Diff for /imach/src/imach.c between versions 1.6 and 1.106

version 1.6, 2001/05/02 17:47:10 version 1.106, 2006/01/19 13:24:36
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.106  2006/01/19 13:24:36  brouard
   individuals from different ages are interviewed on their health status    Some cleaning and links added in html output
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.105  2006/01/05 20:23:19  lievre
   Health expectancies are computed from the transistions observed between    *** empty log message ***
   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 1.104  2005/09/30 16:11:43  lievre
   reach the Maximum Likelihood of the parameters involved in the model.    (Module): sump fixed, loop imx fixed, and simplifications.
   The simplest model is the multinomial logistic model where pij is    (Module): If the status is missing at the last wave but we know
   the probabibility to be observed in state j at the second wave conditional    that the person is alive, then we can code his/her status as -2
   to be observed in state i at the first wave. Therefore the model is:    (instead of missing=-1 in earlier versions) and his/her
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    contributions to the likelihood is 1 - Prob of dying from last
   is a covariate. If you want to have a more complex model than "constant and    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   age", you should modify the program where the markup    the healthy state at last known wave). Version is 0.98
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   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 1.102  2004/09/15 17:31:30  brouard
   individual missed an interview, the information is not rounded or lost, but    Add the possibility to read data file including tab characters.
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.101  2004/09/15 10:38:38  brouard
   observed in state i at age x+h conditional to the observed state i at age    Fix on curr_time
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.100  2004/07/12 18:29:06  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    Add version for Mac OS X. Just define UNIX in Makefile
   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 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.98  2004/05/16 15:05:56  brouard
      New version 0.97 . First attempt to estimate force of mortality
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    directly from the data i.e. without the need of knowing the health
            Institut national d'études démographiques, Paris.    state at each age, but using a Gompertz model: log u =a + b*age .
   This software have been partly granted by Euro-REVES, a concerted action    This is the basic analysis of mortality and should be done before any
   from the European Union.    other analysis, in order to test if the mortality estimated from the
   It is copyrighted identically to a GNU software product, ie programme and    cross-longitudinal survey is different from the mortality estimated
   software can be distributed freely for non commercial use. Latest version    from other sources like vital statistic data.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    The same imach parameter file can be used but the option for mle should be -3.
    
 #include <math.h>    Agnès, who wrote this part of the code, tried to keep most of the
 #include <stdio.h>    former routines in order to include the new code within the former code.
 #include <stdlib.h>  
 #include <unistd.h>    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Current limitations:
 /*#define DEBUG*/    A) Even if you enter covariates, i.e. with the
 #define windows    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    B) There is no computation of Life Expectancy nor Life Table.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.97  2004/02/20 13:25:42  lievre
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Version 0.96d. Population forecasting command line is (temporarily)
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    suppressed.
   
 #define NINTERVMAX 8    Revision 1.96  2003/07/15 15:38:55  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    rewritten within the same printf. Workaround: many printfs.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.95  2003/07/08 07:54:34  brouard
 #define YEARM 12. /* Number of months per year */    * imach.c (Repository):
 #define AGESUP 130    (Repository): Using imachwizard code to output a more meaningful covariance
 #define AGEBASE 40    matrix (cov(a12,c31) instead of numbers.
   
     Revision 1.94  2003/06/27 13:00:02  brouard
 int nvar;    Just cleaning
 static int cptcov;  
 int cptcovn, cptcovage=0;    Revision 1.93  2003/06/25 16:33:55  brouard
 int npar=NPARMAX;    (Module): On windows (cygwin) function asctime_r doesn't
 int nlstate=2; /* Number of live states */    exist so I changed back to asctime which exists.
 int ndeath=1; /* Number of dead states */    (Module): Version 0.96b
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
     Revision 1.92  2003/06/25 16:30:45  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): On windows (cygwin) function asctime_r doesn't
 int maxwav; /* Maxim number of waves */    exist so I changed back to asctime which exists.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.91  2003/06/25 15:30:29  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    * imach.c (Repository): Duplicated warning errors corrected.
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Repository): Elapsed time after each iteration is now output. It
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    helps to forecast when convergence will be reached. Elapsed time
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    is stamped in powell.  We created a new html file for the graphs
 FILE *ficgp, *fichtm;    concerning matrix of covariance. It has extension -cov.htm.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.90  2003/06/24 12:34:15  brouard
  FILE  *ficresvij;    (Module): Some bugs corrected for windows. Also, when
   char fileresv[FILENAMELENGTH];    mle=-1 a template is output in file "or"mypar.txt with the design
  FILE  *ficresvpl;    of the covariance matrix to be input.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.89  2003/06/24 12:30:52  brouard
 #define NR_END 1    (Module): Some bugs corrected for windows. Also, when
 #define FREE_ARG char*    mle=-1 a template is output in file "or"mypar.txt with the design
 #define FTOL 1.0e-10    of the covariance matrix to be input.
   
 #define NRANSI    Revision 1.88  2003/06/23 17:54:56  brouard
 #define ITMAX 200    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
 #define TOL 2.0e-4    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.86  2003/06/17 20:04:08  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.85  2003/06/17 13:12:43  brouard
 #define TINY 1.0e-20    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 static double maxarg1,maxarg2;    prior to the death. In this case, dh was negative and likelihood
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    was wrong (infinity). We still send an "Error" but patch by
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    assuming that the date of death was just one stepm after the
      interview.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Repository): Because some people have very long ID (first column)
 #define rint(a) floor(a+0.5)    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 static double sqrarg;    truncation)
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Repository): No more line truncation errors.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.84  2003/06/13 21:44:43  brouard
 int imx;    * imach.c (Repository): Replace "freqsummary" at a correct
 int stepm;    place. It differs from routine "prevalence" which may be called
 /* Stepm, step in month: minimum step interpolation*/    many times. Probs is memory consuming and must be used with
     parcimony.
 int m,nb;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.83  2003/06/10 13:39:11  lievre
 double **pmmij;    *** empty log message ***
   
 double *weight;    Revision 1.82  2003/06/05 15:57:20  brouard
 int **s; /* Status */    Add log in  imach.c and  fullversion number is now printed.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab;  */
   /*
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */     Interpolated Markov Chain
 double ftolhess; /* Tolerance for computing hessian */  
     Short summary of the programme:
     
 static  int split( char *path, char *dirc, char *name )    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    char *s;                             /* pointer */    first survey ("cross") where individuals from different ages are
    int  l1, l2;                         /* length counters */    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
    l1 = strlen( path );                 /* length of path */    second wave of interviews ("longitudinal") which measure each change
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (if any) in individual health status.  Health expectancies are
    s = strrchr( path, '\\' );           /* find last / */    computed from the time spent in each health state according to a
    if ( s == NULL ) {                   /* no directory, so use current */    model. More health states you consider, more time is necessary to reach the
 #if     defined(__bsd__)                /* get current working directory */    Maximum Likelihood of the parameters involved in the model.  The
       extern char       *getwd( );    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
       if ( getwd( dirc ) == NULL ) {    conditional to be observed in state i at the first wave. Therefore
 #else    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       extern char       *getcwd( );    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    where the markup *Covariates have to be included here again* invites
 #endif    you to do it.  More covariates you add, slower the
          return( GLOCK_ERROR_GETCWD );    convergence.
       }  
       strcpy( name, path );             /* we've got it */    The advantage of this computer programme, compared to a simple
    } else {                             /* strip direcotry from path */    multinomial logistic model, is clear when the delay between waves is not
       s++;                              /* after this, the filename */    identical for each individual. Also, if a individual missed an
       l2 = strlen( s );                 /* length of filename */    intermediate interview, the information is lost, but taken into
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    account using an interpolation or extrapolation.  
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    hPijx is the probability to be observed in state i at age x+h
       dirc[l1-l2] = 0;                  /* add zero */    conditional to the observed state i at age x. The delay 'h' can be
    }    split into an exact number (nh*stepm) of unobserved intermediate
    l1 = strlen( dirc );                 /* length of directory */    states. This elementary transition (by month, quarter,
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    semester or year) is modelled as a multinomial logistic.  The hPx
    return( 0 );                         /* we're done */    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
   
 /******************************************/    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 void replace(char *s, char*t)    
 {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   int i;             Institut national d'études démographiques, Paris.
   int lg=20;    This software have been partly granted by Euro-REVES, a concerted action
   i=0;    from the European Union.
   lg=strlen(t);    It is copyrighted identically to a GNU software product, ie programme and
   for(i=0; i<= lg; i++) {    software can be distributed freely for non commercial use. Latest version
     (s[i] = t[i]);    can be accessed at http://euroreves.ined.fr/imach .
     if (t[i]== '\\') s[i]='/';  
   }    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 nbocc(char *s, char occ)    **********************************************************************/
 {  /*
   int i,j=0;    main
   int lg=20;    read parameterfile
   i=0;    read datafile
   lg=strlen(s);    concatwav
   for(i=0; i<= lg; i++) {    freqsummary
   if  (s[i] == occ ) j++;    if (mle >= 1)
   }      mlikeli
   return j;    print results files
 }    if mle==1 
        computes hessian
 void cutv(char *u,char *v, char*t, char occ)    read end of parameter file: agemin, agemax, bage, fage, estepm
 {        begin-prev-date,...
   int i,lg,j,p=0;    open gnuplot file
   i=0;    open html file
   for(j=0; j<=strlen(t)-1; j++) {    stable prevalence
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;     for age prevalim()
   }    h Pij x
     variance of p varprob
   lg=strlen(t);    forecasting if prevfcast==1 prevforecast call prevalence()
   for(j=0; j<p; j++) {    health expectancies
     (u[j] = t[j]);    Variance-covariance of DFLE
   }    prevalence()
      u[p]='\0';     movingaverage()
     varevsij() 
    for(j=0; j<= lg; j++) {    if popbased==1 varevsij(,popbased)
     if (j>=(p+1))(v[j-p-1] = t[j]);    total life expectancies
   }    Variance of stable prevalence
 }   end
   */
 /********************** nrerror ********************/  
   
 void nrerror(char error_text[])  
 {   
   fprintf(stderr,"ERREUR ...\n");  #include <math.h>
   fprintf(stderr,"%s\n",error_text);  #include <stdio.h>
   exit(1);  #include <stdlib.h>
 }  #include <string.h>
 /*********************** vector *******************/  #include <unistd.h>
 double *vector(int nl, int nh)  
 {  /* #include <sys/time.h> */
   double *v;  #include <time.h>
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #include "timeval.h"
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 /************************ free vector ******************/  #define MAXLINE 256
 void free_vector(double*v, int nl, int nh)  #define GNUPLOTPROGRAM "gnuplot"
 {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free((FREE_ARG)(v+nl-NR_END));  #define FILENAMELENGTH 132
 }  /*#define DEBUG*/
   /*#define windows*/
 /************************ivector *******************************/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int *ivector(long nl,long nh)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 {  
   int *v;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  #define NINTERVMAX 8
 }  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 /******************free ivector **************************/  #define NCOVMAX 8 /* Maximum number of covariates */
 void free_ivector(int *v, long nl, long nh)  #define MAXN 20000
 {  #define YEARM 12. /* Number of months per year */
   free((FREE_ARG)(v+nl-NR_END));  #define AGESUP 130
 }  #define AGEBASE 40
   #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 /******************* imatrix *******************************/  #ifdef UNIX
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define DIRSEPARATOR '/'
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define ODIRSEPARATOR '\\'
 {  #else
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define DIRSEPARATOR '\\'
   int **m;  #define ODIRSEPARATOR '/'
    #endif
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  /* $Id$ */
   if (!m) nrerror("allocation failure 1 in matrix()");  /* $State$ */
   m += NR_END;  
   m -= nrl;  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
    char fullversion[]="$Revision$ $Date$"; 
    int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   /* allocate rows and set pointers to them */  int nvar;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int npar=NPARMAX;
   m[nrl] += NR_END;  int nlstate=2; /* Number of live states */
   m[nrl] -= ncl;  int ndeath=1; /* Number of dead states */
    int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int popbased=0;
    
   /* return pointer to array of pointers to rows */  int *wav; /* Number of waves for this individuual 0 is possible */
   return m;  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 
 /****************** free_imatrix *************************/                     to the likelihood and the sum of weights (done by funcone)*/
 void free_imatrix(m,nrl,nrh,ncl,nch)  int mle, weightopt;
       int **m;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       long nch,ncl,nrh,nrl;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
      /* free an int matrix allocated by imatrix() */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  double jmean; /* Mean space between 2 waves */
   free((FREE_ARG) (m+nrl-NR_END));  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 /******************* matrix *******************************/  FILE *ficlog, *ficrespow;
 double **matrix(long nrl, long nrh, long ncl, long nch)  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  long ipmx; /* Number of contributions */
   double **m;  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *ficresilk;
   m += NR_END;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m -= nrl;  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  FILE *ficreseij;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char filerese[FILENAMELENGTH];
   m[nrl] += NR_END;  FILE  *ficresvij;
   m[nrl] -= ncl;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char fileresvpl[FILENAMELENGTH];
   return m;  char title[MAXLINE];
 }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 /*************************free matrix ************************/  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char command[FILENAMELENGTH];
 {  int  outcmd=0;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 }  
   char filelog[FILENAMELENGTH]; /* Log file */
 /******************* ma3x *******************************/  char filerest[FILENAMELENGTH];
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char fileregp[FILENAMELENGTH];
 {  char popfile[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   if (!m) nrerror("allocation failure 1 in matrix()");  struct timezone tzp;
   m += NR_END;  extern int gettimeofday();
   m -= nrl;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  extern long time();
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char strcurr[80], strfor[80];
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #define NR_END 1
   #define FREE_ARG char*
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define FTOL 1.0e-10
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define NRANSI 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define ITMAX 200 
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  #define TOL 2.0e-4 
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  #define CGOLD 0.3819660 
    #define ZEPS 1.0e-10 
   for (i=nrl+1; i<=nrh; i++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  #define GOLD 1.618034 
       m[i][j]=m[i][j-1]+nlay;  #define GLIMIT 100.0 
   }  #define TINY 1.0e-20 
   return m;  
 }  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /*************************free ma3x ************************/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define rint(a) floor(a+0.5)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  static double sqrarg;
 }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /***************** f1dim *************************/  int agegomp= AGEGOMP;
 extern int ncom;  
 extern double *pcom,*xicom;  int imx; 
 extern double (*nrfunc)(double []);  int stepm=1;
    /* Stepm, step in month: minimum step interpolation*/
 double f1dim(double x)  
 {  int estepm;
   int j;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   double f;  
   double *xt;  int m,nb;
    long *num;
   xt=vector(1,ncom);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   f=(*nrfunc)(xt);  double **pmmij, ***probs;
   free_vector(xt,1,ncom);  double *ageexmed,*agecens;
   return f;  double dateintmean=0;
 }  
   double *weight;
 /*****************brent *************************/  int **s; /* Status */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   int iter;  double *lsurv, *lpop, *tpop;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftemp;  double ftolhess; /* Tolerance for computing hessian */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  /**************** split *************************/
    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   a=(ax < cx ? ax : cx);  {
   b=(ax > cx ? ax : cx);    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   x=w=v=bx;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   fw=fv=fx=(*f)(x);    */ 
   for (iter=1;iter<=ITMAX;iter++) {    char  *ss;                            /* pointer */
     xm=0.5*(a+b);    int   l1, l2;                         /* length counters */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    l1 = strlen(path );                   /* length of path */
     printf(".");fflush(stdout);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 #ifdef DEBUG    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     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 ( ss == NULL ) {                   /* no directory, so use current */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 #endif        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      /* get current working directory */
       *xmin=x;      /*    extern  char* getcwd ( char *buf , int len);*/
       return fx;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     }        return( GLOCK_ERROR_GETCWD );
     ftemp=fu;      }
     if (fabs(e) > tol1) {      strcpy( name, path );               /* we've got it */
       r=(x-w)*(fx-fv);    } else {                              /* strip direcotry from path */
       q=(x-v)*(fx-fw);      ss++;                               /* after this, the filename */
       p=(x-v)*q-(x-w)*r;      l2 = strlen( ss );                  /* length of filename */
       q=2.0*(q-r);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       if (q > 0.0) p = -p;      strcpy( name, ss );         /* save file name */
       q=fabs(q);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       etemp=e;      dirc[l1-l2] = 0;                    /* add zero */
       e=d;    }
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    l1 = strlen( dirc );                  /* length of directory */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    /*#ifdef windows
       else {    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
         d=p/q;  #else
         u=x+d;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
         if (u-a < tol2 || b-u < tol2)  #endif
           d=SIGN(tol1,xm-x);    */
       }    ss = strrchr( name, '.' );            /* find last / */
     } else {    if (ss >0){
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      ss++;
     }      strcpy(ext,ss);                     /* save extension */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      l1= strlen( name);
     fu=(*f)(u);      l2= strlen(ss)+1;
     if (fu <= fx) {      strncpy( finame, name, l1-l2);
       if (u >= x) a=x; else b=x;      finame[l1-l2]= 0;
       SHFT(v,w,x,u)    }
         SHFT(fv,fw,fx,fu)    return( 0 );                          /* we're done */
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  
             v=w;  /******************************************/
             w=u;  
             fv=fw;  void replace_back_to_slash(char *s, char*t)
             fw=fu;  {
           } else if (fu <= fv || v == x || v == w) {    int i;
             v=u;    int lg=0;
             fv=fu;    i=0;
           }    lg=strlen(t);
         }    for(i=0; i<= lg; i++) {
   }      (s[i] = t[i]);
   nrerror("Too many iterations in brent");      if (t[i]== '\\') s[i]='/';
   *xmin=x;    }
   return fx;  }
 }  
   int nbocc(char *s, char occ)
 /****************** mnbrak ***********************/  {
     int i,j=0;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    int lg=20;
             double (*func)(double))    i=0;
 {    lg=strlen(s);
   double ulim,u,r,q, dum;    for(i=0; i<= lg; i++) {
   double fu;    if  (s[i] == occ ) j++;
      }
   *fa=(*func)(*ax);    return j;
   *fb=(*func)(*bx);  }
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  void cutv(char *u,char *v, char*t, char occ)
       SHFT(dum,*fb,*fa,dum)  {
       }    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   *cx=(*bx)+GOLD*(*bx-*ax);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   *fc=(*func)(*cx);       gives u="abcedf" and v="ghi2j" */
   while (*fb > *fc) {    int i,lg,j,p=0;
     r=(*bx-*ax)*(*fb-*fc);    i=0;
     q=(*bx-*cx)*(*fb-*fa);    for(j=0; j<=strlen(t)-1; j++) {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    }
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    lg=strlen(t);
       fu=(*func)(u);    for(j=0; j<p; j++) {
     } else if ((*cx-u)*(u-ulim) > 0.0) {      (u[j] = t[j]);
       fu=(*func)(u);    }
       if (fu < *fc) {       u[p]='\0';
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))     for(j=0; j<= lg; j++) {
           }      if (j>=(p+1))(v[j-p-1] = t[j]);
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    }
       u=ulim;  }
       fu=(*func)(u);  
     } else {  /********************** nrerror ********************/
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  void nrerror(char error_text[])
     }  {
     SHFT(*ax,*bx,*cx,u)    fprintf(stderr,"ERREUR ...\n");
       SHFT(*fa,*fb,*fc,fu)    fprintf(stderr,"%s\n",error_text);
       }    exit(EXIT_FAILURE);
 }  }
   /*********************** vector *******************/
 /*************** linmin ************************/  double *vector(int nl, int nh)
   {
 int ncom;    double *v;
 double *pcom,*xicom;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 double (*nrfunc)(double []);    if (!v) nrerror("allocation failure in vector");
      return v-nl+NR_END;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  }
 {  
   double brent(double ax, double bx, double cx,  /************************ free vector ******************/
                double (*f)(double), double tol, double *xmin);  void free_vector(double*v, int nl, int nh)
   double f1dim(double x);  {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    free((FREE_ARG)(v+nl-NR_END));
               double *fc, double (*func)(double));  }
   int j;  
   double xx,xmin,bx,ax;  /************************ivector *******************************/
   double fx,fb,fa;  int *ivector(long nl,long nh)
    {
   ncom=n;    int *v;
   pcom=vector(1,n);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   xicom=vector(1,n);    if (!v) nrerror("allocation failure in ivector");
   nrfunc=func;    return v-nl+NR_END;
   for (j=1;j<=n;j++) {  }
     pcom[j]=p[j];  
     xicom[j]=xi[j];  /******************free ivector **************************/
   }  void free_ivector(int *v, long nl, long nh)
   ax=0.0;  {
   xx=1.0;    free((FREE_ARG)(v+nl-NR_END));
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /************************lvector *******************************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  long *lvector(long nl,long nh)
 #endif  {
   for (j=1;j<=n;j++) {    long *v;
     xi[j] *= xmin;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     p[j] += xi[j];    if (!v) nrerror("allocation failure in ivector");
   }    return v-nl+NR_END;
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  
 }  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
 /*************** powell ************************/  {
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    free((FREE_ARG)(v+nl-NR_END));
             double (*func)(double []))  }
 {  
   void linmin(double p[], double xi[], int n, double *fret,  /******************* imatrix *******************************/
               double (*func)(double []));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   int i,ibig,j;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double del,t,*pt,*ptt,*xit;  { 
   double fp,fptt;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double *xits;    int **m; 
   pt=vector(1,n);    
   ptt=vector(1,n);    /* allocate pointers to rows */ 
   xit=vector(1,n);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   xits=vector(1,n);    if (!m) nrerror("allocation failure 1 in matrix()"); 
   *fret=(*func)(p);    m += NR_END; 
   for (j=1;j<=n;j++) pt[j]=p[j];    m -= nrl; 
   for (*iter=1;;++(*iter)) {    
     fp=(*fret);    
     ibig=0;    /* allocate rows and set pointers to them */ 
     del=0.0;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for (i=1;i<=n;i++)    m[nrl] += NR_END; 
       printf(" %d %.12f",i, p[i]);    m[nrl] -= ncl; 
     printf("\n");    
     for (i=1;i<=n;i++) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    
       fptt=(*fret);    /* return pointer to array of pointers to rows */ 
 #ifdef DEBUG    return m; 
       printf("fret=%lf \n",*fret);  } 
 #endif  
       printf("%d",i);fflush(stdout);  /****************** free_imatrix *************************/
       linmin(p,xit,n,fret,func);  void free_imatrix(m,nrl,nrh,ncl,nch)
       if (fabs(fptt-(*fret)) > del) {        int **m;
         del=fabs(fptt-(*fret));        long nch,ncl,nrh,nrl; 
         ibig=i;       /* free an int matrix allocated by imatrix() */ 
       }  { 
 #ifdef DEBUG    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       printf("%d %.12e",i,(*fret));    free((FREE_ARG) (m+nrl-NR_END)); 
       for (j=1;j<=n;j++) {  } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
       for(j=1;j<=n;j++)  {
         printf(" p=%.12e",p[j]);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       printf("\n");    double **m;
 #endif  
     }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    if (!m) nrerror("allocation failure 1 in matrix()");
 #ifdef DEBUG    m += NR_END;
       int k[2],l;    m -= nrl;
       k[0]=1;  
       k[1]=-1;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       printf("Max: %.12e",(*func)(p));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for (j=1;j<=n;j++)    m[nrl] += NR_END;
         printf(" %.12e",p[j]);    m[nrl] -= ncl;
       printf("\n");  
       for(l=0;l<=1;l++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         for (j=1;j<=n;j++) {    return m;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);     */
         }  }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /*************************free matrix ************************/
 #endif  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
       free_vector(xit,1,n);    free((FREE_ARG)(m+nrl-NR_END));
       free_vector(xits,1,n);  }
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  /******************* ma3x *******************************/
       return;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for (j=1;j<=n;j++) {    double ***m;
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       pt[j]=p[j];    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     fptt=(*func)(ptt);    m -= nrl;
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       if (t < 0.0) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         linmin(p,xit,n,fret,func);    m[nrl] += NR_END;
         for (j=1;j<=n;j++) {    m[nrl] -= ncl;
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         }  
 #ifdef DEBUG    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         for(j=1;j<=n;j++)    m[nrl][ncl] += NR_END;
           printf(" %.12e",xit[j]);    m[nrl][ncl] -= nll;
         printf("\n");    for (j=ncl+1; j<=nch; j++) 
 #endif      m[nrl][j]=m[nrl][j-1]+nlay;
       }    
     }    for (i=nrl+1; i<=nrh; i++) {
   }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 }      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
 /**** Prevalence limit ****************/    }
     return m; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    /*  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)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    */
      matrix by transitions matrix until convergence is reached */  }
   
   int i, ii,j,k;  /*************************free ma3x ************************/
   double min, max, maxmin, maxmax,sumnew=0.;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double **matprod2();  {
   double **out, cov[NCOVMAX], **pmij();    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double **newm;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double agefin, delaymax=50 ; /* Max number of years to converge */    free((FREE_ARG)(m+nrl-NR_END));
   }
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  /*************** function subdirf ***********/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char *subdirf(char fileres[])
     }  {
     /* Caution optionfilefiname is hidden */
    cov[1]=1.;    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/"); /* Add to the right */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,fileres);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    return tmpout;
     newm=savm;  }
     /* Covariates have to be included here again */  
      cov[2]=agefin;  /*************** function subdirf2 ***********/
    char *subdirf2(char fileres[], char *preop)
       for (k=1; k<=cptcovn;k++) {  {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];    
     /* Caution optionfilefiname is hidden */
 /*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
       for (k=1; k<=cptcovage;k++)    strcat(tmpout,preop);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcat(tmpout,fileres);
        return tmpout;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   
     savm=oldm;  /*************** function subdirf3 ***********/
     oldm=newm;  char *subdirf3(char fileres[], char *preop, char *preop2)
     maxmax=0.;  {
     for(j=1;j<=nlstate;j++){    
       min=1.;    /* Caution optionfilefiname is hidden */
       max=0.;    strcpy(tmpout,optionfilefiname);
       for(i=1; i<=nlstate; i++) {    strcat(tmpout,"/");
         sumnew=0;    strcat(tmpout,preop);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    strcat(tmpout,preop2);
         prlim[i][j]= newm[i][j]/(1-sumnew);    strcat(tmpout,fileres);
         max=FMAX(max,prlim[i][j]);    return tmpout;
         min=FMIN(min,prlim[i][j]);  }
       }  
       maxmin=max-min;  /***************** f1dim *************************/
       maxmax=FMAX(maxmax,maxmin);  extern int ncom; 
     }  extern double *pcom,*xicom;
     if(maxmax < ftolpl){  extern double (*nrfunc)(double []); 
       return prlim;   
     }  double f1dim(double x) 
   }  { 
 }    int j; 
     double f;
 /*************** transition probabilities **********/    double *xt; 
    
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    xt=vector(1,ncom); 
 {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double s1, s2;    f=(*nrfunc)(xt); 
   /*double t34;*/    free_vector(xt,1,ncom); 
   int i,j,j1, nc, ii, jj;    return f; 
   } 
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;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 += param[i][j][nc]*cov[nc];*/  { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int iter; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    double a,b,d,etemp;
       }    double fu,fv,fw,fx;
       ps[i][j]=s2;    double ftemp;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     }    double e=0.0; 
     for(j=i+1; j<=nlstate+ndeath;j++){   
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    a=(ax < cx ? ax : cx); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    b=(ax > cx ? ax : cx); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    x=w=v=bx; 
       }    fw=fv=fx=(*f)(x); 
       ps[i][j]=s2;    for (iter=1;iter<=ITMAX;iter++) { 
     }      xm=0.5*(a+b); 
   }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for(i=1; i<= nlstate; i++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      s1=0;      printf(".");fflush(stdout);
     for(j=1; j<i; j++)      fprintf(ficlog,".");fflush(ficlog);
       s1+=exp(ps[i][j]);  #ifdef DEBUG
     for(j=i+1; j<=nlstate+ndeath; j++)      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       s1+=exp(ps[i][j]);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     ps[i][i]=1./(s1+1.);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(j=1; j<i; j++)  #endif
       ps[i][j]= exp(ps[i][j])*ps[i][i];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for(j=i+1; j<=nlstate+ndeath; j++)        *xmin=x; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        return fx; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      } 
   } /* end i */      ftemp=fu;
       if (fabs(e) > tol1) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        r=(x-w)*(fx-fv); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        q=(x-v)*(fx-fw); 
       ps[ii][jj]=0;        p=(x-v)*q-(x-w)*r; 
       ps[ii][ii]=1;        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
   }        q=fabs(q); 
         etemp=e; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        e=d; 
     for(jj=1; jj<= nlstate+ndeath; jj++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
      printf("%lf ",ps[ii][jj]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
    }        else { 
     printf("\n ");          d=p/q; 
     }          u=x+d; 
     printf("\n ");printf("%lf ",cov[2]);*/          if (u-a < tol2 || b-u < tol2) 
 /*            d=SIGN(tol1,xm-x); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        } 
   goto end;*/      } else { 
     return ps;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 }      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 /**************** Product of 2 matrices ******************/      fu=(*f)(u); 
       if (fu <= fx) { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        if (u >= x) a=x; else b=x; 
 {        SHFT(v,w,x,u) 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          SHFT(fv,fw,fx,fu) 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          } else { 
   /* in, b, out are matrice of pointers which should have been initialized            if (u < x) a=u; else b=u; 
      before: only the contents of out is modified. The function returns            if (fu <= fw || w == x) { 
      a pointer to pointers identical to out */              v=w; 
   long i, j, k;              w=u; 
   for(i=nrl; i<= nrh; i++)              fv=fw; 
     for(k=ncolol; k<=ncoloh; k++)              fw=fu; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)            } else if (fu <= fv || v == x || v == w) { 
         out[i][k] +=in[i][j]*b[j][k];              v=u; 
               fv=fu; 
   return out;            } 
 }          } 
     } 
     nrerror("Too many iterations in brent"); 
 /************* Higher Matrix Product ***************/    *xmin=x; 
     return fx; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  } 
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /****************** mnbrak ***********************/
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step              double (*func)(double)) 
      (typically every 2 years instead of every month which is too big).  { 
      Model is determined by parameters x and covariates have to be    double ulim,u,r,q, dum;
      included manually here.    double fu; 
    
      */    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
   int i, j, d, h, k;    if (*fb > *fa) { 
   double **out, cov[NCOVMAX];      SHFT(dum,*ax,*bx,dum) 
   double **newm;        SHFT(dum,*fb,*fa,dum) 
         } 
   /* Hstepm could be zero and should return the unit matrix */    *cx=(*bx)+GOLD*(*bx-*ax); 
   for (i=1;i<=nlstate+ndeath;i++)    *fc=(*func)(*cx); 
     for (j=1;j<=nlstate+ndeath;j++){    while (*fb > *fc) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      r=(*bx-*ax)*(*fb-*fc); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      q=(*bx-*cx)*(*fb-*fa); 
     }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for(h=1; h <=nhstepm; h++){      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     for(d=1; d <=hstepm; d++){      if ((*bx-u)*(u-*cx) > 0.0) { 
       newm=savm;        fu=(*func)(u); 
       /* Covariates have to be included here again */      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       cov[1]=1.;        fu=(*func)(u); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        if (fu < *fc) { 
       if (cptcovn>0){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        u=ulim; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        fu=(*func)(u); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      } else { 
       savm=oldm;        u=(*cx)+GOLD*(*cx-*bx); 
       oldm=newm;        fu=(*func)(u); 
     }      } 
     for(i=1; i<=nlstate+ndeath; i++)      SHFT(*ax,*bx,*cx,u) 
       for(j=1;j<=nlstate+ndeath;j++) {        SHFT(*fa,*fb,*fc,fu) 
         po[i][j][h]=newm[i][j];        } 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  } 
          */  
       }  /*************** linmin ************************/
   } /* end h */  
   return po;  int ncom; 
 }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
    
 /*************** log-likelihood *************/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 double func( double *x)  { 
 {    double brent(double ax, double bx, double cx, 
   int i, ii, j, k, mi, d, kk;                 double (*f)(double), double tol, double *xmin); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double f1dim(double x); 
   double **out;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double sw; /* Sum of weights */                double *fc, double (*func)(double)); 
   double lli; /* Individual log likelihood */    int j; 
   long ipmx;    double xx,xmin,bx,ax; 
   /*extern weight */    double fx,fb,fa;
   /* We are differentiating ll according to initial status */   
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    ncom=n; 
   /*for(i=1;i<imx;i++)    pcom=vector(1,n); 
 printf(" %d\n",s[4][i]);    xicom=vector(1,n); 
   */    nrfunc=func; 
   cov[1]=1.;    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      xicom[j]=xi[j]; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    } 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    ax=0.0; 
        for(mi=1; mi<= wav[i]-1; mi++){    xx=1.0; 
       for (ii=1;ii<=nlstate+ndeath;ii++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
             for(d=0; d<dh[mi][i]; d++){  #ifdef DEBUG
               newm=savm;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               for (kk=1; kk<=cptcovage;kk++) {  #endif
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    for (j=1;j<=n;j++) { 
                  /*printf("%d %d",kk,Tage[kk]);*/      xi[j] *= xmin; 
               }      p[j] += xi[j]; 
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/    } 
               /*cov[3]=pow(cov[2],2)/1000.;*/    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  } 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
           savm=oldm;  char *asc_diff_time(long time_sec, char ascdiff[])
           oldm=newm;  {
     long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
       } /* end mult */    sec_left = (time_sec) % (60*60*24);
        hours = (sec_left) / (60*60) ;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    sec_left = (sec_left) %(60*60);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    minutes = (sec_left) /60;
       ipmx +=1;    sec_left = (sec_left) % (60);
       sw += weight[i];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    return ascdiff;
     } /* end of wave */  }
   } /* end of individual */  
   /*************** powell ************************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */              double (*func)(double [])) 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  { 
   return -l;    void linmin(double p[], double xi[], int n, double *fret, 
 }                double (*func)(double [])); 
     int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 /*********** Maximum Likelihood Estimation ***************/    double fp,fptt;
     double *xits;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    int niterf, itmp;
 {  
   int i,j, iter;    pt=vector(1,n); 
   double **xi,*delti;    ptt=vector(1,n); 
   double fret;    xit=vector(1,n); 
   xi=matrix(1,npar,1,npar);    xits=vector(1,n); 
   for (i=1;i<=npar;i++)    *fret=(*func)(p); 
     for (j=1;j<=npar;j++)    for (j=1;j<=n;j++) pt[j]=p[j]; 
       xi[i][j]=(i==j ? 1.0 : 0.0);    for (*iter=1;;++(*iter)) { 
   printf("Powell\n");      fp=(*fret); 
   powell(p,xi,npar,ftol,&iter,&fret,func);      ibig=0; 
       del=0.0; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      last_time=curr_time;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));      (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);
 }      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 /**** Computes Hessian and covariance matrix ***/      */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))     for (i=1;i<=n;i++) {
 {        printf(" %d %.12f",i, p[i]);
   double  **a,**y,*x,pd;        fprintf(ficlog," %d %.12lf",i, p[i]);
   double **hess;        fprintf(ficrespow," %.12lf", p[i]);
   int i, j,jk;      }
   int *indx;      printf("\n");
       fprintf(ficlog,"\n");
   double hessii(double p[], double delta, int theta, double delti[]);      fprintf(ficrespow,"\n");fflush(ficrespow);
   double hessij(double p[], double delti[], int i, int j);      if(*iter <=3){
   void lubksb(double **a, int npar, int *indx, double b[]) ;        tm = *localtime(&curr_time.tv_sec);
   void ludcmp(double **a, int npar, int *indx, double *d) ;        strcpy(strcurr,asctime(&tm));
   /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
   hess=matrix(1,npar,1,npar);        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   printf("\nCalculation of the hessian matrix. Wait...\n");          strcurr[itmp-1]='\0';
   for (i=1;i<=npar;i++){        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     printf("%d",i);fflush(stdout);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     hess[i][i]=hessii(p,ftolhess,i,delti);        for(niterf=10;niterf<=30;niterf+=10){
     /*printf(" %f ",p[i]);*/          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   }          tmf = *localtime(&forecast_time.tv_sec);
   /*      asctime_r(&tmf,strfor); */
   for (i=1;i<=npar;i++) {          strcpy(strfor,asctime(&tmf));
     for (j=1;j<=npar;j++)  {          itmp = strlen(strfor);
       if (j>i) {          if(strfor[itmp-1]=='\n')
         printf(".%d%d",i,j);fflush(stdout);          strfor[itmp-1]='\0';
         hess[i][j]=hessij(p,delti,i,j);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         hess[j][i]=hess[i][j];          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }        }
     }      }
   }      for (i=1;i<=n;i++) { 
   printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  #ifdef DEBUG
          printf("fret=%lf \n",*fret);
   a=matrix(1,npar,1,npar);        fprintf(ficlog,"fret=%lf \n",*fret);
   y=matrix(1,npar,1,npar);  #endif
   x=vector(1,npar);        printf("%d",i);fflush(stdout);
   indx=ivector(1,npar);        fprintf(ficlog,"%d",i);fflush(ficlog);
   for (i=1;i<=npar;i++)        linmin(p,xit,n,fret,func); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        if (fabs(fptt-(*fret)) > del) { 
   ludcmp(a,npar,indx,&pd);          del=fabs(fptt-(*fret)); 
           ibig=i; 
   for (j=1;j<=npar;j++) {        } 
     for (i=1;i<=npar;i++) x[i]=0;  #ifdef DEBUG
     x[j]=1;        printf("%d %.12e",i,(*fret));
     lubksb(a,npar,indx,x);        fprintf(ficlog,"%d %.12e",i,(*fret));
     for (i=1;i<=npar;i++){        for (j=1;j<=n;j++) {
       matcov[i][j]=x[i];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     }          printf(" x(%d)=%.12e",j,xit[j]);
   }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   printf("\n#Hessian matrix#\n");        for(j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) {          printf(" p=%.12e",p[j]);
     for (j=1;j<=npar;j++) {          fprintf(ficlog," p=%.12e",p[j]);
       printf("%.3e ",hess[i][j]);        }
     }        printf("\n");
     printf("\n");        fprintf(ficlog,"\n");
   }  #endif
       } 
   /* Recompute Inverse */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        int k[2],l;
   ludcmp(a,npar,indx,&pd);        k[0]=1;
         k[1]=-1;
   /*  printf("\n#Hessian matrix recomputed#\n");        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (j=1;j<=npar;j++) {        for (j=1;j<=n;j++) {
     for (i=1;i<=npar;i++) x[i]=0;          printf(" %.12e",p[j]);
     x[j]=1;          fprintf(ficlog," %.12e",p[j]);
     lubksb(a,npar,indx,x);        }
     for (i=1;i<=npar;i++){        printf("\n");
       y[i][j]=x[i];        fprintf(ficlog,"\n");
       printf("%.3e ",y[i][j]);        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
     printf("\n");            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   */            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(a,1,npar,1,npar);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   free_matrix(y,1,npar,1,npar);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   free_vector(x,1,npar);        }
   free_ivector(indx,1,npar);  #endif
   free_matrix(hess,1,npar,1,npar);  
   
         free_vector(xit,1,n); 
 }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 /*************** hessian matrix ****************/        free_vector(pt,1,n); 
 double hessii( double x[], double delta, int theta, double delti[])        return; 
 {      } 
   int i;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   int l=1, lmax=20;      for (j=1;j<=n;j++) { 
   double k1,k2;        ptt[j]=2.0*p[j]-pt[j]; 
   double p2[NPARMAX+1];        xit[j]=p[j]-pt[j]; 
   double res;        pt[j]=p[j]; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      } 
   double fx;      fptt=(*func)(ptt); 
   int k=0,kmax=10;      if (fptt < fp) { 
   double l1;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   fx=func(x);          linmin(p,xit,n,fret,func); 
   for (i=1;i<=npar;i++) p2[i]=x[i];          for (j=1;j<=n;j++) { 
   for(l=0 ; l <=lmax; l++){            xi[j][ibig]=xi[j][n]; 
     l1=pow(10,l);            xi[j][n]=xit[j]; 
     delts=delt;          }
     for(k=1 ; k <kmax; k=k+1){  #ifdef DEBUG
       delt = delta*(l1*k);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       p2[theta]=x[theta] +delt;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       k1=func(p2)-fx;          for(j=1;j<=n;j++){
       p2[theta]=x[theta]-delt;            printf(" %.12e",xit[j]);
       k2=func(p2)-fx;            fprintf(ficlog," %.12e",xit[j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */          }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          printf("\n");
                fprintf(ficlog,"\n");
 #ifdef DEBUG  #endif
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        }
 #endif      } 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    } 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  } 
         k=kmax;  
       }  /**** Prevalence limit (stable prevalence)  ****************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         delts=delt;       matrix by transitions matrix until convergence is reached */
       }  
     }    int i, ii,j,k;
   }    double min, max, maxmin, maxmax,sumnew=0.;
   delti[theta]=delts;    double **matprod2();
   return res;    double **out, cov[NCOVMAX], **pmij();
      double **newm;
 }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
 double hessij( double x[], double delti[], int thetai,int thetaj)    for (ii=1;ii<=nlstate+ndeath;ii++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   int i;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int l=1, l1, lmax=20;      }
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];     cov[1]=1.;
   int k;   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fx=func(x);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for (k=1; k<=2; k++) {      newm=savm;
     for (i=1;i<=npar;i++) p2[i]=x[i];      /* Covariates have to be included here again */
     p2[thetai]=x[thetai]+delti[thetai]/k;       cov[2]=agefin;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    
     k1=func(p2)-fx;        for (k=1; k<=cptcovn;k++) {
            cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetai]=x[thetai]+delti[thetai]/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]]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k2=func(p2)-fx;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
          /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetai]=x[thetai]-delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      savm=oldm;
 #ifdef DEBUG      oldm=newm;
     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);      maxmax=0.;
 #endif      for(j=1;j<=nlstate;j++){
   }        min=1.;
   return res;        max=0.;
 }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
 /************** Inverse of matrix **************/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 void ludcmp(double **a, int n, int *indx, double *d)          prlim[i][j]= newm[i][j]/(1-sumnew);
 {          max=FMAX(max,prlim[i][j]);
   int i,imax,j,k;          min=FMIN(min,prlim[i][j]);
   double big,dum,sum,temp;        }
   double *vv;        maxmin=max-min;
          maxmax=FMAX(maxmax,maxmin);
   vv=vector(1,n);      }
   *d=1.0;      if(maxmax < ftolpl){
   for (i=1;i<=n;i++) {        return prlim;
     big=0.0;      }
     for (j=1;j<=n;j++)    }
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /*************** transition probabilities ***************/ 
   }  
   for (j=1;j<=n;j++) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    double s1, s2;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    /*double t34;*/
       a[i][j]=sum;    int i,j,j1, nc, ii, jj;
     }  
     big=0.0;      for(i=1; i<= nlstate; i++){
     for (i=j;i<=n;i++) {        for(j=1; j<i;j++){
       sum=a[i][j];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<j;k++)            /*s2 += param[i][j][nc]*cov[nc];*/
         sum -= a[i][k]*a[k][j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       a[i][j]=sum;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       if ( (dum=vv[i]*fabs(sum)) >= big) {          }
         big=dum;          ps[i][j]=s2;
         imax=i;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       }        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
     if (j != imax) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<=n;k++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         dum=a[imax][k];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         a[imax][k]=a[j][k];          }
         a[j][k]=dum;          ps[i][j]=s2;
       }        }
       *d = -(*d);      }
       vv[imax]=vv[j];      /*ps[3][2]=1;*/
     }      
     indx[j]=imax;      for(i=1; i<= nlstate; i++){
     if (a[j][j] == 0.0) a[j][j]=TINY;        s1=0;
     if (j != n) {        for(j=1; j<i; j++)
       dum=1.0/(a[j][j]);          s1+=exp(ps[i][j]);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(j=i+1; j<=nlstate+ndeath; j++)
     }          s1+=exp(ps[i][j]);
   }        ps[i][i]=1./(s1+1.);
   free_vector(vv,1,n);  /* Doesn't work */        for(j=1; j<i; j++)
 ;          ps[i][j]= exp(ps[i][j])*ps[i][i];
 }        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
 void lubksb(double **a, int n, int *indx, double b[])        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {      } /* end i */
   int i,ii=0,ip,j;      
   double sum;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
          for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=n;i++) {          ps[ii][jj]=0;
     ip=indx[i];          ps[ii][ii]=1;
     sum=b[ip];        }
     b[ip]=b[i];      }
     if (ii)      
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     b[i]=sum;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   }  /*         printf("ddd %lf ",ps[ii][jj]); */
   for (i=n;i>=1;i--) {  /*       } */
     sum=b[i];  /*       printf("\n "); */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*        } */
     b[i]=sum/a[i][i];  /*        printf("\n ");printf("%lf ",cov[2]); */
   }         /*
 }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
 /************ Frequencies ********************/      return ps;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  }
 {  /* Some frequencies */  
    /**************** Product of 2 matrices ******************/
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double *pp;  {
   double pos;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   FILE *ficresp;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   char fileresp[FILENAMELENGTH];    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
   pp=vector(1,nlstate);       a pointer to pointers identical to out */
     long i, j, k;
   strcpy(fileresp,"p");    for(i=nrl; i<= nrh; i++)
   strcat(fileresp,fileres);      for(k=ncolol; k<=ncoloh; k++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     printf("Problem with prevalence resultfile: %s\n", fileresp);          out[i][k] +=in[i][j]*b[j][k];
     exit(0);  
   }    return out;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  
   
   j=cptcovn;  /************* Higher Matrix Product ***************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   for(k1=1; k1<=j;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    /* Computes the transition matrix starting at age 'age' over 
        j1++;       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         for (i=-1; i<=nlstate+ndeath; i++)         nhstepm*hstepm matrices. 
          for (jk=-1; jk<=nlstate+ndeath; jk++)         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
            for(m=agemin; m <= agemax+3; m++)       (typically every 2 years instead of every month which is too big 
              freq[i][jk][m]=0;       for the memory).
               Model is determined by parameters x and covariates have to be 
        for (i=1; i<=imx; i++) {       included manually here. 
          bool=1;  
          if  (cptcovn>0) {       */
            for (z1=1; z1<=cptcovn; z1++)  
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;    int i, j, d, h, k;
          }    double **out, cov[NCOVMAX];
           if (bool==1) {    double **newm;
            for(m=firstpass; m<=lastpass-1; m++){  
              if(agev[m][i]==0) agev[m][i]=agemax+1;    /* Hstepm could be zero and should return the unit matrix */
              if(agev[m][i]==1) agev[m][i]=agemax+2;    for (i=1;i<=nlstate+ndeath;i++)
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for (j=1;j<=nlstate+ndeath;j++){
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        oldm[i][j]=(i==j ? 1.0 : 0.0);
            }        po[i][j][0]=(i==j ? 1.0 : 0.0);
          }      }
        }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         if  (cptcovn>0) {    for(h=1; h <=nhstepm; h++){
          fprintf(ficresp, "\n#Variable");      for(d=1; d <=hstepm; d++){
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);        newm=savm;
        }        /* Covariates have to be included here again */
        fprintf(ficresp, "\n#");        cov[1]=1.;
        for(i=1; i<=nlstate;i++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        fprintf(ficresp, "\n");        for (k=1; k<=cptcovage;k++)
                  cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for (k=1; k<=cptcovprod;k++)
     if(i==(int)agemax+3)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf("Total");  
     else  
       printf("Age %d", i);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for(jk=1; jk <=nlstate ; jk++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         pp[jk] += freq[jk][m][i];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){        oldm=newm;
       for(m=-1, pos=0; m <=0 ; m++)      }
         pos += freq[jk][m][i];      for(i=1; i<=nlstate+ndeath; i++)
       if(pp[jk]>=1.e-10)        for(j=1;j<=nlstate+ndeath;j++) {
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          po[i][j][h]=newm[i][j];
       else          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);           */
     }        }
     for(jk=1; jk <=nlstate ; jk++){    } /* end h */
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    return po;
         pp[jk] += freq[jk][m][i];  }
     }  
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];  /*************** log-likelihood *************/
     for(jk=1; jk <=nlstate ; jk++){  double func( double *x)
       if(pos>=1.e-5)  {
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    int i, ii, j, k, mi, d, kk;
       else    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double **out;
       if( i <= (int) agemax){    double sw; /* Sum of weights */
         if(pos>=1.e-5)    double lli; /* Individual log likelihood */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    int s1, s2;
       else    double bbh, survp;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    long ipmx;
       }    /*extern weight */
     }    /* We are differentiating ll according to initial status */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for(m=-1; m <=nlstate+ndeath; m++)    /*for(i=1;i<imx;i++) 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      printf(" %d\n",s[4][i]);
     if(i <= (int) agemax)    */
       fprintf(ficresp,"\n");    cov[1]=1.;
     printf("\n");  
     }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
  }    if(mle==1){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fclose(ficresp);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(mi=1; mi<= wav[i]-1; mi++){
   free_vector(pp,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 }  /* End of Freq */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************* Waves Concatenation ***************/            }
           for(d=0; d<dh[mi][i]; d++){
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for (kk=1; kk<=cptcovage;kk++) {
      Death is a valid wave (if date is known).              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      and mw[mi+1][i]. dh depends on stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      */            savm=oldm;
             oldm=newm;
   int i, mi, m;          } /* end mult */
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        
 float sum=0.;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
   for(i=1; i<=imx; i++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     mi=0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     m=firstpass;           * the nearest (and in case of equal distance, to the lowest) interval but now
     while(s[m][i] <= nlstate){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       if(s[m][i]>=1)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         mw[++mi][i]=m;           * probability in order to take into account the bias as a fraction of the way
       if(m >=lastpass)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         break;           * -stepm/2 to stepm/2 .
       else           * For stepm=1 the results are the same as for previous versions of Imach.
         m++;           * For stepm > 1 the results are less biased than in previous versions. 
     }/* end while */           */
     if (s[m][i] > nlstate){          s1=s[mw[mi][i]][i];
       mi++;     /* Death is another wave */          s2=s[mw[mi+1][i]][i];
       /* if(mi==0)  never been interviewed correctly before death */          bbh=(double)bh[mi][i]/(double)stepm; 
          /* Only death is a correct wave */          /* bias bh is positive if real duration
       mw[mi][i]=m;           * 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]));*/
     wav[i]=mi;          if( s2 > nlstate){ 
     if(mi==0)            /* i.e. if s2 is a death state and if the date of death is known 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);               then the contribution to the likelihood is the probability to 
   }               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
   for(i=1; i<=imx; i++){               minus probability to die before dh-stepm . 
     for(mi=1; mi<wav[i];mi++){               In version up to 0.92 likelihood was computed
       if (stepm <=0)          as if date of death was unknown. Death was treated as any other
         dh[mi][i]=1;          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
         if (s[mw[mi+1][i]][i] > nlstate) {          to consider that at each interview the state was recorded
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          (healthy, disable or death) and IMaCh was corrected; but when we
           if(j=0) j=1;  /* Survives at least one month after exam */          introduced the exact date of death then we should have modified
         }          the contribution of an exact death to the likelihood. This new
         else{          contribution is smaller and very dependent of the step unit
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          stepm. It is no more the probability to die between last interview
           k=k+1;          and month of death but the probability to survive from last
           if (j >= jmax) jmax=j;          interview up to one month before death multiplied by the
           else if (j <= jmin)jmin=j;          probability to die within a month. Thanks to Chris
           sum=sum+j;          Jackson for correcting this bug.  Former versions increased
         }          mortality artificially. The bad side is that we add another loop
         jk= j/stepm;          which slows down the processing. The difference can be up to 10%
         jl= j -jk*stepm;          lower mortality.
         ju= j -(jk+1)*stepm;            */
         if(jl <= -ju)            lli=log(out[s1][s2] - savm[s1][s2]);
           dh[mi][i]=jk;  
         else  
           dh[mi][i]=jk+1;          } else if  (s2==-2) {
         if(dh[mi][i]==0)            for (j=1,survp=0. ; j<=nlstate; j++) 
           dh[mi][i]=1; /* At least one step */              survp += out[s1][j];
       }            lli= survp;
     }          }
   }          
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);          else if  (s2==-4) {
 }            for (j=3,survp=0. ; j<=nlstate; j++) 
 /*********** Tricode ****************************/              survp += out[s1][j];
 void tricode(int *Tvar, int **nbcode, int imx)            lli= survp;
 {          }
   int Ndum[80],ij=1, k, j, i, Ntvar[20];          
   int cptcode=0;          else if  (s2==-5) {
   for (k=0; k<79; k++) Ndum[k]=0;            for (j=1,survp=0. ; j<=2; j++) 
   for (k=1; k<=7; k++) ncodemax[k]=0;              survp += out[s1][j];
             lli= survp;
   for (j=1; j<=cptcovn; j++) {          }
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;          else{
       if (ij > cptcode) cptcode=ij;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/          } 
     for (i=0; i<=cptcode; i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if(Ndum[i]!=0) ncodemax[j]++;          /*if(lli ==000.0)*/
     }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
     ij=1;          sw += weight[i];
     for (i=1; i<=ncodemax[j]; i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (k=0; k<=79; k++) {        } /* end of wave */
         if (Ndum[k] != 0) {      } /* end of individual */
           nbcode[Tvar[j]][ij]=k;    }  else if(mle==2){
           ij++;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if (ij > ncodemax[j]) break;        for(mi=1; mi<= wav[i]-1; mi++){
       }            for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
   }                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<=dh[mi][i]; d++){
 /*********** Health Expectancies ****************/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /* Health expectancies */            }
   int i, j, nhstepm, hstepm, h;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double age, agelim,hf;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***p3mat;            savm=oldm;
              oldm=newm;
   fprintf(ficreseij,"# Health expectancies\n");          } /* end mult */
   fprintf(ficreseij,"# Age");        
   for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
     for(j=1; j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
       fprintf(ficreseij," %1d-%1d",i,j);          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficreseij,"\n");          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;
   hstepm=1*YEARM; /*  Every j years of age (in month) */          sw += weight[i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   agelim=AGESUP;      } /* end of individual */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }  else if(mle==3){  /* exponential inter-extrapolation */
     /* nhstepm age range expressed in number of stepm */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     /* Typically if 20 years = 20*12/6=40 stepm */        for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) hstepm=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            for (j=1;j<=nlstate+ndeath;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              savm[ii][j]=(ii==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1; i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<=nlstate;j++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            }
           eij[i][j][(int)age] +=p3mat[i][j][h];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
     hf=1;            oldm=newm;
     if (stepm >= YEARM) hf=stepm/YEARM;          } /* end mult */
     fprintf(ficreseij,"%.0f",age );        
     for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
       for(j=1; j<=nlstate;j++){          s2=s[mw[mi+1][i]][i];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          bbh=(double)bh[mi][i]/(double)stepm; 
       }          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 */
     fprintf(ficreseij,"\n");          ipmx +=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }        } /* end of wave */
       } /* end of individual */
 /************ Variance ******************/    }else if (mle==4){  /* ml=4 no inter-extrapolation */
 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)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* Variance of health expectancies */        for(mi=1; mi<= wav[i]-1; mi++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **newm;            for (j=1;j<=nlstate+ndeath;j++){
   double **dnewm,**doldm;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k, cptcode;            }
    double *xp;          for(d=0; d<dh[mi][i]; d++){
   double **gp, **gm;            newm=savm;
   double ***gradg, ***trgradg;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***p3mat;            for (kk=1; kk<=cptcovage;kk++) {
   double age,agelim;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int theta;            }
           
    fprintf(ficresvij,"# Covariances of life expectancies\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficresvij,"# Age");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=nlstate;i++)            savm=oldm;
     for(j=1; j<=nlstate;j++)            oldm=newm;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          } /* end mult */
   fprintf(ficresvij,"\n");        
           s1=s[mw[mi][i]][i];
   xp=vector(1,npar);          s2=s[mw[mi+1][i]][i];
   dnewm=matrix(1,nlstate,1,npar);          if( s2 > nlstate){ 
   doldm=matrix(1,nlstate,1,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
   hstepm=1*YEARM; /* Every year of age */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          }
   agelim = AGESUP;          ipmx +=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          sw += weight[i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (stepm >= YEARM) hstepm=1;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        } /* end of wave */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end of individual */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     gp=matrix(0,nhstepm,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gm=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(theta=1; theta <=npar; theta++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (j=1;j<=nlstate+ndeath;j++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<= nlstate; j++){            newm=savm;
         for(h=0; h<=nhstepm; h++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
       }          
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=npar; i++) /* Computes gradient */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            savm=oldm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              oldm=newm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          } /* end mult */
       for(j=1; j<= nlstate; j++){        
         for(h=0; h<=nhstepm; h++){          s1=s[mw[mi][i]][i];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          ipmx +=1;
       }          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]);*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        } /* end of wave */
         }      } /* end of individual */
     } /* End theta */    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(h=0; h<=nhstepm; h++)    return -l;
       for(j=1; j<=nlstate;j++)  }
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  /*************** log-likelihood *************/
   double funcone( double *x)
     for(i=1;i<=nlstate;i++)  {
       for(j=1;j<=nlstate;j++)    /* Same as likeli but slower because of a lot of printf and if */
         vareij[i][j][(int)age] =0.;    int i, ii, j, k, mi, d, kk;
     for(h=0;h<=nhstepm;h++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       for(k=0;k<=nhstepm;k++){    double **out;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double lli; /* Individual log likelihood */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double llt;
         for(i=1;i<=nlstate;i++)    int s1, s2;
           for(j=1;j<=nlstate;j++)    double bbh, survp;
             vareij[i][j][(int)age] += doldm[i][j];    /*extern weight */
       }    /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     h=1;    /*for(i=1;i<imx;i++) 
     if (stepm >= YEARM) h=stepm/YEARM;      printf(" %d\n",s[4][i]);
     fprintf(ficresvij,"%.0f ",age );    */
     for(i=1; i<=nlstate;i++)    cov[1]=1.;
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }  
     fprintf(ficresvij,"\n");    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_matrix(gp,0,nhstepm,1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_matrix(gm,0,nhstepm,1,nlstate);      for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          for (j=1;j<=nlstate+ndeath;j++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* End age */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
   free_vector(xp,1,npar);        for(d=0; d<dh[mi][i]; d++){
   free_matrix(doldm,1,nlstate,1,npar);          newm=savm;
   free_matrix(dnewm,1,nlstate,1,nlstate);          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];
           }
 /************ Variance of prevlim ******************/          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 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)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {          savm=oldm;
   /* Variance of prevalence limit */          oldm=newm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        } /* end mult */
   double **newm;        
   double **dnewm,**doldm;        s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm;        s2=s[mw[mi+1][i]][i];
   int k, cptcode;        bbh=(double)bh[mi][i]/(double)stepm; 
   double *xp;        /* bias is positive if real duration
   double *gp, *gm;         * is higher than the multiple of stepm and negative otherwise.
   double **gradg, **trgradg;         */
   double age,agelim;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   int theta;          lli=log(out[s1][s2] - savm[s1][s2]);
            } else if (mle==1){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   fprintf(ficresvpl,"# Age");        } else if(mle==2){
   for(i=1; i<=nlstate;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 */
       fprintf(ficresvpl," %1d-%1d",i,i);        } else if(mle==3){  /* exponential inter-extrapolation */
   fprintf(ficresvpl,"\n");          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
   xp=vector(1,npar);          lli=log(out[s1][s2]); /* Original formula */
   dnewm=matrix(1,nlstate,1,npar);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   doldm=matrix(1,nlstate,1,nlstate);          lli=log(out[s1][s2]); /* Original formula */
          } /* End of if */
   hstepm=1*YEARM; /* Every year of age */        ipmx +=1;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        sw += weight[i];
   agelim = AGESUP;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  /*       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]); */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if(globpr){
     if (stepm >= YEARM) hstepm=1;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   %10.6f %10.6f %10.6f ", \
     gradg=matrix(1,npar,1,nlstate);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     gp=vector(1,nlstate);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     gm=vector(1,nlstate);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
     for(theta=1; theta <=npar; theta++){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(i=1; i<=npar; i++){ /* Computes gradient */          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } /* end of wave */
       for(i=1;i<=nlstate;i++)    } /* end of individual */
         gp[i] = prlim[i][i];    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);    if(globpr==0){ /* First time we count the contributions and weights */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      gipmx=ipmx;
       for(i=1;i<=nlstate;i++)      gsw=sw;
         gm[i] = prlim[i][i];    }
     return -l;
       for(i=1;i<=nlstate;i++)  }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */  
   /*************** function likelione ***********/
     trgradg =matrix(1,nlstate,1,npar);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     for(j=1; j<=nlstate;j++)    /* This routine should help understanding what is done with 
       for(theta=1; theta <=npar; theta++)       the selection of individuals/waves and
         trgradg[j][theta]=gradg[theta][j];       to check the exact contribution to the likelihood.
        Plotting could be done.
     for(i=1;i<=nlstate;i++)     */
       varpl[i][(int)age] =0.;    int k;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    if(*globpri !=0){ /* Just counts and sums, no printings */
     for(i=1;i<=nlstate;i++)      strcpy(fileresilk,"ilk"); 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     fprintf(ficresvpl,"%.0f ",age );        printf("Problem with resultfile: %s\n", fileresilk);
     for(i=1; i<=nlstate;i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      }
     fprintf(ficresvpl,"\n");      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");
     free_vector(gp,1,nlstate);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     free_vector(gm,1,nlstate);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     free_matrix(gradg,1,npar,1,nlstate);      for(k=1; k<=nlstate; k++) 
     free_matrix(trgradg,1,nlstate,1,npar);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   } /* End age */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    *fretone=(*funcone)(p);
   free_matrix(dnewm,1,nlstate,1,nlstate);    if(*globpri !=0){
       fclose(ficresilk);
 }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     } 
     return;
 /***********************************************/  }
 /**************** Main Program *****************/  
 /***********************************************/  
   /*********** Maximum Likelihood Estimation ***************/
 /*int main(int argc, char *argv[])*/  
 int main()  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
     int i,j, iter;
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;    double **xi;
   double agedeb, agefin,hf;    double fret;
   double agemin=1.e20, agemax=-1.e20;    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   double fret;    xi=matrix(1,npar,1,npar);
   double **xi,tmp,delta;    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   double dum; /* Dummy variable */        xi[i][j]=(i==j ? 1.0 : 0.0);
   double ***p3mat;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int *indx;    strcpy(filerespow,"pow"); 
   char line[MAXLINE], linepar[MAXLINE];    strcat(filerespow,fileres);
   char title[MAXLINE];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      printf("Problem with resultfile: %s\n", filerespow);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   char filerest[FILENAMELENGTH];    }
   char fileregp[FILENAMELENGTH];    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    for (i=1;i<=nlstate;i++)
   int firstobs=1, lastobs=10;      for(j=1;j<=nlstate+ndeath;j++)
   int sdeb, sfin; /* Status at beginning and end */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   int c,  h , cpt,l;    fprintf(ficrespow,"\n");
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;    powell(p,xi,npar,ftol,&iter,&fret,func);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
      fclose(ficrespow);
   int hstepm, nhstepm;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double bage, fage, age, agelim, agebase;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double ftolpl=FTOL;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **prlim;  
   double *severity;  }
   double ***param; /* Matrix of parameters */  
   double  *p;  /**** Computes Hessian and covariance matrix ***/
   double **matcov; /* Matrix of covariance */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double ***delti3; /* Scale */  {
   double *delti; /* Scale */    double  **a,**y,*x,pd;
   double ***eij, ***vareij;    double **hess;
   double **varpl; /* Variances of prevalence limits by age */    int i, j,jk;
   double *epj, vepp;    int *indx;
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   char z[1]="c", occ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
 #include <sys/time.h>    void ludcmp(double **a, int npar, int *indx, double *d) ;
 #include <time.h>    double gompertz(double p[]);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    hess=matrix(1,npar,1,npar);
   /* long total_usecs;  
   struct timeval start_time, end_time;    printf("\nCalculation of the hessian matrix. Wait...\n");
      fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
   printf("\nIMACH, Version 0.64a");     
   printf("\nEnter the parameter file name: ");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
 #ifdef windows      /*  printf(" %f ",p[i]);
   scanf("%s",pathtot);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   getcwd(pathcd, size);    }
   /*cygwin_split_path(pathtot,path,optionfile);    
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for (i=1;i<=npar;i++) {
   /* cutv(path,optionfile,pathtot,'\\');*/      for (j=1;j<=npar;j++)  {
         if (j>i) { 
 split(pathtot, path,optionfile);          printf(".%d%d",i,j);fflush(stdout);
   chdir(path);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   replace(pathc,path);          hess[i][j]=hessij(p,delti,i,j,func,npar);
 #endif          
 #ifdef unix          hess[j][i]=hess[i][j];    
   scanf("%s",optionfile);          /*printf(" %lf ",hess[i][j]);*/
 #endif        }
       }
 /*-------- arguments in the command line --------*/    }
     printf("\n");
   strcpy(fileres,"r");    fprintf(ficlog,"\n");
   strcat(fileres, optionfile);  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /*---------arguments file --------*/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    a=matrix(1,npar,1,npar);
     printf("Problem with optionfile %s\n",optionfile);    y=matrix(1,npar,1,npar);
     goto end;    x=vector(1,npar);
   }    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
   strcpy(filereso,"o");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   strcat(filereso,fileres);    ludcmp(a,npar,indx,&pd);
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   /* Reads comments: lines beginning with '#' */      lubksb(a,npar,indx,x);
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1;i<=npar;i++){ 
     ungetc(c,ficpar);        matcov[i][j]=x[i];
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    }
     fputs(line,ficparo);  
   }    printf("\n#Hessian matrix#\n");
   ungetc(c,ficpar);    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   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);      for (j=1;j<=npar;j++) { 
   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);        printf("%.3e ",hess[i][j]);
   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);        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
   covar=matrix(0,NCOVMAX,1,n);          printf("\n");
   if (strlen(model)<=1) cptcovn=0;      fprintf(ficlog,"\n");
   else {    }
     j=0;  
     j=nbocc(model,'+');    /* Recompute Inverse */
     cptcovn=j+1;    for (i=1;i<=npar;i++)
   }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    /*  printf("\n#Hessian matrix recomputed#\n");
    
   /* Read guess parameters */    for (j=1;j<=npar;j++) {
   /* Reads comments: lines beginning with '#' */      for (i=1;i<=npar;i++) x[i]=0;
   while((c=getc(ficpar))=='#' && c!= EOF){      x[j]=1;
     ungetc(c,ficpar);      lubksb(a,npar,indx,x);
     fgets(line, MAXLINE, ficpar);      for (i=1;i<=npar;i++){ 
     puts(line);        y[i][j]=x[i];
     fputs(line,ficparo);        printf("%.3e ",y[i][j]);
   }        fprintf(ficlog,"%.3e ",y[i][j]);
   ungetc(c,ficpar);      }
        printf("\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      fprintf(ficlog,"\n");
     for(i=1; i <=nlstate; i++)    }
     for(j=1; j <=nlstate+ndeath-1; j++){    */
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);    free_matrix(a,1,npar,1,npar);
       printf("%1d%1d",i,j);    free_matrix(y,1,npar,1,npar);
       for(k=1; k<=ncovmodel;k++){    free_vector(x,1,npar);
         fscanf(ficpar," %lf",&param[i][j][k]);    free_ivector(indx,1,npar);
         printf(" %lf",param[i][j][k]);    free_matrix(hess,1,npar,1,npar);
         fprintf(ficparo," %lf",param[i][j][k]);  
       }  
       fscanf(ficpar,"\n");  }
       printf("\n");  
       fprintf(ficparo,"\n");  /*************** hessian matrix ****************/
     }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
    {
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    int i;
   p=param[1][1];    int l=1, lmax=20;
      double k1,k2;
   /* Reads comments: lines beginning with '#' */    double p2[NPARMAX+1];
   while((c=getc(ficpar))=='#' && c!= EOF){    double res;
     ungetc(c,ficpar);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     fgets(line, MAXLINE, ficpar);    double fx;
     puts(line);    int k=0,kmax=10;
     fputs(line,ficparo);    double l1;
   }  
   ungetc(c,ficpar);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for(l=0 ; l <=lmax; l++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      l1=pow(10,l);
   for(i=1; i <=nlstate; i++){      delts=delt;
     for(j=1; j <=nlstate+ndeath-1; j++){      for(k=1 ; k <kmax; k=k+1){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        delt = delta*(l1*k);
       printf("%1d%1d",i,j);        p2[theta]=x[theta] +delt;
       fprintf(ficparo,"%1d%1d",i1,j1);        k1=func(p2)-fx;
       for(k=1; k<=ncovmodel;k++){        p2[theta]=x[theta]-delt;
         fscanf(ficpar,"%le",&delti3[i][j][k]);        k2=func(p2)-fx;
         printf(" %le",delti3[i][j][k]);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         fprintf(ficparo," %le",delti3[i][j][k]);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       }        
       fscanf(ficpar,"\n");  #ifdef DEBUG
       printf("\n");        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficparo,"\n");        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   delti=delti3[1][1];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
            k=kmax;
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     ungetc(c,ficpar);          k=kmax; l=lmax*10.;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     fputs(line,ficparo);          delts=delt;
   }        }
   ungetc(c,ficpar);      }
      }
   matcov=matrix(1,npar,1,npar);    delti[theta]=delts;
   for(i=1; i <=npar; i++){    return res; 
     fscanf(ficpar,"%s",&str);    
     printf("%s",str);  }
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       fscanf(ficpar," %le",&matcov[i][j]);  {
       printf(" %.5le",matcov[i][j]);    int i;
       fprintf(ficparo," %.5le",matcov[i][j]);    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
     fscanf(ficpar,"\n");    double p2[NPARMAX+1];
     printf("\n");    int k;
     fprintf(ficparo,"\n");  
   }    fx=func(x);
   for(i=1; i <=npar; i++)    for (k=1; k<=2; k++) {
     for(j=i+1;j<=npar;j++)      for (i=1;i<=npar;i++) p2[i]=x[i];
       matcov[i][j]=matcov[j][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
          p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   printf("\n");      k1=func(p2)-fx;
     
       p2[thetai]=x[thetai]+delti[thetai]/k;
     /*-------- data file ----------*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if((ficres =fopen(fileres,"w"))==NULL) {      k2=func(p2)-fx;
       printf("Problem with resultfile: %s\n", fileres);goto end;    
     }      p2[thetai]=x[thetai]-delti[thetai]/k;
     fprintf(ficres,"#%s\n",version);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          k3=func(p2)-fx;
     if((fic=fopen(datafile,"r"))==NULL)    {    
       printf("Problem with datafile: %s\n", datafile);goto end;      p2[thetai]=x[thetai]-delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
     n= lastobs;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     severity = vector(1,maxwav);  #ifdef DEBUG
     outcome=imatrix(1,maxwav+1,1,n);      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);
     num=ivector(1,n);      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);
     moisnais=vector(1,n);  #endif
     annais=vector(1,n);    }
     moisdc=vector(1,n);    return res;
     andc=vector(1,n);  }
     agedc=vector(1,n);  
     cod=ivector(1,n);  /************** Inverse of matrix **************/
     weight=vector(1,n);  void ludcmp(double **a, int n, int *indx, double *d) 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  { 
     mint=matrix(1,maxwav,1,n);    int i,imax,j,k; 
     anint=matrix(1,maxwav,1,n);    double big,dum,sum,temp; 
     s=imatrix(1,maxwav+1,1,n);    double *vv; 
     adl=imatrix(1,maxwav+1,1,n);       
     tab=ivector(1,NCOVMAX);    vv=vector(1,n); 
     ncodemax=ivector(1,8);    *d=1.0; 
     for (i=1;i<=n;i++) { 
     i=1;      big=0.0; 
     while (fgets(line, MAXLINE, fic) != NULL)    {      for (j=1;j<=n;j++) 
       if ((i >= firstobs) && (i <=lastobs)) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
              if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         for (j=maxwav;j>=1;j--){      vv[i]=1.0/big; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    } 
           strcpy(line,stra);    for (j=1;j<=n;j++) { 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for (i=1;i<j;i++) { 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        sum=a[i][j]; 
         }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                a[i][j]=sum; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      big=0.0; 
       for (i=j;i<=n;i++) { 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        sum=a[i][j]; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        a[i][j]=sum; 
         for (j=ncov;j>=1;j--){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          big=dum; 
         }          imax=i; 
         num[i]=atol(stra);        } 
       } 
         /*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]));*/      if (j != imax) { 
         for (k=1;k<=n;k++) { 
         i=i+1;          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
     }          a[j][k]=dum; 
         } 
     /*scanf("%d",i);*/        *d = -(*d); 
   imx=i-1; /* Number of individuals */        vv[imax]=vv[j]; 
       } 
   /* Calculation of the number of parameter from char model*/      indx[j]=imax; 
   Tvar=ivector(1,15);          if (a[j][j] == 0.0) a[j][j]=TINY; 
   Tage=ivector(1,15);            if (j != n) { 
            dum=1.0/(a[j][j]); 
   if (strlen(model) >1){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     j=0, j1=0;      } 
     j=nbocc(model,'+');    } 
     j1=nbocc(model,'*');    free_vector(vv,1,n);  /* Doesn't work */
     cptcovn=j+1;  ;
      } 
     strcpy(modelsav,model);  
     if (j==0) {  void lubksb(double **a, int n, int *indx, double b[]) 
       if (j1==0){  { 
        cutv(stra,strb,modelsav,'V');    int i,ii=0,ip,j; 
        Tvar[1]=atoi(strb);    double sum; 
       }   
       else if (j1==1) {    for (i=1;i<=n;i++) { 
        cutv(stra,strb,modelsav,'*');      ip=indx[i]; 
        /*      printf("stra=%s strb=%s modelsav=%s ",stra,strb,modelsav);*/      sum=b[ip]; 
        Tage[1]=1; cptcovage++;      b[ip]=b[i]; 
        if (strcmp(stra,"age")==0) {      if (ii) 
          cutv(strd,strc,strb,'V');        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
          Tvar[1]=atoi(strc);      else if (sum) ii=i; 
        }      b[i]=sum; 
        else if (strcmp(strb,"age")==0) {    } 
          cutv(strd,strc,stra,'V');    for (i=n;i>=1;i--) { 
          Tvar[1]=atoi(strc);      sum=b[i]; 
        }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        else {printf("Error"); exit(0);}      b[i]=sum/a[i][i]; 
       }    } 
     }  } 
     else {  
       for(i=j; i>=1;i--){  /************ Frequencies ********************/
         cutv(stra,strb,modelsav,'+');  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[])
         /*printf("%s %s %s\n", stra,strb,modelsav);*/  {  /* Some frequencies */
         if (strchr(strb,'*')) {    
           cutv(strd,strc,strb,'*');    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           if (strcmp(strc,"age")==0) {    int first;
             cutv(strb,stre,strd,'V');    double ***freq; /* Frequencies */
             Tvar[i+1]=atoi(stre);    double *pp, **prop;
             cptcovage++;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             Tage[cptcovage]=i+1;    FILE *ficresp;
             printf("stre=%s ", stre);    char fileresp[FILENAMELENGTH];
           }    
           else if (strcmp(strd,"age")==0) {    pp=vector(1,nlstate);
             cutv(strb,stre,strc,'V');    prop=matrix(1,nlstate,iagemin,iagemax+3);
             Tvar[i+1]=atoi(stre);    strcpy(fileresp,"p");
             cptcovage++;    strcat(fileresp,fileres);
             Tage[cptcovage]=i+1;    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(strb,stre,strc,'V');      exit(0);
             Tvar[i+1]=ncov+1;    }
             cutv(strb,strc,strd,'V');    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(stre)][k]*covar[atoi(strc)][k];    
           }    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         else {  
           cutv(strd,strc,strb,'V');    first=1;
           /* printf("%s %s %s", strd,strc,strb);*/  
     for(k1=1; k1<=j;k1++){
         Tvar[i+1]=atoi(strc);      for(i1=1; i1<=ncodemax[k1];i1++){
         }        j1++;
         strcpy(modelsav,stra);          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
       cutv(strd,strc,stra,'V');        for (i=-5; i<=nlstate+ndeath; i++)  
       Tvar[1]=atoi(strc);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
   }              freq[i][jk][m]=0;
   
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);      for (i=1; i<=nlstate; i++)  
      scanf("%d ",i);*/        for(m=iagemin; m <= iagemax+3; m++)
     fclose(fic);          prop[i][m]=0;
         
    if(mle==1){        dateintsum=0;
     if (weightopt != 1) { /* Maximisation without weights*/        k2cpt=0;
       for(i=1;i<=n;i++) weight[i]=1.0;        for (i=1; i<=imx; i++) {
     }          bool=1;
     /*-calculation of age at interview from date of interview and age at death -*/          if  (cptcovn>0) {
     agev=matrix(1,maxwav,1,imx);            for (z1=1; z1<=cptcoveff; z1++) 
                  if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for (i=1; i<=imx; i++)  {                bool=0;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          }
       for(m=1; (m<= maxwav); m++){          if (bool==1){
         if(s[m][i] >0){            for(m=firstpass; m<=lastpass; m++){
           if (s[m][i] == nlstate+1) {              k2=anint[m][i]+(mint[m][i]/12.);
             if(agedc[i]>0)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
               if(moisdc[i]!=99 && andc[i]!=9999)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               agev[m][i]=agedc[i];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             else{                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                if (m<lastpass) {
               agev[m][i]=-1;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           }                }
           else if(s[m][i] !=9){ /* Should no more exist */                
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
             if(mint[m][i]==99 || anint[m][i]==9999)                  dateintsum=dateintsum+k2;
               agev[m][i]=1;                  k2cpt++;
             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);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             }  fprintf(ficresp, "#Local time at start: %s", strstart);
             /*agev[m][i]=anint[m][i]-annais[i];*/        if  (cptcovn>0) {
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficresp, "\n#********** Variable "); 
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           else { /* =9 */          fprintf(ficresp, "**********\n#");
             agev[m][i]=1;        }
             s[m][i]=-1;        for(i=1; i<=nlstate;i++) 
           }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         }        fprintf(ficresp, "\n");
         else /*= 0 Unknown */        
           agev[m][i]=1;        for(i=iagemin; i <= iagemax+3; i++){
       }          if(i==iagemax+3){
                fprintf(ficlog,"Total");
     }          }else{
     for (i=1; i<=imx; i++)  {            if(first==1){
       for(m=1; (m<= maxwav); m++){              first=0;
         if (s[m][i] > (nlstate+ndeath)) {              printf("See log file for details...\n");
           printf("Error: Wrong value in nlstate or ndeath\n");              }
           goto end;            fprintf(ficlog,"Age %d", i);
         }          }
       }          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          }
           for(jk=1; jk <=nlstate ; jk++){
     free_vector(severity,1,maxwav);            for(m=-1, pos=0; m <=0 ; m++)
     free_imatrix(outcome,1,maxwav+1,1,n);              pos += freq[jk][m][i];
     free_vector(moisnais,1,n);            if(pp[jk]>=1.e-10){
     free_vector(annais,1,n);              if(first==1){
     free_matrix(mint,1,maxwav,1,n);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_matrix(anint,1,maxwav,1,n);              }
     free_vector(moisdc,1,n);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_vector(andc,1,n);            }else{
               if(first==1)
                    printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     wav=ivector(1,imx);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          }
      
     /* Concatenates waves */          for(jk=1; jk <=nlstate ; jk++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
           }       
       Tcode=ivector(1,100);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
    nbcode=imatrix(1,nvar,1,8);              pos += pp[jk];
    ncodemax[1]=1;            posprop += prop[jk][i];
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);          }
            for(jk=1; jk <=nlstate ; jk++){
    codtab=imatrix(1,100,1,10);            if(pos>=1.e-5){
    h=0;              if(first==1)
    m=pow(2,cptcovn);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    for(k=1;k<=cptcovn; k++){            }else{
      for(i=1; i <=(m/pow(2,k));i++){              if(first==1)
        for(j=1; j <= ncodemax[k]; j++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            h++;            }
            if (h>m) h=1;codtab[h][k]=j;            if( i <= iagemax){
          }              if(pos>=1.e-5){
        }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      }                /*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]);*/
               }
    /* for(i=1; i <=m ;i++){              else
      for(k=1; k <=cptcovn; k++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);            }
      }          }
      printf("\n");          
    }          for(jk=-1; jk <=nlstate+ndeath; jk++)
    scanf("%d",i);*/            for(m=-1; m <=nlstate+ndeath; m++)
                  if(freq[jk][m][i] !=0 ) {
    /* Calculates basic frequencies. Computes observed prevalence at single age              if(first==1)
        and prints on file fileres'p'. */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(i <= iagemax)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficresp,"\n");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(first==1)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            printf("Others in log...\n");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          fprintf(ficlog,"\n");
            }
     /* 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) */    dateintmean=dateintsum/k2cpt; 
       
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
        free_vector(pp,1,nlstate);
     /*--------- results files --------------*/    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     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);    /* End of Freq */
      }
    jk=1;  
    fprintf(ficres,"# Parameters\n");  /************ Prevalence ********************/
    printf("# Parameters\n");  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
    for(i=1,jk=1; i <=nlstate; i++){  {  
      for(k=1; k <=(nlstate+ndeath); k++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        if (k != i)       in each health status at the date of interview (if between dateprev1 and dateprev2).
          {       We still use firstpass and lastpass as another selection.
            printf("%d%d ",i,k);    */
            fprintf(ficres,"%1d%1d ",i,k);   
            for(j=1; j <=ncovmodel; j++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
              printf("%f ",p[jk]);    double ***freq; /* Frequencies */
              fprintf(ficres,"%f ",p[jk]);    double *pp, **prop;
              jk++;    double pos,posprop; 
            }    double  y2; /* in fractional years */
            printf("\n");    int iagemin, iagemax;
            fprintf(ficres,"\n");  
          }    iagemin= (int) agemin;
      }    iagemax= (int) agemax;
    }    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /* Computing hessian and covariance matrix */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     ftolhess=ftol; /* Usually correct */    j1=0;
     hesscov(matcov, p, npar, delti, ftolhess, func);    
     fprintf(ficres,"# Scales\n");    j=cptcoveff;
     printf("# Scales\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      for(i=1,jk=1; i <=nlstate; i++){    
       for(j=1; j <=nlstate+ndeath; j++){    for(k1=1; k1<=j;k1++){
         if (j!=i) {      for(i1=1; i1<=ncodemax[k1];i1++){
           fprintf(ficres,"%1d%1d",i,j);        j1++;
           printf("%1d%1d",i,j);        
           for(k=1; k<=ncovmodel;k++){        for (i=1; i<=nlstate; i++)  
             printf(" %.5e",delti[jk]);          for(m=iagemin; m <= iagemax+3; m++)
             fprintf(ficres," %.5e",delti[jk]);            prop[i][m]=0.0;
             jk++;       
           }        for (i=1; i<=imx; i++) { /* Each individual */
           printf("\n");          bool=1;
           fprintf(ficres,"\n");          if  (cptcovn>0) {
         }            for (z1=1; z1<=cptcoveff; z1++) 
       }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       }                bool=0;
              } 
     k=1;          if (bool==1) { 
     fprintf(ficres,"# Covariance\n");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     printf("# Covariance\n");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     for(i=1;i<=npar;i++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       /*  if (k>nlstate) k=1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       i1=(i-1)/(ncovmodel*nlstate)+1;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[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); 
       printf("%s%d%d",alph[k],i1,tab[i]);*/                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       fprintf(ficres,"%3d",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]]);*/
       printf("%3d",i);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(j=1; j<=i;j++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
         fprintf(ficres," %.5e",matcov[i][j]);                } 
         printf(" %.5e",matcov[i][j]);              }
       }            } /* end selection of waves */
       fprintf(ficres,"\n");          }
       printf("\n");        }
       k++;        for(i=iagemin; i <= iagemax+3; i++){  
     }          
              for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     while((c=getc(ficpar))=='#' && c!= EOF){            posprop += prop[jk][i]; 
       ungetc(c,ficpar);          } 
       fgets(line, MAXLINE, ficpar);  
       puts(line);          for(jk=1; jk <=nlstate ; jk++){     
       fputs(line,ficparo);            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
     ungetc(c,ficpar);                probs[i][jk][j1]= prop[jk][i]/posprop;
                } 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            } 
              }/* end jk */ 
     if (fage <= 2) {        }/* end i */ 
       bage = agemin;      } /* end i1 */
       fage = agemax;    } /* end k1 */
     }    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /*free_vector(pp,1,nlstate);*/
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 /*------------ gnuplot -------------*/  }  /* End of prevalence */
 chdir(pathcd);  
   if((ficgp=fopen("graph.plt","w"))==NULL) {  /************* Waves Concatenation ***************/
     printf("Problem with file graph.gp");goto end;  
   }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 #ifdef windows  {
   fprintf(ficgp,"cd \"%s\" \n",pathc);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 #endif       Death is a valid wave (if date is known).
 m=pow(2,cptcovn);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
  /* 1eme*/       and mw[mi+1][i]. dh depends on stepm.
   for (cpt=1; cpt<= nlstate ; cpt ++) {       */
    for (k1=1; k1<= m ; k1 ++) {  
     int i, mi, m;
 #ifdef windows    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     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);       double sum=0., jmean=0.;*/
 #endif    int first;
 #ifdef unix    int j, k=0,jk, ju, jl;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    double sum=0.;
 #endif    first=0;
     jmin=1e+5;
 for (i=1; i<= nlstate ; i ++) {    jmax=-1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    jmean=0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(i=1; i<=imx; i++){
 }      mi=0;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      m=firstpass;
     for (i=1; i<= nlstate ; i ++) {      while(s[m][i] <= nlstate){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          mw[++mi][i]=m;
 }        if(m >=lastpass)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          break;
      for (i=1; i<= nlstate ; i ++) {        else
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          m++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }/* end while */
 }        if (s[m][i] > nlstate){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        mi++;     /* Death is another wave */
 #ifdef unix        /* if(mi==0)  never been interviewed correctly before death */
 fprintf(ficgp,"\nset ter gif small size 400,300");           /* Only death is a correct wave */
 #endif        mw[mi][i]=m;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      }
    }  
   }      wav[i]=mi;
   /*2 eme*/      if(mi==0){
         nbwarn++;
   for (k1=1; k1<= m ; k1 ++) {        if(first==0){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
              first=1;
     for (i=1; i<= nlstate+1 ; i ++) {        }
       k=2*i;        if(first==1){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       for (j=1; j<= nlstate+1 ; j ++) {        }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      } /* end mi==0 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } /* End individuals */
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    for(i=1; i<=imx; i++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      for(mi=1; mi<wav[i];mi++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        if (stepm <=0)
       for (j=1; j<= nlstate+1 ; j ++) {          dh[mi][i]=1;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        else{
         else fprintf(ficgp," \%%*lf (\%%*lf)");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 }              if (agedc[i] < 2*AGESUP) {
       fprintf(ficgp,"\" t\"\" w l 0,");              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              if(j==0) j=1;  /* Survives at least one month after exam */
       for (j=1; j<= nlstate+1 ; j ++) {              else if(j<0){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                nberr++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 }                  j=1; /* Temporary Dangerous patch */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                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);
       else fprintf(ficgp,"\" t\"\" w l 0,");                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);              }
   }              k=k+1;
                if (j >= jmax) jmax=j;
   /*3eme*/              if (j <= jmin) jmin=j;
               sum=sum+j;
   for (k1=1; k1<= m ; k1 ++) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       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);          }
       for (i=1; i< nlstate ; i ++) {          else{
         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);            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,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }            k=k+1;
   }            if (j >= jmax) jmax=j;
              else if (j <= jmin)jmin=j;
   /* CV preval stat */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   for (k1=1; k1<= m ; k1 ++) {            /*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]);*/
     for (cpt=1; cpt<nlstate ; cpt ++) {            if(j<0){
       k=3;              nberr++;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for (i=1; i< nlstate ; i ++)              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         fprintf(ficgp,"+$%d",k+i+1);            }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            sum=sum+j;
                }
       l=3+(nlstate+ndeath)*cpt;          jk= j/stepm;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          jl= j -jk*stepm;
       for (i=1; i< nlstate ; i ++) {          ju= j -(jk+1)*stepm;
         l=3+(nlstate+ndeath)*cpt;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         fprintf(ficgp,"+$%d",l+i+1);            if(jl==0){
       }              dh[mi][i]=jk;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                bh[mi][i]=0;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            }else{ /* We want a negative bias in order to only have interpolation ie
     }                    * at the price of an extra matrix product in likelihood */
   }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   /* proba elementaires */            }
    for(i=1,jk=1; i <=nlstate; i++){          }else{
     for(k=1; k <=(nlstate+ndeath); k++){            if(jl <= -ju){
       if (k != i) {              dh[mi][i]=jk;
         for(j=1; j <=ncovmodel; j++){              bh[mi][i]=jl;       /* bias is positive if real duration
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/                                   * is higher than the multiple of stepm and negative otherwise.
           /*fprintf(ficgp,"%s",alph[1]);*/                                   */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            }
           jk++;            else{
           fprintf(ficgp,"\n");              dh[mi][i]=jk+1;
         }              bh[mi][i]=ju;
       }            }
     }            if(dh[mi][i]==0){
     }              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   for(jk=1; jk <=m; jk++) {              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);            }
    i=1;          } /* end if mle */
    for(k2=1; k2<=nlstate; k2++) {        }
      k3=i;      } /* end wave */
      for(k=1; k<=(nlstate+ndeath); k++) {    }
        if (k != k2){    jmean=sum/k;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         for(j=3; j <=ncovmodel; j++)   }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         fprintf(ficgp,")/(1");  /*********** Tricode ****************************/
          void tricode(int *Tvar, int **nbcode, int imx)
         for(k1=1; k1 <=nlstate; k1++){    {
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    
           for(j=3; j <=ncovmodel; j++)    int Ndum[20],ij=1, k, j, i, maxncov=19;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int cptcode=0;
           fprintf(ficgp,")");    cptcoveff=0; 
         }   
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    for (k=0; k<maxncov; k++) Ndum[k]=0;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    for (k=1; k<=7; k++) ncodemax[k]=0;
         i=i+ncovmodel;  
        }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
      }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
    }                                 modality*/ 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   }        Ndum[ij]++; /*store the modality */
            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   fclose(ficgp);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                             Tvar[j]. If V=sex and male is 0 and 
 chdir(path);                                         female is 1, then  cptcode=1.*/
     free_matrix(agev,1,maxwav,1,imx);      }
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      for (i=0; i<=cptcode; i++) {
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        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 */
          }
     free_imatrix(s,1,maxwav+1,1,n);  
          ij=1; 
          for (i=1; i<=ncodemax[j]; i++) {
     free_ivector(num,1,n);        for (k=0; k<= maxncov; k++) {
     free_vector(agedc,1,n);          if (Ndum[k] != 0) {
     free_vector(weight,1,n);            nbcode[Tvar[j]][ij]=k; 
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     fclose(ficparo);            
     fclose(ficres);            ij++;
    }          }
              if (ij > ncodemax[j]) break; 
    /*________fin mle=1_________*/        }  
          } 
     }  
    
     /* No more information from the sample is required now */   for (k=0; k< maxncov; k++) Ndum[k]=0;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){   for (i=1; i<=ncovmodel-2; i++) { 
     ungetc(c,ficpar);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     fgets(line, MAXLINE, ficpar);     ij=Tvar[i];
     puts(line);     Ndum[ij]++;
     fputs(line,ficparo);   }
   }  
   ungetc(c,ficpar);   ij=1;
     for (i=1; i<= maxncov; i++) {
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);     if((Ndum[i]!=0) && (i<=ncovcol)){
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);       Tvaraff[ij]=i; /*For printing */
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       ij++;
 /*--------- index.htm --------*/     }
    }
   if((fichtm=fopen("index.htm","w"))==NULL)    {   
     printf("Problem with index.htm \n");goto end;   cptcoveff=ij-1; /*Number of simple covariates*/
   }  }
   
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n  /*********** Health Expectancies ****************/
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  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[] )
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  {
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    /* Health expectancies */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    double age, agelim, hf;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    double ***p3mat,***varhe;
         - 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);    double **dnewm,**doldm;
     double *xp;
  fprintf(fichtm," <li>Graphs</li>\n<p>");    double **gp, **gm;
     double ***gradg, ***trgradg;
  m=cptcovn;    int theta;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
  j1=0;    xp=vector(1,npar);
  for(k1=1; k1<=m;k1++){    dnewm=matrix(1,nlstate*nlstate,1,npar);
    for(i1=1; i1<=ncodemax[k1];i1++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
        j1++;    
        if (cptcovn > 0) {    fprintf(ficreseij,"# Local time at start: %s", strstart);
          fprintf(fichtm,"<hr>************ Results for covariates");    fprintf(ficreseij,"# Health expectancies\n");
          for (cpt=1; cpt<=cptcovn;cpt++)    fprintf(ficreseij,"# Age");
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);    for(i=1; i<=nlstate;i++)
          fprintf(fichtm," ************\n<hr>");      for(j=1; j<=nlstate;j++)
        }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    fprintf(ficreseij,"\n");
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      
        for(cpt=1; cpt<nlstate;cpt++){    if(estepm < stepm){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      printf ("Problem %d lower than %d\n",estepm, stepm);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    }
        }    else  hstepm=estepm;   
     for(cpt=1; cpt<=nlstate;cpt++) {    /* We compute the life expectancy from trapezoids spaced every estepm months
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident     * This is mainly to measure the difference between two models: for example
 interval) in state (%d): v%s%d%d.gif <br>     * if stepm=24 months pijx are given only every 2 years and by summing them
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       * we are calculating an estimate of the Life Expectancy assuming a linear 
      }     * progression in between and thus overestimating or underestimating according
      for(cpt=1; cpt<=nlstate;cpt++) {     * to the curvature of the survival function. If, for the same date, we 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     * to compare the new estimate of Life expectancy with the same linear 
      }     * hypothesis. A more precise result, taking into account a more precise
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     * curvature will be obtained if estepm is as small as stepm. */
 health expectancies in states (1) and (2): e%s%d.gif<br>  
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    /* For example we decided to compute the life expectancy with the smallest unit */
 fprintf(fichtm,"\n</body>");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
    }       nhstepm is the number of hstepm from age to agelim 
  }       nstepm is the number of stepm from age to agelin. 
 fclose(fichtm);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   /*--------------- Prevalence limit --------------*/    /* 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
   strcpy(filerespl,"pl");       means that if the survival funtion is printed only each two years of age and if
   strcat(filerespl,fileres);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       results. So we changed our mind and took the option of the best precision.
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");    agelim=AGESUP;
   fprintf(ficrespl,"#Age ");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      /* nhstepm age range expressed in number of stepm */
   fprintf(ficrespl,"\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   prlim=matrix(1,nlstate,1,nlstate);      /* if (stepm >= YEARM) hstepm=1;*/
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   k=0;  
   agebase=agemin;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   agelim=agemax;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   ftolpl=1.e-10;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   i1=cptcovn;   
   if (cptcovn < 1){i1=1;}  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      /* Computing  Variances of health expectancies */
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       for(theta=1; theta <=npar; theta++){
         fprintf(ficrespl,"\n#******");        for(i=1; i<=npar; i++){ 
         for(j=1;j<=cptcovn;j++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           fprintf(ficrespl," V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);        }
         fprintf(ficrespl,"******\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            
         for (age=agebase; age<=agelim; age++){        cptj=0;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(j=1; j<= nlstate; j++){
           fprintf(ficrespl,"%.0f",age );          for(i=1; i<=nlstate; i++){
           for(i=1; i<=nlstate;i++)            cptj=cptj+1;
           fprintf(ficrespl," %.5f", prlim[i][i]);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           fprintf(ficrespl,"\n");              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         }            }
       }          }
     }        }
   fclose(ficrespl);       
   /*------------- h Pij x at various ages ------------*/       
          for(i=1; i<=npar; i++) 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        
   }        cptj=0;
   printf("Computing pij: result on file '%s' \n", filerespij);        for(j=1; j<= nlstate; j++){
            for(i=1;i<=nlstate;i++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;            cptj=cptj+1;
   if (stepm<=24) stepsize=2;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
   agelim=AGESUP;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   hstepm=stepsize*YEARM; /* Every year of age */            }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          }
          }
   k=0;        for(j=1; j<= nlstate*nlstate; j++)
   for(cptcov=1;cptcov<=i1;cptcov++){          for(h=0; h<=nhstepm-1; h++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       k=k+1;          }
         fprintf(ficrespij,"\n#****** ");       } 
         for(j=1;j<=cptcovn;j++)     
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  /* End theta */
         fprintf(ficrespij,"******\n");  
               trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       for(h=0; h<=nhstepm-1; h++)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(j=1; j<=nlstate*nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(theta=1; theta <=npar; theta++)
           oldm=oldms;savm=savms;            trgradg[h][j][theta]=gradg[h][theta][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)       for(i=1;i<=nlstate*nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)        for(j=1;j<=nlstate*nlstate;j++)
               fprintf(ficrespij," %1d-%1d",i,j);          varhe[i][j][(int)age] =0.;
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){       printf("%d|",(int)age);fflush(stdout);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             for(i=1; i<=nlstate;i++)       for(h=0;h<=nhstepm-1;h++){
               for(j=1; j<=nlstate+ndeath;j++)        for(k=0;k<=nhstepm-1;k++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             fprintf(ficrespij,"\n");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           }          for(i=1;i<=nlstate*nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1;j<=nlstate*nlstate;j++)
           fprintf(ficrespij,"\n");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }        }
     }      }
   }      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   fclose(ficrespij);        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   /*---------- Health expectancies and variances ------------*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
   strcpy(filerest,"t");  /* 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]);*/
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {          }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }      fprintf(ficreseij,"%3.0f",age );
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      cptj=0;
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   strcpy(filerese,"e");          cptj++;
   strcat(filerese,fileres);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   if((ficreseij=fopen(filerese,"w"))==NULL) {        }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      fprintf(ficreseij,"\n");
   }     
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
  strcpy(fileresv,"v");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   strcat(fileresv,fileres);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }    printf("\n");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fprintf(ficlog,"\n");
   
   k=0;    free_vector(xp,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       k=k+1;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       fprintf(ficrest,"\n#****** ");  }
       for(j=1;j<=cptcovn;j++)  
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  /************ Variance ******************/
       fprintf(ficrest,"******\n");  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(ficreseij,"\n#****** ");    /* Variance of health expectancies */
       for(j=1;j<=cptcovn;j++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    /* double **newm;*/
       fprintf(ficreseij,"******\n");    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
       fprintf(ficresvij,"\n#****** ");    int i, j, nhstepm, hstepm, h, nstepm ;
       for(j=1;j<=cptcovn;j++)    int k, cptcode;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double *xp;
       fprintf(ficresvij,"******\n");    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double **gradgp, **trgradgp; /* for var p point j */
       oldm=oldms;savm=savms;    double *gpp, *gmp; /* for var p point j */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double ***p3mat;
       oldm=oldms;savm=savms;    double age,agelim, hf;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double ***mobaverage;
          int theta;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    char digit[4];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    char digitp[25];
       fprintf(ficrest,"\n");  
            char fileresprobmorprev[FILENAMELENGTH];
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;    if(popbased==1){
       epj=vector(1,nlstate+1);      if(mobilav!=0)
       for(age=bage; age <=fage ;age++){        strcpy(digitp,"-populbased-mobilav-");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      else strcpy(digitp,"-populbased-nomobil-");
         fprintf(ficrest," %.0f",age);    }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    else 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      strcpy(digitp,"-stablbased-");
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }    if (mobilav!=0) {
           epj[nlstate+1] +=epj[j];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         for(i=1, vepp=0.;i <=nlstate;i++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           for(j=1;j <=nlstate;j++)        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             vepp += vareij[i][j][(int)age];      }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    }
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    strcpy(fileresprobmorprev,"prmorprev"); 
         }    sprintf(digit,"%-d",ij);
         fprintf(ficrest,"\n");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   }    strcat(fileresprobmorprev,fileres);
            if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
  fclose(ficreseij);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
  fclose(ficresvij);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   fclose(ficrest);    }
   fclose(ficpar);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_vector(epj,1,nlstate+1);   
   /*  scanf("%d ",i); */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   /*------- Variance limit prevalence------*/      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 strcpy(fileresvpl,"vpl");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   strcat(fileresvpl,fileres);      fprintf(ficresprobmorprev," p.%-d SE",j);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      for(i=1; i<=nlstate;i++)
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     exit(0);    }  
   }    fprintf(ficresprobmorprev,"\n");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
  k=0;    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");
  for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*   } */
      k=k+1;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      fprintf(ficresvpl,"\n#****** ");   fprintf(ficresvij, "#Local time at start: %s", strstart);
      for(j=1;j<=cptcovn;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(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    fprintf(ficresvij,"# Age");
      fprintf(ficresvpl,"******\n");    for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      oldm=oldms;savm=savms;    fprintf(ficresvij,"\n");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }    xp=vector(1,npar);
  }    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   fclose(ficresvpl);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    gmp=vector(nlstate+1,nlstate+ndeath);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      
      if(estepm < stepm){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      printf ("Problem %d lower than %d\n",estepm, stepm);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    else  hstepm=estepm;   
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* 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. 
   free_matrix(matcov,1,npar,1,npar);       nhstepm is the number of hstepm from age to agelim 
   free_vector(delti,1,npar);       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   printf("End of Imach\n");       survival function given by stepm (the optimization length). Unfortunately it
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       means that if the survival funtion is printed every two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /* 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);*/       results. So we changed our mind and took the option of the best precision.
   /*printf("Total time was %d uSec.\n", total_usecs);*/    */
   /*------ End -----------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
  end:    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #ifdef windows      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  chdir(pathcd);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 #endif      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  system("wgnuplot graph.plt");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
 #ifdef windows      gm=matrix(0,nhstepm,1,nlstate);
   while (z[0] != 'q') {  
     chdir(pathcd);  
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      for(theta=1; theta <=npar; theta++){
     scanf("%s",z);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     if (z[0] == 'c') system("./imach");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     else if (z[0] == 'e') {        }
       chdir(path);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       system("index.htm");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }  
     else if (z[0] == 'q') exit(0);        if (popbased==1) {
   }          if(mobilav ==0){
 #endif            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];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         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];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm 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 */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         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 */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of 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);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

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  Added in v.1.106


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