax,j,k; 
     if((fic=fopen(datafile,"r"))==NULL)    {    double big,dum,sum,temp; 
       printf("Problem with datafile: %s\n", datafile);goto end;    double *vv; 
     }   
     vv=vector(1,n); 
     n= lastobs;    *d=1.0; 
     severity = vector(1,maxwav);    for (i=1;i<=n;i++) { 
     outcome=imatrix(1,maxwav+1,1,n);      big=0.0; 
     num=ivector(1,n);      for (j=1;j<=n;j++) 
     moisnais=vector(1,n);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     annais=vector(1,n);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     moisdc=vector(1,n);      vv[i]=1.0/big; 
     andc=vector(1,n);    } 
     agedc=vector(1,n);    for (j=1;j<=n;j++) { 
     cod=ivector(1,n);      for (i=1;i<j;i++) { 
     weight=vector(1,n);        sum=a[i][j]; 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     mint=matrix(1,maxwav,1,n);        a[i][j]=sum; 
     anint=matrix(1,maxwav,1,n);      } 
     s=imatrix(1,maxwav+1,1,n);      big=0.0; 
     adl=imatrix(1,maxwav+1,1,n);          for (i=j;i<=n;i++) { 
     tab=ivector(1,NCOVMAX);        sum=a[i][j]; 
     ncodemax=ivector(1,8);        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
     i=1;        a[i][j]=sum; 
     while (fgets(line, MAXLINE, fic) != NULL)    {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       if ((i >= firstobs) && (i <=lastobs)) {          big=dum; 
                  imax=i; 
         for (j=maxwav;j>=1;j--){        } 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      } 
           strcpy(line,stra);      if (j != imax) { 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (k=1;k<=n;k++) { 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          dum=a[imax][k]; 
         }          a[imax][k]=a[j][k]; 
                  a[j][k]=dum; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        *d = -(*d); 
         vv[imax]=vv[j]; 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      if (j != n) { 
         for (j=ncov;j>=1;j--){        dum=1.0/(a[j][j]); 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         }      } 
         num[i]=atol(stra);    } 
     free_vector(vv,1,n);  /* Doesn't work */
         /*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]));*/  ;
   } 
         i=i+1;  
       }  void lubksb(double **a, int n, int *indx, double b[]) 
     }  { 
     int i,ii=0,ip,j; 
     /*scanf("%d",i);*/    double sum; 
   imx=i-1; /* Number of individuals */   
     for (i=1;i<=n;i++) { 
   /* Calculation of the number of parameter from char model*/      ip=indx[i]; 
   Tvar=ivector(1,15);      sum=b[ip]; 
   Tprod=ivector(1,15);      b[ip]=b[i]; 
   Tvaraff=ivector(1,15);      if (ii) 
   Tvard=imatrix(1,15,1,2);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   Tage=ivector(1,15);            else if (sum) ii=i; 
          b[i]=sum; 
   if (strlen(model) >1){    } 
     j=0, j1=0, k1=1, k2=1;    for (i=n;i>=1;i--) { 
     j=nbocc(model,'+');      sum=b[i]; 
     j1=nbocc(model,'*');      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     cptcovn=j+1;      b[i]=sum/a[i][i]; 
     cptcovprod=j1;    } 
      } 
     strcpy(modelsav,model);  
    if (j==0) {  /************ Frequencies ********************/
       if (j1==0){  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[])
         cutv(stra,strb,modelsav,'V');  {  /* Some frequencies */
         Tvar[1]=atoi(strb);    
       }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       else if (j1==1) {    int first;
         cutv(stra,strb,modelsav,'*');    double ***freq; /* Frequencies */
         Tage[1]=1; cptcovage++;    double *pp, **prop;
         if (strcmp(stra,"age")==0) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           cptcovprod--;    FILE *ficresp;
           cutv(strd,strc,strb,'V');    char fileresp[FILENAMELENGTH];
           Tvar[1]=atoi(strc);    
         }    pp=vector(1,nlstate);
         else if (strcmp(strb,"age")==0) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
           cptcovprod--;    strcpy(fileresp,"p");
           cutv(strd,strc,stra,'V');    strcat(fileresp,fileres);
           Tvar[1]=atoi(strc);    if((ficresp=fopen(fileresp,"w"))==NULL) {
         }      printf("Problem with prevalence resultfile: %s\n", fileresp);
         else {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           cutv(strd,strc,strb,'V');      exit(0);
           cutv(stre,strd,stra,'V');    }
           Tvar[1]=ncov+1;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           for (k=1; k<=lastobs;k++)    j1=0;
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];    
         }    j=cptcoveff;
         /*printf("%s %s %s\n", stra,strb,modelsav);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 printf("%d ",Tvar[1]);  
 scanf("%d",i);*/    first=1;
       }  
     }    for(k1=1; k1<=j;k1++){
    else {      for(i1=1; i1<=ncodemax[k1];i1++){
       for(i=j; i>=1;i--){        j1++;
         cutv(stra,strb,modelsav,'+');        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         /*printf("%s %s %s\n", stra,strb,modelsav);          scanf("%d", i);*/
           scanf("%d",i);*/        for (i=-5; i<=nlstate+ndeath; i++)  
         if (strchr(strb,'*')) {          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           cutv(strd,strc,strb,'*');            for(m=iagemin; m <= iagemax+3; m++)
           if (strcmp(strc,"age")==0) {              freq[i][jk][m]=0;
             cptcovprod--;  
             cutv(strb,stre,strd,'V');      for (i=1; i<=nlstate; i++)  
             Tvar[i+1]=atoi(stre);        for(m=iagemin; m <= iagemax+3; m++)
             cptcovage++;          prop[i][m]=0;
             Tage[cptcovage]=i+1;        
             printf("stre=%s ", stre);        dateintsum=0;
           }        k2cpt=0;
           else if (strcmp(strd,"age")==0) {        for (i=1; i<=imx; i++) {
             cptcovprod--;          bool=1;
             cutv(strb,stre,strc,'V');          if  (cptcovn>0) {
             Tvar[i+1]=atoi(stre);            for (z1=1; z1<=cptcoveff; z1++) 
             cptcovage++;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             Tage[cptcovage]=i+1;                bool=0;
           }          }
           else {          if (bool==1){
             cutv(strb,stre,strc,'V');            for(m=firstpass; m<=lastpass; m++){
             Tvar[i+1]=ncov+k1;              k2=anint[m][i]+(mint[m][i]/12.);
             cutv(strb,strc,strd,'V');              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             Tprod[k1]=i+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             Tvard[k1][1]=atoi(strc);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             Tvard[k1][2]=atoi(stre);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
             Tvar[cptcovn+k2]=Tvard[k1][1];                if (m<lastpass) {
             Tvar[cptcovn+k2+1]=Tvard[k1][2];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             for (k=1; k<=lastobs;k++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                }
             k1++;                
             k2=k2+2;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           }                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
         else {                }
           cutv(strd,strc,strb,'V');                /*}*/
           /* printf("%s %s %s", strd,strc,strb);*/            }
           Tvar[i+1]=atoi(strc);          }
         }        }
         strcpy(modelsav,stra);           
       }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       cutv(strd,strc,stra,'V');  fprintf(ficresp, "#Local time at start: %s", strstart);
       Tvar[1]=atoi(strc);        if  (cptcovn>0) {
     }          fprintf(ficresp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* for (i=1; i<=5; i++)          fprintf(ficresp, "**********\n#");
      printf("i=%d %d ",i,Tvar[i]);*/        }
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/        for(i=1; i<=nlstate;i++) 
  /*printf("cptcovprod=%d ", cptcovprod);*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /*  scanf("%d ",i);*/        fprintf(ficresp, "\n");
     fclose(fic);        
         for(i=iagemin; i <= iagemax+3; i++){
     /*  if(mle==1){*/          if(i==iagemax+3){
     if (weightopt != 1) { /* Maximisation without weights*/            fprintf(ficlog,"Total");
       for(i=1;i<=n;i++) weight[i]=1.0;          }else{
     }            if(first==1){
     /*-calculation of age at interview from date of interview and age at death -*/              first=0;
     agev=matrix(1,maxwav,1,imx);              printf("See log file for details...\n");
                }
     for (i=1; i<=imx; i++)  {            fprintf(ficlog,"Age %d", i);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          }
       for(m=1; (m<= maxwav); m++){          for(jk=1; jk <=nlstate ; jk++){
         if(s[m][i] >0){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           if (s[m][i] == nlstate+1) {              pp[jk] += freq[jk][m][i]; 
             if(agedc[i]>0)          }
               if(moisdc[i]!=99 && andc[i]!=9999)          for(jk=1; jk <=nlstate ; jk++){
               agev[m][i]=agedc[i];            for(m=-1, pos=0; m <=0 ; m++)
             else{              pos += freq[jk][m][i];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            if(pp[jk]>=1.e-10){
               agev[m][i]=-1;              if(first==1){
             }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }              }
           else if(s[m][i] !=9){ /* Should no more exist */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            }else{
             if(mint[m][i]==99 || anint[m][i]==9999)              if(first==1)
               agev[m][i]=1;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             else if(agev[m][i] <agemin){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               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){          for(jk=1; jk <=nlstate ; jk++){
               agemax=agev[m][i];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/              pp[jk] += freq[jk][m][i];
             }          }       
             /*agev[m][i]=anint[m][i]-annais[i];*/          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             /*   agev[m][i] = age[i]+2*m;*/            pos += pp[jk];
           }            posprop += prop[jk][i];
           else { /* =9 */          }
             agev[m][i]=1;          for(jk=1; jk <=nlstate ; jk++){
             s[m][i]=-1;            if(pos>=1.e-5){
           }              if(first==1)
         }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         else /*= 0 Unknown */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           agev[m][i]=1;            }else{
       }              if(first==1)
                    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for (i=1; i<=imx; i++)  {            }
       for(m=1; (m<= maxwav); m++){            if( i <= iagemax){
         if (s[m][i] > (nlstate+ndeath)) {              if(pos>=1.e-5){
           printf("Error: Wrong value in nlstate or ndeath\n");                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           goto end;                /*probs[i][jk][j1]= pp[jk]/pos;*/
         }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       }              }
     }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            }
           }
     free_vector(severity,1,maxwav);          
     free_imatrix(outcome,1,maxwav+1,1,n);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     free_vector(moisnais,1,n);            for(m=-1; m <=nlstate+ndeath; m++)
     free_vector(annais,1,n);              if(freq[jk][m][i] !=0 ) {
     free_matrix(mint,1,maxwav,1,n);              if(first==1)
     free_matrix(anint,1,maxwav,1,n);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     free_vector(moisdc,1,n);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     free_vector(andc,1,n);              }
           if(i <= iagemax)
                fprintf(ficresp,"\n");
     wav=ivector(1,imx);          if(first==1)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            printf("Others in log...\n");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficlog,"\n");
            }
     /* Concatenates waves */      }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    }
     dateintmean=dateintsum/k2cpt; 
    
       Tcode=ivector(1,100);    fclose(ficresp);
       nbcode=imatrix(1,nvar,1,8);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       ncodemax[1]=1;    free_vector(pp,1,nlstate);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
          /* End of Freq */
    codtab=imatrix(1,100,1,10);  }
    h=0;  
    m=pow(2,cptcoveff);  /************ Prevalence ********************/
    void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
    for(k=1;k<=cptcoveff; k++){  {  
      for(i=1; i <=(m/pow(2,k));i++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        for(j=1; j <= ncodemax[k]; j++){       in each health status at the date of interview (if between dateprev1 and dateprev2).
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){       We still use firstpass and lastpass as another selection.
            h++;    */
            if (h>m) h=1;codtab[h][k]=j;   
          }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
        }    double ***freq; /* Frequencies */
      }    double *pp, **prop;
    }    double pos,posprop; 
     double  y2; /* in fractional years */
     int iagemin, iagemax;
    /*for(i=1; i <=m ;i++){  
      for(k=1; k <=cptcovn; k++){    iagemin= (int) agemin;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    iagemax= (int) agemax;
      }    /*pp=vector(1,nlstate);*/
      printf("\n");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
    }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
    scanf("%d",i);*/    j1=0;
        
    /* Calculates basic frequencies. Computes observed prevalence at single age    j=cptcoveff;
        and prints on file fileres'p'. */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    
     for(k1=1; k1<=j;k1++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i1=1; i1<=ncodemax[k1];i1++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        j1++;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i<=nlstate; i++)  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          for(m=iagemin; m <= iagemax+3; m++)
                prop[i][m]=0.0;
     /* 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] */        for (i=1; i<=imx; i++) { /* Each individual */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          bool=1;
           if  (cptcovn>0) {
     if(mle==1){            for (z1=1; z1<=cptcoveff; z1++) 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     }                bool=0;
              } 
     /*--------- results files --------------*/          if (bool==1) { 
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                  y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
    jk=1;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
    fprintf(ficres,"# Parameters\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
    printf("# Parameters\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
    for(i=1,jk=1; i <=nlstate; i++){                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
      for(k=1; k <=(nlstate+ndeath); k++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
        if (k != i)                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
          {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
            printf("%d%d ",i,k);                  prop[s[m][i]][iagemax+3] += weight[i]; 
            fprintf(ficres,"%1d%1d ",i,k);                } 
            for(j=1; j <=ncovmodel; j++){              }
              printf("%f ",p[jk]);            } /* end selection of waves */
              fprintf(ficres,"%f ",p[jk]);          }
              jk++;        }
            }        for(i=iagemin; i <= iagemax+3; i++){  
            printf("\n");          
            fprintf(ficres,"\n");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
          }            posprop += prop[jk][i]; 
      }          } 
    }  
  if(mle==1){          for(jk=1; jk <=nlstate ; jk++){     
     /* Computing hessian and covariance matrix */            if( i <=  iagemax){ 
     ftolhess=ftol; /* Usually correct */              if(posprop>=1.e-5){ 
     hesscov(matcov, p, npar, delti, ftolhess, func);                probs[i][jk][j1]= prop[jk][i]/posprop;
  }              } 
     fprintf(ficres,"# Scales\n");            } 
     printf("# Scales\n");          }/* end jk */ 
      for(i=1,jk=1; i <=nlstate; i++){        }/* end i */ 
       for(j=1; j <=nlstate+ndeath; j++){      } /* end i1 */
         if (j!=i) {    } /* end k1 */
           fprintf(ficres,"%1d%1d",i,j);    
           printf("%1d%1d",i,j);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           for(k=1; k<=ncovmodel;k++){    /*free_vector(pp,1,nlstate);*/
             printf(" %.5e",delti[jk]);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
             fprintf(ficres," %.5e",delti[jk]);  }  /* End of prevalence */
             jk++;  
           }  /************* Waves Concatenation ***************/
           printf("\n");  
           fprintf(ficres,"\n");  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)
         }  {
       }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       }       Death is a valid wave (if date is known).
           mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     k=1;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     fprintf(ficres,"# Covariance\n");       and mw[mi+1][i]. dh depends on stepm.
     printf("# Covariance\n");       */
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;    int i, mi, m;
       i1=(i-1)/(ncovmodel*nlstate)+1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);       double sum=0., jmean=0.;*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/    int first;
       fprintf(ficres,"%3d",i);    int j, k=0,jk, ju, jl;
       printf("%3d",i);    double sum=0.;
       for(j=1; j<=i;j++){    first=0;
         fprintf(ficres," %.5e",matcov[i][j]);    jmin=1e+5;
         printf(" %.5e",matcov[i][j]);    jmax=-1;
       }    jmean=0.;
       fprintf(ficres,"\n");    for(i=1; i<=imx; i++){
       printf("\n");      mi=0;
       k++;      m=firstpass;
     }      while(s[m][i] <= nlstate){
            if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     while((c=getc(ficpar))=='#' && c!= EOF){          mw[++mi][i]=m;
       ungetc(c,ficpar);        if(m >=lastpass)
       fgets(line, MAXLINE, ficpar);          break;
       puts(line);        else
       fputs(line,ficparo);          m++;
     }      }/* end while */
     ungetc(c,ficpar);      if (s[m][i] > nlstate){
          mi++;     /* Death is another wave */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        /* if(mi==0)  never been interviewed correctly before death */
               /* Only death is a correct wave */
     if (fage <= 2) {        mw[mi][i]=m;
       bage = agemin;      }
       fage = agemax;  
     }      wav[i]=mi;
       if(mi==0){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        nbwarn++;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        if(first==0){
           printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
              first=1;
 /*------------ gnuplot -------------*/        }
 chdir(pathcd);        if(first==1){
   if((ficgp=fopen("graph.plt","w"))==NULL) {          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     printf("Problem with file graph.gp");goto end;        }
   }      } /* end mi==0 */
 #ifdef windows    } /* End individuals */
   fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif    for(i=1; i<=imx; i++){
 m=pow(2,cptcoveff);      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
  /* 1eme*/          dh[mi][i]=1;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        else{
    for (k1=1; k1<= m ; k1 ++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
 #ifdef windows              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     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);              if(j==0) j=1;  /* Survives at least one month after exam */
 #endif              else if(j<0){
 #ifdef unix                nberr++;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                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]);
 #endif                j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
 for (i=1; i<= nlstate ; i ++) {                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]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              }
 }              k=k+1;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              if (j >= jmax) jmax=j;
     for (i=1; i<= nlstate ; i ++) {              if (j <= jmin) jmin=j;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              sum=sum+j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            }
      for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 }    /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix            k=k+1;
 fprintf(ficgp,"\nset ter gif small size 400,300");            if (j >= jmax) jmax=j;
 #endif            else if (j <= jmin)jmin=j;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
    }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   }            if(j<0){
   /*2 eme*/              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]);
   for (k1=1; k1<= m ; k1 ++) {              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]);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            }
                sum=sum+j;
     for (i=1; i<= nlstate+1 ; i ++) {          }
       k=2*i;          jk= j/stepm;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          jl= j -jk*stepm;
       for (j=1; j<= nlstate+1 ; j ++) {          ju= j -(jk+1)*stepm;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if(jl==0){
 }                dh[mi][i]=jk;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              bh[mi][i]=0;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            }else{ /* We want a negative bias in order to only have interpolation ie
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                    * at the price of an extra matrix product in likelihood */
       for (j=1; j<= nlstate+1 ; j ++) {              dh[mi][i]=jk+1;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              bh[mi][i]=ju;
         else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }            }else{
       fprintf(ficgp,"\" t\"\" w l 0,");            if(jl <= -ju){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              dh[mi][i]=jk;
       for (j=1; j<= nlstate+1 ; j ++) {              bh[mi][i]=jl;       /* bias is positive if real duration
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                                   * is higher than the multiple of stepm and negative otherwise.
   else fprintf(ficgp," \%%*lf (\%%*lf)");                                   */
 }              }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            else{
       else fprintf(ficgp,"\" t\"\" w l 0,");              dh[mi][i]=jk+1;
     }              bh[mi][i]=ju;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            }
   }            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   /*3eme*/              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   for (k1=1; k1<= m ; k1 ++) {            }
     for (cpt=1; cpt<= nlstate ; cpt ++) {          } /* end if mle */
       k=2+nlstate*(cpt-1);        }
       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);      } /* end wave */
       for (i=1; i< nlstate ; i ++) {    }
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    jmean=sum/k;
       }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     }   }
   }  
    /*********** Tricode ****************************/
   /* CV preval stat */  void tricode(int *Tvar, int **nbcode, int imx)
   for (k1=1; k1<= m ; k1 ++) {  {
     for (cpt=1; cpt<nlstate ; cpt ++) {    
       k=3;    int Ndum[20],ij=1, k, j, i, maxncov=19;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    int cptcode=0;
       for (i=1; i< nlstate ; i ++)    cptcoveff=0; 
         fprintf(ficgp,"+$%d",k+i+1);   
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    for (k=0; k<maxncov; k++) Ndum[k]=0;
          for (k=1; k<=7; k++) ncodemax[k]=0;
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i< nlstate ; i ++) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         l=3+(nlstate+ndeath)*cpt;                                 modality*/ 
         fprintf(ficgp,"+$%d",l+i+1);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       }        Ndum[ij]++; /*store the modality */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     }                                         Tvar[j]. If V=sex and male is 0 and 
   }                                         female is 1, then  cptcode=1.*/
       }
   /* proba elementaires */  
    for(i=1,jk=1; i <=nlstate; i++){      for (i=0; i<=cptcode; i++) {
     for(k=1; k <=(nlstate+ndeath); k++){        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 */
       if (k != i) {      }
         for(j=1; j <=ncovmodel; j++){  
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      ij=1; 
           /*fprintf(ficgp,"%s",alph[1]);*/      for (i=1; i<=ncodemax[j]; i++) {
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        for (k=0; k<= maxncov; k++) {
           jk++;          if (Ndum[k] != 0) {
           fprintf(ficgp,"\n");            nbcode[Tvar[j]][ij]=k; 
         }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       }            
     }            ij++;
     }          }
           if (ij > ncodemax[j]) break; 
   for(jk=1; jk <=m; jk++) {        }  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      } 
    i=1;    }  
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;   for (k=0; k< maxncov; k++) Ndum[k]=0;
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){   for (i=1; i<=ncovmodel-2; i++) { 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 ij=1;     ij=Tvar[i];
         for(j=3; j <=ncovmodel; j++) {     Ndum[ij]++;
           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++;   ij=1;
           }   for (i=1; i<= maxncov; i++) {
           else     if((Ndum[i]!=0) && (i<=ncovcol)){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       Tvaraff[ij]=i; /*For printing */
         }       ij++;
           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);   cptcoveff=ij-1; /*Number of simple covariates*/
 ij=1;  }
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  /*********** Health Expectancies ****************/
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  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[] )
           }  
           else  {
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Health expectancies */
           }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
           fprintf(ficgp,")");    double age, agelim, hf;
         }    double ***p3mat,***varhe;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double **dnewm,**doldm;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double *xp;
         i=i+ncovmodel;    double **gp, **gm;
        }    double ***gradg, ***trgradg;
      }    int theta;
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   }    xp=vector(1,npar);
        dnewm=matrix(1,nlstate*nlstate,1,npar);
   fclose(ficgp);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
        
 chdir(path);    fprintf(ficreseij,"# Local time at start: %s", strstart);
     free_matrix(agev,1,maxwav,1,imx);    fprintf(ficreseij,"# Health expectancies\n");
     free_ivector(wav,1,imx);    fprintf(ficreseij,"# Age");
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    for(i=1; i<=nlstate;i++)
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      for(j=1; j<=nlstate;j++)
            fprintf(ficreseij," %1d-%1d (SE)",i,j);
     free_imatrix(s,1,maxwav+1,1,n);    fprintf(ficreseij,"\n");
      
        if(estepm < stepm){
     free_ivector(num,1,n);      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_vector(agedc,1,n);    }
     free_vector(weight,1,n);    else  hstepm=estepm;   
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    /* We compute the life expectancy from trapezoids spaced every estepm months
     fclose(ficparo);     * This is mainly to measure the difference between two models: for example
     fclose(ficres);     * if stepm=24 months pijx are given only every 2 years and by summing them
     /*  }*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
         * progression in between and thus overestimating or underestimating according
    /*________fin mle=1_________*/     * to the curvature of the survival function. If, for the same date, we 
         * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
     /* No more information from the sample is required now */     * curvature will be obtained if estepm is as small as stepm. */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    /* For example we decided to compute the life expectancy with the smallest unit */
     ungetc(c,ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fgets(line, MAXLINE, ficpar);       nhstepm is the number of hstepm from age to agelim 
     puts(line);       nstepm is the number of stepm from age to agelin. 
     fputs(line,ficparo);       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like estepm months */
   ungetc(c,ficpar);    /* 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
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       means that if the survival funtion is printed only each two years of age and if
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       results. So we changed our mind and took the option of the best precision.
 /*--------- index.htm --------*/    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if((fichtm=fopen("index.htm","w"))==NULL)    {  
     printf("Problem with index.htm \n");goto end;    agelim=AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      /* if (stepm >= YEARM) hstepm=1;*/
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  fprintf(fichtm," <li>Graphs</li>\n<p>");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
  j1=0;      /* Computing  Variances of health expectancies */
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){       for(theta=1; theta <=npar; theta++){
        j1++;        for(i=1; i<=npar; i++){ 
        if (cptcovn > 0) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          fprintf(fichtm,"<hr>************ Results for covariates");        }
          for (cpt=1; cpt<=cptcoveff;cpt++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    
          fprintf(fichtm," ************\n<hr>");        cptj=0;
        }        for(j=1; j<= nlstate; j++){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          for(i=1; i<=nlstate; i++){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                cptj=cptj+1;
        for(cpt=1; cpt<nlstate;cpt++){            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            }
        }          }
     for(cpt=1; cpt<=nlstate;cpt++) {        }
        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(i=1; i<=npar; i++) 
      }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      for(cpt=1; cpt<=nlstate;cpt++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         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);        cptj=0;
      }        for(j=1; j<= nlstate; j++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          for(i=1;i<=nlstate;i++){
 health expectancies in states (1) and (2): e%s%d.gif<br>            cptj=cptj+1;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 fprintf(fichtm,"\n</body>");  
    }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  }            }
 fclose(fichtm);          }
         }
   /*--------------- Prevalence limit --------------*/        for(j=1; j<= nlstate*nlstate; j++)
            for(h=0; h<=nhstepm-1; h++){
   strcpy(filerespl,"pl");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   strcat(filerespl,fileres);          }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       } 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;     
   }  /* End theta */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);       for(h=0; h<=nhstepm-1; h++)
   fprintf(ficrespl,"\n");        for(j=1; j<=nlstate*nlstate;j++)
            for(theta=1; theta <=npar; theta++)
   prlim=matrix(1,nlstate,1,nlstate);            trgradg[h][j][theta]=gradg[h][theta][j];
   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 */       for(i=1;i<=nlstate*nlstate;i++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1;j<=nlstate*nlstate;j++)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          varhe[i][j][(int)age] =0.;
   k=0;  
   agebase=agemin;       printf("%d|",(int)age);fflush(stdout);
   agelim=agemax;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   ftolpl=1.e-10;       for(h=0;h<=nhstepm-1;h++){
   i1=cptcoveff;        for(k=0;k<=nhstepm-1;k++){
   if (cptcovn < 1){i1=1;}          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   for(cptcov=1;cptcov<=i1;cptcov++){          for(i=1;i<=nlstate*nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(j=1;j<=nlstate*nlstate;j++)
         k=k+1;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        }
         fprintf(ficrespl,"\n#******");      }
         for(j=1;j<=cptcoveff;j++)      /* Computing expectancies */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1; i<=nlstate;i++)
         fprintf(ficrespl,"******\n");        for(j=1; j<=nlstate;j++)
                  for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         for (age=agebase; age<=agelim; age++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            
           fprintf(ficrespl,"%.0f",age );  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);          }
           fprintf(ficrespl,"\n");  
         }      fprintf(ficreseij,"%3.0f",age );
       }      cptj=0;
     }      for(i=1; i<=nlstate;i++)
   fclose(ficrespl);        for(j=1; j<=nlstate;j++){
   /*------------- h Pij x at various ages ------------*/          cptj++;
            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      fprintf(ficreseij,"\n");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;     
   }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   printf("Computing pij: result on file '%s' \n", filerespij);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   if (stepm<=24) stepsize=2;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }
   agelim=AGESUP;    printf("\n");
   hstepm=stepsize*YEARM; /* Every year of age */    fprintf(ficlog,"\n");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
      free_vector(xp,1,npar);
   k=0;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       k=k+1;  }
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)  /************ Variance ******************/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  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(ficrespij,"******\n");  {
            /* Variance of health expectancies */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* double **newm;*/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double **dnewm,**doldm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewmp,**doldmp;
           oldm=oldms;savm=savms;    int i, j, nhstepm, hstepm, h, nstepm ;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int k, cptcode;
           fprintf(ficrespij,"# Age");    double *xp;
           for(i=1; i<=nlstate;i++)    double **gp, **gm;  /* for var eij */
             for(j=1; j<=nlstate+ndeath;j++)    double ***gradg, ***trgradg; /*for var eij */
               fprintf(ficrespij," %1d-%1d",i,j);    double **gradgp, **trgradgp; /* for var p point j */
           fprintf(ficrespij,"\n");    double *gpp, *gmp; /* for var p point j */
           for (h=0; h<=nhstepm; h++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    double ***p3mat;
             for(i=1; i<=nlstate;i++)    double age,agelim, hf;
               for(j=1; j<=nlstate+ndeath;j++)    double ***mobaverage;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    int theta;
             fprintf(ficrespij,"\n");    char digit[4];
           }    char digitp[25];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    char fileresprobmorprev[FILENAMELENGTH];
         }  
     }    if(popbased==1){
   }      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
   fclose(ficrespij);      else strcpy(digitp,"-populbased-nomobil-");
     }
   /*---------- Health expectancies and variances ------------*/    else 
       strcpy(digitp,"-stablbased-");
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    if (mobilav!=0) {
   if((ficrest=fopen(filerest,"w"))==NULL) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   strcpy(filerese,"e");  
   strcat(filerese,fileres);    strcpy(fileresprobmorprev,"prmorprev"); 
   if((ficreseij=fopen(filerese,"w"))==NULL) {    sprintf(digit,"%-d",ij);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
  strcpy(fileresv,"v");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   strcat(fileresv,fileres);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   k=0;    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   for(cptcov=1;cptcov<=i1;cptcov++){    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);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       k=k+1;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficrest,"\n#****** ");      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(j=1;j<=cptcoveff;j++)      for(i=1; i<=nlstate;i++)
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       fprintf(ficrest,"******\n");    }  
     fprintf(ficresprobmorprev,"\n");
       fprintf(ficreseij,"\n#****** ");    fprintf(ficgp,"\n# Routine varevsij");
       for(j=1;j<=cptcoveff;j++)    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
       fprintf(ficreseij,"******\n");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
       fprintf(ficresvij,"\n#****** ");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++)   fprintf(ficresvij, "#Local time at start: %s", strstart);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
       fprintf(ficresvij,"******\n");    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(j=1; j<=nlstate;j++)
       oldm=oldms;savm=savms;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      fprintf(ficresvij,"\n");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    xp=vector(1,npar);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    dnewm=matrix(1,nlstate,1,npar);
          doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficrest,"\n");  
            gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       hf=1;    gpp=vector(nlstate+1,nlstate+ndeath);
       if (stepm >= YEARM) hf=stepm/YEARM;    gmp=vector(nlstate+1,nlstate+ndeath);
       epj=vector(1,nlstate+1);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for(age=bage; age <=fage ;age++){    
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if(estepm < stepm){
         fprintf(ficrest," %.0f",age);      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    else  hstepm=estepm;   
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    /* 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. 
           epj[nlstate+1] +=epj[j];       nhstepm is the number of hstepm from age to agelim 
         }       nstepm is the number of stepm from age to agelin. 
         for(i=1, vepp=0.;i <=nlstate;i++)       Look at hpijx to understand the reason of that which relies in memory size
           for(j=1;j <=nlstate;j++)       and note for a fixed period like k years */
             vepp += vareij[i][j][(int)age];    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));       survival function given by stepm (the optimization length). Unfortunately it
         for(j=1;j <=nlstate;j++){       means that if the survival funtion is printed every two years of age and if
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));       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.
         fprintf(ficrest,"\n");    */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }    agelim = AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  fclose(ficreseij);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  fclose(ficresvij);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficrest);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   fclose(ficpar);      gp=matrix(0,nhstepm,1,nlstate);
   free_vector(epj,1,nlstate+1);      gm=matrix(0,nhstepm,1,nlstate);
   /*  scanf("%d ",i); */  
   
   /*------- Variance limit prevalence------*/        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 strcpy(fileresvpl,"vpl");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcat(fileresvpl,fileres);        }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     exit(0);  
   }        if (popbased==1) {
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
  k=0;              prlim[i][i]=probs[(int)age][i][ij];
  for(cptcov=1;cptcov<=i1;cptcov++){          }else{ /* mobilav */ 
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(i=1; i<=nlstate;i++)
      k=k+1;              prlim[i][i]=mobaverage[(int)age][i][ij];
      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");        for(j=1; j<= nlstate; j++){
                for(h=0; h<=nhstepm; h++){
      varpl=matrix(1,nlstate,(int) bage, (int) fage);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
      oldm=oldms;savm=savms;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          }
    }        }
  }        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   fclose(ficresvpl);           as a weighted average of prlim.
         */
   /*---------- End : free ----------------*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }    
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        /* end probability of death */
    
          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   
          if (popbased==1) {
   free_matrix(matcov,1,npar,1,npar);          if(mobilav ==0){
   free_vector(delti,1,npar);            for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   printf("End of Imach\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          }
          }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for(j=1; j<= nlstate; j++){
   /*------ End -----------*/          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
  end:              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 #ifdef windows          }
  chdir(pathcd);        }
 #endif        /* This for computing probability of death (h=1 means
  system("wgnuplot graph.plt");           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
 #ifdef windows        */
   while (z[0] != 'q') {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     chdir(pathcd);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     printf("\nType e to edit output files, c to start again, and q for exiting: ");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     scanf("%s",z);        }    
     if (z[0] == 'c') system("./imach");        /* end probability of death */
     else if (z[0] == 'e') {  
       chdir(path);        for(j=1; j<= nlstate; j++) /* vareij */
       system("index.htm");          for(h=0; h<=nhstepm; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     else if (z[0] == 'q') exit(0);          }
   }  
 #endif        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         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++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ 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[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     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 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     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((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     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);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficresprob, "#Local time at start: %s", strstart);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           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(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           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\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           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);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 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><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              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> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    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   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     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 parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (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);
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,"\"");
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
     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);
     }
   }
   
   
   
Removed from v.1.7  
changed lines
  Added in v.1.107

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