Diff for /imach/src/imach.c between versions 1.8 and 1.109

version 1.8, 2001/05/02 17:54:31 version 1.109, 2006/01/24 19:37:15
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 1.109  2006/01/24 19:37:15  brouard
   individuals from different ages are interviewed on their health status    (Module): Comments (lines starting with a #) are allowed in data.
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.108  2006/01/19 18:05:42  lievre
   Health expectancies are computed from the transistions observed between    Gnuplot problem appeared...
   waves and are computed for each degree of severity of disability (number    To be fixed
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.107  2006/01/19 16:20:37  brouard
   The simplest model is the multinomial logistic model where pij is    Test existence of gnuplot in imach path
   the probabibility to be observed in state j at the second wave conditional  
   to be observed in state i at the first wave. Therefore the model is:    Revision 1.106  2006/01/19 13:24:36  brouard
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Some cleaning and links added in html output
   is a covariate. If you want to have a more complex model than "constant and  
   age", you should modify the program where the markup    Revision 1.105  2006/01/05 20:23:19  lievre
     *Covariates have to be included here again* invites you to do it.    *** empty log message ***
   More covariates you add, less is the speed of the convergence.  
     Revision 1.104  2005/09/30 16:11:43  lievre
   The advantage that this computer programme claims, comes from that if the    (Module): sump fixed, loop imx fixed, and simplifications.
   delay between waves is not identical for each individual, or if some    (Module): If the status is missing at the last wave but we know
   individual missed an interview, the information is not rounded or lost, but    that the person is alive, then we can code his/her status as -2
   taken into account using an interpolation or extrapolation.    (instead of missing=-1 in earlier versions) and his/her
   hPijx is the probability to be    contributions to the likelihood is 1 - Prob of dying from last
   observed in state i at age x+h conditional to the observed state i at age    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   x. The delay 'h' can be split into an exact number (nh*stepm) of    the healthy state at last known wave). Version is 0.98
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.103  2005/09/30 15:54:49  lievre
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    (Module): sump fixed, loop imx fixed, and simplifications.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.102  2004/09/15 17:31:30  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Add the possibility to read data file including tab characters.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.101  2004/09/15 10:38:38  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Fix on curr_time
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.100  2004/07/12 18:29:06  brouard
   from the European Union.    Add version for Mac OS X. Just define UNIX in Makefile
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.99  2004/06/05 08:57:40  brouard
   can be accessed at http://euroreves.ined.fr/imach .    *** empty log message ***
   **********************************************************************/  
      Revision 1.98  2004/05/16 15:05:56  brouard
 #include <math.h>    New version 0.97 . First attempt to estimate force of mortality
 #include <stdio.h>    directly from the data i.e. without the need of knowing the health
 #include <stdlib.h>    state at each age, but using a Gompertz model: log u =a + b*age .
 #include <unistd.h>    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 #define MAXLINE 256    cross-longitudinal survey is different from the mortality estimated
 #define FILENAMELENGTH 80    from other sources like vital statistic data.
 /*#define DEBUG*/  
 #define windows    The same imach parameter file can be used but the option for mle should be -3.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Current limitations:
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    A) Even if you enter covariates, i.e. with the
 #define NCOVMAX 8 /* Maximum number of covariates */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define MAXN 20000    B) There is no computation of Life Expectancy nor Life Table.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.97  2004/02/20 13:25:42  lievre
 #define AGEBASE 40    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
   
 int nvar;    Revision 1.96  2003/07/15 15:38:55  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 int npar=NPARMAX;    rewritten within the same printf. Workaround: many printfs.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.95  2003/07/08 07:54:34  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 int *wav; /* Number of waves for this individuual 0 is possible */    matrix (cov(a12,c31) instead of numbers.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.94  2003/06/27 13:00:02  brouard
 int mle, weightopt;    Just cleaning
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.93  2003/06/25 16:33:55  brouard
 double jmean; /* Mean space between 2 waves */    (Module): On windows (cygwin) function asctime_r doesn't
 double **oldm, **newm, **savm; /* Working pointers to matrices */    exist so I changed back to asctime which exists.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Version 0.96b
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Revision 1.92  2003/06/25 16:30:45  brouard
 FILE *ficreseij;    (Module): On windows (cygwin) function asctime_r doesn't
   char filerese[FILENAMELENGTH];    exist so I changed back to asctime which exists.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.91  2003/06/25 15:30:29  brouard
  FILE  *ficresvpl;    * imach.c (Repository): Duplicated warning errors corrected.
   char fileresvpl[FILENAMELENGTH];    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 #define NR_END 1    is stamped in powell.  We created a new html file for the graphs
 #define FREE_ARG char*    concerning matrix of covariance. It has extension -cov.htm.
 #define FTOL 1.0e-10  
     Revision 1.90  2003/06/24 12:34:15  brouard
 #define NRANSI    (Module): Some bugs corrected for windows. Also, when
 #define ITMAX 200    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 #define TOL 2.0e-4  
     Revision 1.89  2003/06/24 12:30:52  brouard
 #define CGOLD 0.3819660    (Module): Some bugs corrected for windows. Also, when
 #define ZEPS 1.0e-10    mle=-1 a template is output in file "or"mypar.txt with the design
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    of the covariance matrix to be input.
   
 #define GOLD 1.618034    Revision 1.88  2003/06/23 17:54:56  brouard
 #define GLIMIT 100.0    * 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 TINY 1.0e-20  
     Revision 1.87  2003/06/18 12:26:01  brouard
 static double maxarg1,maxarg2;    Version 0.96
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.86  2003/06/17 20:04:08  brouard
      (Module): Change position of html and gnuplot routines and added
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    routine fileappend.
 #define rint(a) floor(a+0.5)  
     Revision 1.85  2003/06/17 13:12:43  brouard
 static double sqrarg;    * imach.c (Repository): Check when date of death was earlier that
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    current date of interview. It may happen when the death was just
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 int imx;    assuming that the date of death was just one stepm after the
 int stepm;    interview.
 /* Stepm, step in month: minimum step interpolation*/    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 int m,nb;    memory allocation. But we also truncated to 8 characters (left
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    truncation)
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Repository): No more line truncation errors.
 double **pmmij;  
     Revision 1.84  2003/06/13 21:44:43  brouard
 double *weight;    * imach.c (Repository): Replace "freqsummary" at a correct
 int **s; /* Status */    place. It differs from routine "prevalence" which may be called
 double *agedc, **covar, idx;    many times. Probs is memory consuming and must be used with
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  */
   /*
    l1 = strlen( path );                 /* length of path */     Interpolated Markov Chain
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Short summary of the programme:
    if ( s == NULL ) {                   /* no directory, so use current */    
 #if     defined(__bsd__)                /* get current working directory */    This program computes Healthy Life Expectancies from
       extern char       *getwd( );    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
       if ( getwd( dirc ) == NULL ) {    interviewed on their health status or degree of disability (in the
 #else    case of a health survey which is our main interest) -2- at least a
       extern char       *getcwd( );    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    computed from the time spent in each health state according to a
 #endif    model. More health states you consider, more time is necessary to reach the
          return( GLOCK_ERROR_GETCWD );    Maximum Likelihood of the parameters involved in the model.  The
       }    simplest model is the multinomial logistic model where pij is the
       strcpy( name, path );             /* we've got it */    probability to be observed in state j at the second wave
    } else {                             /* strip direcotry from path */    conditional to be observed in state i at the first wave. Therefore
       s++;                              /* after this, the filename */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       l2 = strlen( s );                 /* length of filename */    'age' is age and 'sex' is a covariate. If you want to have a more
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    complex model than "constant and age", you should modify the program
       strcpy( name, s );                /* save file name */    where the markup *Covariates have to be included here again* invites
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    you to do it.  More covariates you add, slower the
       dirc[l1-l2] = 0;                  /* add zero */    convergence.
    }  
    l1 = strlen( dirc );                 /* length of directory */    The advantage of this computer programme, compared to a simple
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    multinomial logistic model, is clear when the delay between waves is not
    return( 0 );                         /* we're done */    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
   
 /******************************************/    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 void replace(char *s, char*t)    split into an exact number (nh*stepm) of unobserved intermediate
 {    states. This elementary transition (by month, quarter,
   int i;    semester or year) is modelled as a multinomial logistic.  The hPx
   int lg=20;    matrix is simply the matrix product of nh*stepm elementary matrices
   i=0;    and the contribution of each individual to the likelihood is simply
   lg=strlen(t);    hPijx.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Also this programme outputs the covariance matrix of the parameters but also
     if (t[i]== '\\') s[i]='/';    of the life expectancies. It also computes the stable prevalence. 
   }    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 int nbocc(char *s, char occ)    This software have been partly granted by Euro-REVES, a concerted action
 {    from the European Union.
   int i,j=0;    It is copyrighted identically to a GNU software product, ie programme and
   int lg=20;    software can be distributed freely for non commercial use. Latest version
   i=0;    can be accessed at http://euroreves.ined.fr/imach .
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   if  (s[i] == occ ) j++;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   }    
   return j;    **********************************************************************/
 }  /*
     main
 void cutv(char *u,char *v, char*t, char occ)    read parameterfile
 {    read datafile
   int i,lg,j,p=0;    concatwav
   i=0;    freqsummary
   for(j=0; j<=strlen(t)-1; j++) {    if (mle >= 1)
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      mlikeli
   }    print results files
     if mle==1 
   lg=strlen(t);       computes hessian
   for(j=0; j<p; j++) {    read end of parameter file: agemin, agemax, bage, fage, estepm
     (u[j] = t[j]);        begin-prev-date,...
   }    open gnuplot file
      u[p]='\0';    open html file
     stable prevalence
    for(j=0; j<= lg; j++) {     for age prevalim()
     if (j>=(p+1))(v[j-p-1] = t[j]);    h Pij x
   }    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /********************** nrerror ********************/    Variance-covariance of DFLE
     prevalence()
 void nrerror(char error_text[])     movingaverage()
 {    varevsij() 
   fprintf(stderr,"ERREUR ...\n");    if popbased==1 varevsij(,popbased)
   fprintf(stderr,"%s\n",error_text);    total life expectancies
   exit(1);    Variance of stable prevalence
 }   end
 /*********************** vector *******************/  */
 double *vector(int nl, int nh)  
 {  
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));   
   if (!v) nrerror("allocation failure in vector");  #include <math.h>
   return v-nl+NR_END;  #include <stdio.h>
 }  #include <stdlib.h>
   #include <string.h>
 /************************ free vector ******************/  #include <unistd.h>
 void free_vector(double*v, int nl, int nh)  
 {  #include <limits.h>
   free((FREE_ARG)(v+nl-NR_END));  #include <sys/types.h>
 }  #include <sys/stat.h>
   #include <errno.h>
 /************************ivector *******************************/  extern int errno;
 int *ivector(long nl,long nh)  
 {  /* #include <sys/time.h> */
   int *v;  #include <time.h>
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #include "timeval.h"
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 /******************free ivector **************************/  #define MAXLINE 256
 void free_ivector(int *v, long nl, long nh)  
 {  #define GNUPLOTPROGRAM "gnuplot"
   free((FREE_ARG)(v+nl-NR_END));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 }  #define FILENAMELENGTH 132
   
 /******************* imatrix *******************************/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   int **m;  
    #define NINTERVMAX 8
   /* allocate pointers to rows */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NCOVMAX 8 /* Maximum number of covariates */
   m += NR_END;  #define MAXN 20000
   m -= nrl;  #define YEARM 12. /* Number of months per year */
    #define AGESUP 130
    #define AGEBASE 40
   /* allocate rows and set pointers to them */  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #ifdef UNIX
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define DIRSEPARATOR '/'
   m[nrl] += NR_END;  #define CHARSEPARATOR "/"
   m[nrl] -= ncl;  #define ODIRSEPARATOR '\\'
    #else
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define DIRSEPARATOR '\\'
    #define CHARSEPARATOR "\\"
   /* return pointer to array of pointers to rows */  #define ODIRSEPARATOR '/'
   return m;  #endif
 }  
   /* $Id$ */
 /****************** free_imatrix *************************/  /* $State$ */
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
       long nch,ncl,nrh,nrl;  char fullversion[]="$Revision$ $Date$"; 
      /* free an int matrix allocated by imatrix() */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   free((FREE_ARG) (m+nrl-NR_END));  int npar=NPARMAX;
 }  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
 /******************* matrix *******************************/  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double **matrix(long nrl, long nrh, long ncl, long nch)  int popbased=0;
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int *wav; /* Number of waves for this individuual 0 is possible */
   double **m;  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int gipmx, gsw; /* Global variables on the number of contributions 
   if (!m) nrerror("allocation failure 1 in matrix()");                     to the likelihood and the sum of weights (done by funcone)*/
   m += NR_END;  int mle, weightopt;
   m -= nrl;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   m[nrl] += NR_END;  double jmean; /* Mean space between 2 waves */
   m[nrl] -= ncl;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   return m;  FILE *ficlog, *ficrespow;
 }  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 /*************************free matrix ************************/  long ipmx; /* Number of contributions */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /******************* ma3x *******************************/  FILE *fichtm, *fichtmcov; /* Html File */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  FILE  *ficresvij;
   double ***m;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileresvpl[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char title[MAXLINE];
   m += NR_END;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m -= nrl;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char command[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int  outcmd=0;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char fileregp[FILENAMELENGTH];
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char popfile[FILENAMELENGTH];
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
    struct timezone tzp;
   for (i=nrl+1; i<=nrh; i++) {  extern int gettimeofday();
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     for (j=ncl+1; j<=nch; j++)  long time_value;
       m[i][j]=m[i][j-1]+nlay;  extern long time();
   }  char strcurr[80], strfor[80];
   return m;  
 }  char *endptr;
   long lval;
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define NR_END 1
 {  #define FREE_ARG char*
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define FTOL 1.0e-10
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #define NRANSI 
 }  #define ITMAX 200 
   
 /***************** f1dim *************************/  #define TOL 2.0e-4 
 extern int ncom;  
 extern double *pcom,*xicom;  #define CGOLD 0.3819660 
 extern double (*nrfunc)(double []);  #define ZEPS 1.0e-10 
    #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double f1dim(double x)  
 {  #define GOLD 1.618034 
   int j;  #define GLIMIT 100.0 
   double f;  #define TINY 1.0e-20 
   double *xt;  
    static double maxarg1,maxarg2;
   xt=vector(1,ncom);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   f=(*nrfunc)(xt);    
   free_vector(xt,1,ncom);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   return f;  #define rint(a) floor(a+0.5)
 }  
   static double sqrarg;
 /*****************brent *************************/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  int agegomp= AGEGOMP;
   int iter;  
   double a,b,d,etemp;  int imx; 
   double fu,fv,fw,fx;  int stepm=1;
   double ftemp;  /* Stepm, step in month: minimum step interpolation*/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  int m,nb;
   x=w=v=bx;  long *num;
   fw=fv=fx=(*f)(x);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   for (iter=1;iter<=ITMAX;iter++) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     xm=0.5*(a+b);  double **pmmij, ***probs;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  double *ageexmed,*agecens;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  double dateintmean=0;
     printf(".");fflush(stdout);  
 #ifdef DEBUG  double *weight;
     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);  int **s; /* Status */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  double *agedc, **covar, idx;
 #endif  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double *lsurv, *lpop, *tpop;
       *xmin=x;  
       return fx;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     }  double ftolhess; /* Tolerance for computing hessian */
     ftemp=fu;  
     if (fabs(e) > tol1) {  /**************** split *************************/
       r=(x-w)*(fx-fv);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       q=2.0*(q-r);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       if (q > 0.0) p = -p;    */ 
       q=fabs(q);    char  *ss;                            /* pointer */
       etemp=e;    int   l1, l2;                         /* length counters */
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    l1 = strlen(path );                   /* length of path */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       else {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         d=p/q;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
         u=x+d;      strcpy( name, path );               /* we got the fullname name because no directory */
         if (u-a < tol2 || b-u < tol2)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
           d=SIGN(tol1,xm-x);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       }      /* get current working directory */
     } else {      /*    extern  char* getcwd ( char *buf , int len);*/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     }        return( GLOCK_ERROR_GETCWD );
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      }
     fu=(*f)(u);      /* got dirc from getcwd*/
     if (fu <= fx) {      printf(" DIRC = %s \n",dirc);
       if (u >= x) a=x; else b=x;    } else {                              /* strip direcotry from path */
       SHFT(v,w,x,u)      ss++;                               /* after this, the filename */
         SHFT(fv,fw,fx,fu)      l2 = strlen( ss );                  /* length of filename */
         } else {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           if (u < x) a=u; else b=u;      strcpy( name, ss );         /* save file name */
           if (fu <= fw || w == x) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
             v=w;      dirc[l1-l2] = 0;                    /* add zero */
             w=u;      printf(" DIRC2 = %s \n",dirc);
             fv=fw;    }
             fw=fu;    /* We add a separator at the end of dirc if not exists */
           } else if (fu <= fv || v == x || v == w) {    l1 = strlen( dirc );                  /* length of directory */
             v=u;    if( dirc[l1-1] != DIRSEPARATOR ){
             fv=fu;      dirc[l1] =  DIRSEPARATOR;
           }      dirc[l1+1] = 0; 
         }      printf(" DIRC3 = %s \n",dirc);
   }    }
   nrerror("Too many iterations in brent");    ss = strrchr( name, '.' );            /* find last / */
   *xmin=x;    if (ss >0){
   return fx;      ss++;
 }      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 /****************** mnbrak ***********************/      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      finame[l1-l2]= 0;
             double (*func)(double))    }
 {  
   double ulim,u,r,q, dum;    return( 0 );                          /* we're done */
   double fu;  }
    
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  /******************************************/
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  void replace_back_to_slash(char *s, char*t)
       SHFT(dum,*fb,*fa,dum)  {
       }    int i;
   *cx=(*bx)+GOLD*(*bx-*ax);    int lg=0;
   *fc=(*func)(*cx);    i=0;
   while (*fb > *fc) {    lg=strlen(t);
     r=(*bx-*ax)*(*fb-*fc);    for(i=0; i<= lg; i++) {
     q=(*bx-*cx)*(*fb-*fa);      (s[i] = t[i]);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      if (t[i]== '\\') s[i]='/';
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    }
     ulim=(*bx)+GLIMIT*(*cx-*bx);  }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  int nbocc(char *s, char occ)
     } else if ((*cx-u)*(u-ulim) > 0.0) {  {
       fu=(*func)(u);    int i,j=0;
       if (fu < *fc) {    int lg=20;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    i=0;
           SHFT(*fb,*fc,fu,(*func)(u))    lg=strlen(s);
           }    for(i=0; i<= lg; i++) {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    if  (s[i] == occ ) j++;
       u=ulim;    }
       fu=(*func)(u);    return j;
     } else {  }
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  void cutv(char *u,char *v, char*t, char occ)
     }  {
     SHFT(*ax,*bx,*cx,u)    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       SHFT(*fa,*fb,*fc,fu)       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       }       gives u="abcedf" and v="ghi2j" */
 }    int i,lg,j,p=0;
     i=0;
 /*************** linmin ************************/    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 int ncom;    }
 double *pcom,*xicom;  
 double (*nrfunc)(double []);    lg=strlen(t);
      for(j=0; j<p; j++) {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      (u[j] = t[j]);
 {    }
   double brent(double ax, double bx, double cx,       u[p]='\0';
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);     for(j=0; j<= lg; j++) {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      if (j>=(p+1))(v[j-p-1] = t[j]);
               double *fc, double (*func)(double));    }
   int j;  }
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /********************** nrerror ********************/
    
   ncom=n;  void nrerror(char error_text[])
   pcom=vector(1,n);  {
   xicom=vector(1,n);    fprintf(stderr,"ERREUR ...\n");
   nrfunc=func;    fprintf(stderr,"%s\n",error_text);
   for (j=1;j<=n;j++) {    exit(EXIT_FAILURE);
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  /*********************** vector *******************/
   }  double *vector(int nl, int nh)
   ax=0.0;  {
   xx=1.0;    double *v;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if (!v) nrerror("allocation failure in vector");
 #ifdef DEBUG    return v-nl+NR_END;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  /************************ free vector ******************/
     xi[j] *= xmin;  void free_vector(double*v, int nl, int nh)
     p[j] += xi[j];  {
   }    free((FREE_ARG)(v+nl-NR_END));
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  
 }  /************************ivector *******************************/
   int *ivector(long nl,long nh)
 /*************** powell ************************/  {
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    int *v;
             double (*func)(double []))    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 {    if (!v) nrerror("allocation failure in ivector");
   void linmin(double p[], double xi[], int n, double *fret,    return v-nl+NR_END;
               double (*func)(double []));  }
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  /******************free ivector **************************/
   double fp,fptt;  void free_ivector(int *v, long nl, long nh)
   double *xits;  {
   pt=vector(1,n);    free((FREE_ARG)(v+nl-NR_END));
   ptt=vector(1,n);  }
   xit=vector(1,n);  
   xits=vector(1,n);  /************************lvector *******************************/
   *fret=(*func)(p);  long *lvector(long nl,long nh)
   for (j=1;j<=n;j++) pt[j]=p[j];  {
   for (*iter=1;;++(*iter)) {    long *v;
     fp=(*fret);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     ibig=0;    if (!v) nrerror("allocation failure in ivector");
     del=0.0;    return v-nl+NR_END;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  }
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  /******************free lvector **************************/
     printf("\n");  void free_lvector(long *v, long nl, long nh)
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    free((FREE_ARG)(v+nl-NR_END));
       fptt=(*fret);  }
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  /******************* imatrix *******************************/
 #endif  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       printf("%d",i);fflush(stdout);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       linmin(p,xit,n,fret,func);  { 
       if (fabs(fptt-(*fret)) > del) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         del=fabs(fptt-(*fret));    int **m; 
         ibig=i;    
       }    /* allocate pointers to rows */ 
 #ifdef DEBUG    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       printf("%d %.12e",i,(*fret));    if (!m) nrerror("allocation failure 1 in matrix()"); 
       for (j=1;j<=n;j++) {    m += NR_END; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m -= nrl; 
         printf(" x(%d)=%.12e",j,xit[j]);    
       }    
       for(j=1;j<=n;j++)    /* allocate rows and set pointers to them */ 
         printf(" p=%.12e",p[j]);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       printf("\n");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 #endif    m[nrl] += NR_END; 
     }    m[nrl] -= ncl; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    
 #ifdef DEBUG    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       int k[2],l;    
       k[0]=1;    /* return pointer to array of pointers to rows */ 
       k[1]=-1;    return m; 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /****************** free_imatrix *************************/
       printf("\n");  void free_imatrix(m,nrl,nrh,ncl,nch)
       for(l=0;l<=1;l++) {        int **m;
         for (j=1;j<=n;j++) {        long nch,ncl,nrh,nrl; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];       /* free an int matrix allocated by imatrix() */ 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    free((FREE_ARG) (m+nrl-NR_END)); 
       }  } 
 #endif  
   /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
       free_vector(xit,1,n);  {
       free_vector(xits,1,n);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       free_vector(ptt,1,n);    double **m;
       free_vector(pt,1,n);  
       return;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m += NR_END;
     for (j=1;j<=n;j++) {    m -= nrl;
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       pt[j]=p[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     fptt=(*func)(ptt);    m[nrl] -= ncl;
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if (t < 0.0) {    return m;
         linmin(p,xit,n,fret,func);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         for (j=1;j<=n;j++) {     */
           xi[j][ibig]=xi[j][n];  }
           xi[j][n]=xit[j];  
         }  /*************************free matrix ************************/
 #ifdef DEBUG  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           printf(" %.12e",xit[j]);    free((FREE_ARG)(m+nrl-NR_END));
         printf("\n");  }
 #endif  
       }  /******************* ma3x *******************************/
     }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   }  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /**** Prevalence limit ****************/  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    m -= nrl;
      matrix by transitions matrix until convergence is reached */  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int i, ii,j,k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double min, max, maxmin, maxmax,sumnew=0.;    m[nrl] += NR_END;
   double **matprod2();    m[nrl] -= ncl;
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double agefin, delaymax=50 ; /* Max number of years to converge */  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (ii=1;ii<=nlstate+ndeath;ii++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     for (j=1;j<=nlstate+ndeath;j++){    m[nrl][ncl] += NR_END;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
    cov[1]=1.;    
      for (i=nrl+1; i<=nrh; i++) {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      for (j=ncl+1; j<=nch; j++) 
     newm=savm;        m[i][j]=m[i][j-1]+nlay;
     /* Covariates have to be included here again */    }
      cov[2]=agefin;    return m; 
      /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       for (k=1; k<=cptcovn;k++) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  }
       }  
       for (k=1; k<=cptcovage;k++)  /*************************free ma3x ************************/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       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]]];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    free((FREE_ARG)(m+nrl-NR_END));
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  }
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
     savm=oldm;  {
     oldm=newm;    /* Caution optionfilefiname is hidden */
     maxmax=0.;    strcpy(tmpout,optionfilefiname);
     for(j=1;j<=nlstate;j++){    strcat(tmpout,"/"); /* Add to the right */
       min=1.;    strcat(tmpout,fileres);
       max=0.;    return tmpout;
       for(i=1; i<=nlstate; i++) {  }
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /*************** function subdirf2 ***********/
         prlim[i][j]= newm[i][j]/(1-sumnew);  char *subdirf2(char fileres[], char *preop)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    
       }    /* Caution optionfilefiname is hidden */
       maxmin=max-min;    strcpy(tmpout,optionfilefiname);
       maxmax=FMAX(maxmax,maxmin);    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
     if(maxmax < ftolpl){    strcat(tmpout,fileres);
       return prlim;    return tmpout;
     }  }
   }  
 }  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
 /*************** transition probabilities **********/  {
     
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   double s1, s2;    strcat(tmpout,"/");
   /*double t34;*/    strcat(tmpout,preop);
   int i,j,j1, nc, ii, jj;    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
     for(i=1; i<= nlstate; i++){    return tmpout;
     for(j=1; j<i;j++){  }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /***************** f1dim *************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  extern int ncom; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  extern double *pcom,*xicom;
       }  extern double (*nrfunc)(double []); 
       ps[i][j]=s2;   
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  double f1dim(double x) 
     }  { 
     for(j=i+1; j<=nlstate+ndeath;j++){    int j; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double f;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double *xt; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/   
       }    xt=vector(1,ncom); 
       ps[i][j]=s2;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     }    f=(*nrfunc)(xt); 
   }    free_vector(xt,1,ncom); 
   for(i=1; i<= nlstate; i++){    return f; 
      s1=0;  } 
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  /*****************brent *************************/
     for(j=i+1; j<=nlstate+ndeath; j++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       s1+=exp(ps[i][j]);  { 
     ps[i][i]=1./(s1+1.);    int iter; 
     for(j=1; j<i; j++)    double a,b,d,etemp;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double fu,fv,fw,fx;
     for(j=i+1; j<=nlstate+ndeath; j++)    double ftemp;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    double e=0.0; 
   } /* end i */   
     a=(ax < cx ? ax : cx); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    b=(ax > cx ? ax : cx); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    x=w=v=bx; 
       ps[ii][jj]=0;    fw=fv=fx=(*f)(x); 
       ps[ii][ii]=1;    for (iter=1;iter<=ITMAX;iter++) { 
     }      xm=0.5*(a+b); 
   }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      printf(".");fflush(stdout);
     for(jj=1; jj<= nlstate+ndeath; jj++){      fprintf(ficlog,".");fflush(ficlog);
      printf("%lf ",ps[ii][jj]);  #ifdef DEBUG
    }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     printf("\n ");      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     printf("\n ");printf("%lf ",cov[2]);*/  #endif
 /*      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        *xmin=x; 
   goto end;*/        return fx; 
     return ps;      } 
 }      ftemp=fu;
       if (fabs(e) > tol1) { 
 /**************** Product of 2 matrices ******************/        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        p=(x-v)*q-(x-w)*r; 
 {        q=2.0*(q-r); 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        if (q > 0.0) p = -p; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        q=fabs(q); 
   /* in, b, out are matrice of pointers which should have been initialized        etemp=e; 
      before: only the contents of out is modified. The function returns        e=d; 
      a pointer to pointers identical to out */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   long i, j, k;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for(i=nrl; i<= nrh; i++)        else { 
     for(k=ncolol; k<=ncoloh; k++)          d=p/q; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          u=x+d; 
         out[i][k] +=in[i][j]*b[j][k];          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
   return out;        } 
 }      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 /************* Higher Matrix Product ***************/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      if (fu <= fx) { 
 {        if (u >= x) a=x; else b=x; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        SHFT(v,w,x,u) 
      duration (i.e. until          SHFT(fv,fw,fx,fu) 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          } else { 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step            if (u < x) a=u; else b=u; 
      (typically every 2 years instead of every month which is too big).            if (fu <= fw || w == x) { 
      Model is determined by parameters x and covariates have to be              v=w; 
      included manually here.              w=u; 
               fv=fw; 
      */              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
   int i, j, d, h, k;              v=u; 
   double **out, cov[NCOVMAX];              fv=fu; 
   double **newm;            } 
           } 
   /* Hstepm could be zero and should return the unit matrix */    } 
   for (i=1;i<=nlstate+ndeath;i++)    nrerror("Too many iterations in brent"); 
     for (j=1;j<=nlstate+ndeath;j++){    *xmin=x; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    return fx; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  } 
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /****************** mnbrak ***********************/
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       newm=savm;              double (*func)(double)) 
       /* Covariates have to be included here again */  { 
       cov[1]=1.;    double ulim,u,r,q, dum;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    double fu; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];   
 for (k=1; k<=cptcovage;k++)    *fa=(*func)(*ax); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    *fb=(*func)(*bx); 
    for (k=1; k<=cptcovprod;k++)    if (*fb > *fa) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
         } 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    *cx=(*bx)+GOLD*(*bx-*ax); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    *fc=(*func)(*cx); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    while (*fb > *fc) { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      r=(*bx-*ax)*(*fb-*fc); 
       savm=oldm;      q=(*bx-*cx)*(*fb-*fa); 
       oldm=newm;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for(i=1; i<=nlstate+ndeath; i++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       for(j=1;j<=nlstate+ndeath;j++) {      if ((*bx-u)*(u-*cx) > 0.0) { 
         po[i][j][h]=newm[i][j];        fu=(*func)(u); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
          */        fu=(*func)(u); 
       }        if (fu < *fc) { 
   } /* end h */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   return po;            SHFT(*fb,*fc,fu,(*func)(u)) 
 }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
 /*************** log-likelihood *************/        fu=(*func)(u); 
 double func( double *x)      } else { 
 {        u=(*cx)+GOLD*(*cx-*bx); 
   int i, ii, j, k, mi, d, kk;        fu=(*func)(u); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      } 
   double **out;      SHFT(*ax,*bx,*cx,u) 
   double sw; /* Sum of weights */        SHFT(*fa,*fb,*fc,fu) 
   double lli; /* Individual log likelihood */        } 
   long ipmx;  } 
   /*extern weight */  
   /* We are differentiating ll according to initial status */  /*************** linmin ************************/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  int ncom; 
     printf(" %d\n",s[4][i]);  double *pcom,*xicom;
   */  double (*nrfunc)(double []); 
   cov[1]=1.;   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  { 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double brent(double ax, double bx, double cx, 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];                 double (*f)(double), double tol, double *xmin); 
     for(mi=1; mi<= wav[i]-1; mi++){    double f1dim(double x); 
       for (ii=1;ii<=nlstate+ndeath;ii++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);                double *fc, double (*func)(double)); 
       for(d=0; d<dh[mi][i]; d++){    int j; 
         newm=savm;    double xx,xmin,bx,ax; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    double fx,fb,fa;
         for (kk=1; kk<=cptcovage;kk++) {   
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    ncom=n; 
         }    pcom=vector(1,n); 
            xicom=vector(1,n); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    nrfunc=func; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    for (j=1;j<=n;j++) { 
         savm=oldm;      pcom[j]=p[j]; 
         oldm=newm;      xicom[j]=xi[j]; 
            } 
            ax=0.0; 
       } /* end mult */    xx=1.0; 
          mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  #ifdef DEBUG
       ipmx +=1;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       sw += weight[i];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  #endif
     } /* end of wave */    for (j=1;j<=n;j++) { 
   } /* end of individual */      xi[j] *= xmin; 
       p[j] += xi[j]; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    } 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    free_vector(xicom,1,n); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    free_vector(pcom,1,n); 
   return -l;  } 
 }  
   char *asc_diff_time(long time_sec, char ascdiff[])
   {
 /*********** Maximum Likelihood Estimation ***************/    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    sec_left = (time_sec) % (60*60*24);
 {    hours = (sec_left) / (60*60) ;
   int i,j, iter;    sec_left = (sec_left) %(60*60);
   double **xi,*delti;    minutes = (sec_left) /60;
   double fret;    sec_left = (sec_left) % (60);
   xi=matrix(1,npar,1,npar);    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   for (i=1;i<=npar;i++)    return ascdiff;
     for (j=1;j<=npar;j++)  }
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  /*************** powell ************************/
   powell(p,xi,npar,ftol,&iter,&fret,func);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
 }    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 /**** Computes Hessian and covariance matrix ***/    double fp,fptt;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    double *xits;
 {    int niterf, itmp;
   double  **a,**y,*x,pd;  
   double **hess;    pt=vector(1,n); 
   int i, j,jk;    ptt=vector(1,n); 
   int *indx;    xit=vector(1,n); 
     xits=vector(1,n); 
   double hessii(double p[], double delta, int theta, double delti[]);    *fret=(*func)(p); 
   double hessij(double p[], double delti[], int i, int j);    for (j=1;j<=n;j++) pt[j]=p[j]; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    for (*iter=1;;++(*iter)) { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;      fp=(*fret); 
       ibig=0; 
       del=0.0; 
   hess=matrix(1,npar,1,npar);      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
   printf("\nCalculation of the hessian matrix. Wait...\n");      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);
   for (i=1;i<=npar;i++){      /*    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);
     printf("%d",i);fflush(stdout);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     hess[i][i]=hessii(p,ftolhess,i,delti);      */
     /*printf(" %f ",p[i]);*/     for (i=1;i<=n;i++) {
   }        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
   for (i=1;i<=npar;i++) {        fprintf(ficrespow," %.12lf", p[i]);
     for (j=1;j<=npar;j++)  {      }
       if (j>i) {      printf("\n");
         printf(".%d%d",i,j);fflush(stdout);      fprintf(ficlog,"\n");
         hess[i][j]=hessij(p,delti,i,j);      fprintf(ficrespow,"\n");fflush(ficrespow);
         hess[j][i]=hess[i][j];      if(*iter <=3){
       }        tm = *localtime(&curr_time.tv_sec);
     }        strcpy(strcurr,asctime(&tm));
   }  /*       asctime_r(&tm,strcurr); */
   printf("\n");        forecast_time=curr_time; 
         itmp = strlen(strcurr);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
            strcurr[itmp-1]='\0';
   a=matrix(1,npar,1,npar);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   y=matrix(1,npar,1,npar);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   x=vector(1,npar);        for(niterf=10;niterf<=30;niterf+=10){
   indx=ivector(1,npar);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (i=1;i<=npar;i++)          tmf = *localtime(&forecast_time.tv_sec);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*      asctime_r(&tmf,strfor); */
   ludcmp(a,npar,indx,&pd);          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
   for (j=1;j<=npar;j++) {          if(strfor[itmp-1]=='\n')
     for (i=1;i<=npar;i++) x[i]=0;          strfor[itmp-1]='\0';
     x[j]=1;          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);
     lubksb(a,npar,indx,x);          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<=npar;i++){        }
       matcov[i][j]=x[i];      }
     }      for (i=1;i<=n;i++) { 
   }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   printf("\n#Hessian matrix#\n");  #ifdef DEBUG
   for (i=1;i<=npar;i++) {        printf("fret=%lf \n",*fret);
     for (j=1;j<=npar;j++) {        fprintf(ficlog,"fret=%lf \n",*fret);
       printf("%.3e ",hess[i][j]);  #endif
     }        printf("%d",i);fflush(stdout);
     printf("\n");        fprintf(ficlog,"%d",i);fflush(ficlog);
   }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
   /* Recompute Inverse */          del=fabs(fptt-(*fret)); 
   for (i=1;i<=npar;i++)          ibig=i; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        } 
   ludcmp(a,npar,indx,&pd);  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   /*  printf("\n#Hessian matrix recomputed#\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   for (j=1;j<=npar;j++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (i=1;i<=npar;i++) x[i]=0;          printf(" x(%d)=%.12e",j,xit[j]);
     x[j]=1;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     lubksb(a,npar,indx,x);        }
     for (i=1;i<=npar;i++){        for(j=1;j<=n;j++) {
       y[i][j]=x[i];          printf(" p=%.12e",p[j]);
       printf("%.3e ",y[i][j]);          fprintf(ficlog," p=%.12e",p[j]);
     }        }
     printf("\n");        printf("\n");
   }        fprintf(ficlog,"\n");
   */  #endif
       } 
   free_matrix(a,1,npar,1,npar);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   free_matrix(y,1,npar,1,npar);  #ifdef DEBUG
   free_vector(x,1,npar);        int k[2],l;
   free_ivector(indx,1,npar);        k[0]=1;
   free_matrix(hess,1,npar,1,npar);        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
 }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
 /*************** hessian matrix ****************/          fprintf(ficlog," %.12e",p[j]);
 double hessii( double x[], double delta, int theta, double delti[])        }
 {        printf("\n");
   int i;        fprintf(ficlog,"\n");
   int l=1, lmax=20;        for(l=0;l<=1;l++) {
   double k1,k2;          for (j=1;j<=n;j++) {
   double p2[NPARMAX+1];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   double res;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double fx;          }
   int k=0,kmax=10;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double l1;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   fx=func(x);  #endif
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);        free_vector(xit,1,n); 
     delts=delt;        free_vector(xits,1,n); 
     for(k=1 ; k <kmax; k=k+1){        free_vector(ptt,1,n); 
       delt = delta*(l1*k);        free_vector(pt,1,n); 
       p2[theta]=x[theta] +delt;        return; 
       k1=func(p2)-fx;      } 
       p2[theta]=x[theta]-delt;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       k2=func(p2)-fx;      for (j=1;j<=n;j++) { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        ptt[j]=2.0*p[j]-pt[j]; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        xit[j]=p[j]-pt[j]; 
              pt[j]=p[j]; 
 #ifdef DEBUG      } 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      fptt=(*func)(ptt); 
 #endif      if (fptt < fp) { 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        if (t < 0.0) { 
         k=kmax;          linmin(p,xit,n,fret,func); 
       }          for (j=1;j<=n;j++) { 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            xi[j][ibig]=xi[j][n]; 
         k=kmax; l=lmax*10.;            xi[j][n]=xit[j]; 
       }          }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  #ifdef DEBUG
         delts=delt;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          for(j=1;j<=n;j++){
   }            printf(" %.12e",xit[j]);
   delti[theta]=delts;            fprintf(ficlog," %.12e",xit[j]);
   return res;          }
            printf("\n");
 }          fprintf(ficlog,"\n");
   #endif
 double hessij( double x[], double delti[], int thetai,int thetaj)        }
 {      } 
   int i;    } 
   int l=1, l1, lmax=20;  } 
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];  /**** Prevalence limit (stable prevalence)  ****************/
   int k;  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   fx=func(x);  {
   for (k=1; k<=2; k++) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for (i=1;i<=npar;i++) p2[i]=x[i];       matrix by transitions matrix until convergence is reached */
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    int i, ii,j,k;
     k1=func(p2)-fx;    double min, max, maxmin, maxmax,sumnew=0.;
      double **matprod2();
     p2[thetai]=x[thetai]+delti[thetai]/k;    double **out, cov[NCOVMAX], **pmij();
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double **newm;
     k2=func(p2)-fx;    double agefin, delaymax=50 ; /* Max number of years to converge */
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    for (ii=1;ii<=nlstate+ndeath;ii++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      for (j=1;j<=nlstate+ndeath;j++){
     k3=func(p2)-fx;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;     cov[1]=1.;
     k4=func(p2)-fx;   
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 #ifdef DEBUG    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     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);      newm=savm;
 #endif      /* Covariates have to be included here again */
   }       cov[2]=agefin;
   return res;    
 }        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 /************** Inverse of matrix **************/          /*      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]]);*/
 void ludcmp(double **a, int n, int *indx, double *d)        }
 {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int i,imax,j,k;        for (k=1; k<=cptcovprod;k++)
   double big,dum,sum,temp;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double *vv;  
          /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   vv=vector(1,n);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   *d=1.0;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   for (i=1;i<=n;i++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     big=0.0;  
     for (j=1;j<=n;j++)      savm=oldm;
       if ((temp=fabs(a[i][j])) > big) big=temp;      oldm=newm;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      maxmax=0.;
     vv[i]=1.0/big;      for(j=1;j<=nlstate;j++){
   }        min=1.;
   for (j=1;j<=n;j++) {        max=0.;
     for (i=1;i<j;i++) {        for(i=1; i<=nlstate; i++) {
       sum=a[i][j];          sumnew=0;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       a[i][j]=sum;          prlim[i][j]= newm[i][j]/(1-sumnew);
     }          max=FMAX(max,prlim[i][j]);
     big=0.0;          min=FMIN(min,prlim[i][j]);
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];        maxmin=max-min;
       for (k=1;k<j;k++)        maxmax=FMAX(maxmax,maxmin);
         sum -= a[i][k]*a[k][j];      }
       a[i][j]=sum;      if(maxmax < ftolpl){
       if ( (dum=vv[i]*fabs(sum)) >= big) {        return prlim;
         big=dum;      }
         imax=i;    }
       }  }
     }  
     if (j != imax) {  /*************** transition probabilities ***************/ 
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         a[imax][k]=a[j][k];  {
         a[j][k]=dum;    double s1, s2;
       }    /*double t34;*/
       *d = -(*d);    int i,j,j1, nc, ii, jj;
       vv[imax]=vv[j];  
     }      for(i=1; i<= nlstate; i++){
     indx[j]=imax;        for(j=1; j<i;j++){
     if (a[j][j] == 0.0) a[j][j]=TINY;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     if (j != n) {            /*s2 += param[i][j][nc]*cov[nc];*/
       dum=1.0/(a[j][j]);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     }          }
   }          ps[i][j]=s2;
   free_vector(vv,1,n);  /* Doesn't work */  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
 ;        }
 }        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 void lubksb(double **a, int n, int *indx, double b[])            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   int i,ii=0,ip,j;          }
   double sum;          ps[i][j]=s2;
          }
   for (i=1;i<=n;i++) {      }
     ip=indx[i];      /*ps[3][2]=1;*/
     sum=b[ip];      
     b[ip]=b[i];      for(i=1; i<= nlstate; i++){
     if (ii)        s1=0;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for(j=1; j<i; j++)
     else if (sum) ii=i;          s1+=exp(ps[i][j]);
     b[i]=sum;        for(j=i+1; j<=nlstate+ndeath; j++)
   }          s1+=exp(ps[i][j]);
   for (i=n;i>=1;i--) {        ps[i][i]=1./(s1+1.);
     sum=b[i];        for(j=1; j<i; j++)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     b[i]=sum/a[i][i];        for(j=i+1; j<=nlstate+ndeath; j++)
   }          ps[i][j]= exp(ps[i][j])*ps[i][i];
 }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
 /************ Frequencies ********************/      
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 {  /* Some frequencies */        for(jj=1; jj<= nlstate+ndeath; jj++){
            ps[ii][jj]=0;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          ps[ii][ii]=1;
   double ***freq; /* Frequencies */        }
   double *pp;      }
   double pos;      
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   pp=vector(1,nlstate);  /*         printf("ddd %lf ",ps[ii][jj]); */
   /*       } */
   strcpy(fileresp,"p");  /*       printf("\n "); */
   strcat(fileresp,fileres);  /*        } */
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*        printf("\n ");printf("%lf ",cov[2]); */
     printf("Problem with prevalence resultfile: %s\n", fileresp);         /*
     exit(0);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   }        goto end;*/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      return ps;
   j1=0;  }
   
   j=cptcoveff;  /**************** Product of 2 matrices ******************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   for(k1=1; k1<=j;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        j1++;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    /* in, b, out are matrice of pointers which should have been initialized 
          scanf("%d", i);*/       before: only the contents of out is modified. The function returns
         for (i=-1; i<=nlstate+ndeath; i++)         a pointer to pointers identical to out */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      long i, j, k;
            for(m=agemin; m <= agemax+3; m++)    for(i=nrl; i<= nrh; i++)
              freq[i][jk][m]=0;      for(k=ncolol; k<=ncoloh; k++)
                for(j=ncl,out[i][k]=0.; j<=nch; j++)
        for (i=1; i<=imx; i++) {          out[i][k] +=in[i][j]*b[j][k];
          bool=1;  
          if  (cptcovn>0) {    return out;
            for (z1=1; z1<=cptcoveff; z1++)  }
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;  
          }  /************* Higher Matrix Product ***************/
           if (bool==1) {  
            for(m=firstpass; m<=lastpass-1; m++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
              if(agev[m][i]==0) agev[m][i]=agemax+1;  {
              if(agev[m][i]==1) agev[m][i]=agemax+2;    /* Computes the transition matrix starting at age 'age' over 
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];       'nhstepm*hstepm*stepm' months (i.e. until
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
            }       nhstepm*hstepm matrices. 
          }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        }       (typically every 2 years instead of every month which is too big 
         if  (cptcovn>0) {       for the memory).
          fprintf(ficresp, "\n#********** Variable ");       Model is determined by parameters x and covariates have to be 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       included manually here. 
        fprintf(ficresp, "**********\n#");  
         }       */
        for(i=1; i<=nlstate;i++)  
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    int i, j, d, h, k;
        fprintf(ficresp, "\n");    double **out, cov[NCOVMAX];
            double **newm;
   for(i=(int)agemin; i <= (int)agemax+3; i++){  
     if(i==(int)agemax+3)    /* Hstepm could be zero and should return the unit matrix */
       printf("Total");    for (i=1;i<=nlstate+ndeath;i++)
     else      for (j=1;j<=nlstate+ndeath;j++){
       printf("Age %d", i);        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for(jk=1; jk <=nlstate ; jk++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
         pp[jk] += freq[jk][m][i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
     for(jk=1; jk <=nlstate ; jk++){      for(d=1; d <=hstepm; d++){
       for(m=-1, pos=0; m <=0 ; m++)        newm=savm;
         pos += freq[jk][m][i];        /* Covariates have to be included here again */
       if(pp[jk]>=1.e-10)        cov[1]=1.;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       else        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for (k=1; k<=cptcovage;k++)
     }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovprod;k++)
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         pp[jk] += freq[jk][m][i];  
     }  
     for(jk=1,pos=0; jk <=nlstate ; jk++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       pos += pp[jk];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for(jk=1; jk <=nlstate ; jk++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       if(pos>=1.e-5)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        savm=oldm;
       else        oldm=newm;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      }
       if( i <= (int) agemax){      for(i=1; i<=nlstate+ndeath; i++)
         if(pos>=1.e-5)        for(j=1;j<=nlstate+ndeath;j++) {
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          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]);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           */
       }        }
     }    } /* end h */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    return po;
       for(m=-1; m <=nlstate+ndeath; m++)  }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  /*************** log-likelihood *************/
     printf("\n");  double func( double *x)
     }  {
     }    int i, ii, j, k, mi, d, kk;
  }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   fclose(ficresp);    double sw; /* Sum of weights */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double lli; /* Individual log likelihood */
   free_vector(pp,1,nlstate);    int s1, s2;
     double bbh, survp;
 }  /* End of Freq */    long ipmx;
     /*extern weight */
 /************* Waves Concatenation ***************/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    */
      Death is a valid wave (if date is known).    cov[1]=1.;
      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]    for(k=1; k<=nlstate; k++) ll[k]=0.;
      and mw[mi+1][i]. dh depends on stepm.  
      */    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, mi, m;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for(mi=1; mi<= wav[i]-1; mi++){
      double sum=0., jmean=0.;*/          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 int j, k=0,jk, ju, jl;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      double sum=0.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 jmin=1e+5;            }
  jmax=-1;          for(d=0; d<dh[mi][i]; d++){
 jmean=0.;            newm=savm;
   for(i=1; i<=imx; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     mi=0;            for (kk=1; kk<=cptcovage;kk++) {
     m=firstpass;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     while(s[m][i] <= nlstate){            }
       if(s[m][i]>=1)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         mw[++mi][i]=m;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(m >=lastpass)            savm=oldm;
         break;            oldm=newm;
       else          } /* end mult */
         m++;        
     }/* end while */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     if (s[m][i] > nlstate){          /* But now since version 0.9 we anticipate for bias at large stepm.
       mi++;     /* Death is another wave */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       /* if(mi==0)  never been interviewed correctly before death */           * (in months) between two waves is not a multiple of stepm, we rounded to 
          /* Only death is a correct wave */           * the nearest (and in case of equal distance, to the lowest) interval but now
       mw[mi][i]=m;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
     wav[i]=mi;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     if(mi==0)           * -stepm/2 to stepm/2 .
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);           * For stepm=1 the results are the same as for previous versions of Imach.
   }           * For stepm > 1 the results are less biased than in previous versions. 
            */
   for(i=1; i<=imx; i++){          s1=s[mw[mi][i]][i];
     for(mi=1; mi<wav[i];mi++){          s2=s[mw[mi+1][i]][i];
       if (stepm <=0)          bbh=(double)bh[mi][i]/(double)stepm; 
         dh[mi][i]=1;          /* bias bh is positive if real duration
       else{           * is higher than the multiple of stepm and negative otherwise.
         if (s[mw[mi+1][i]][i] > nlstate) {           */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/          if( s2 > nlstate){ 
           if(j==0) j=1;  /* Survives at least one month after exam */            /* i.e. if s2 is a death state and if the date of death is known 
           k=k+1;               then the contribution to the likelihood is the probability to 
           if (j >= jmax) jmax=j;               die between last step unit time and current  step unit time, 
           else if (j <= jmin)jmin=j;               which is also equal to probability to die before dh 
           sum=sum+j;               minus probability to die before dh-stepm . 
         }               In version up to 0.92 likelihood was computed
         else{          as if date of death was unknown. Death was treated as any other
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          health state: the date of the interview describes the actual state
           /*if ((j<0) || (j>28)) printf("j=%d num=%d ",j,i);*/          and not the date of a change in health state. The former idea was
           k=k+1;          to consider that at each interview the state was recorded
           if (j >= jmax) jmax=j;          (healthy, disable or death) and IMaCh was corrected; but when we
           else if (j <= jmin)jmin=j;          introduced the exact date of death then we should have modified
           sum=sum+j;          the contribution of an exact death to the likelihood. This new
         }          contribution is smaller and very dependent of the step unit
         jk= j/stepm;          stepm. It is no more the probability to die between last interview
         jl= j -jk*stepm;          and month of death but the probability to survive from last
         ju= j -(jk+1)*stepm;          interview up to one month before death multiplied by the
         if(jl <= -ju)          probability to die within a month. Thanks to Chris
           dh[mi][i]=jk;          Jackson for correcting this bug.  Former versions increased
         else          mortality artificially. The bad side is that we add another loop
           dh[mi][i]=jk+1;          which slows down the processing. The difference can be up to 10%
         if(dh[mi][i]==0)          lower mortality.
           dh[mi][i]=1; /* At least one step */            */
       }            lli=log(out[s1][s2] - savm[s1][s2]);
     }  
   }  
   jmean=sum/k;          } else if  (s2==-2) {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            for (j=1,survp=0. ; j<=nlstate; j++) 
 }              survp += out[s1][j];
 /*********** Tricode ****************************/            lli= survp;
 void tricode(int *Tvar, int **nbcode, int imx)          }
 {          
   int Ndum[20],ij=1, k, j, i;          else if  (s2==-4) {
   int cptcode=0;            for (j=3,survp=0. ; j<=nlstate; j++) 
   cptcoveff=0;              survp += out[s1][j];
              lli= survp;
   for (k=0; k<19; k++) Ndum[k]=0;          }
   for (k=1; k<=7; k++) ncodemax[k]=0;          
           else if  (s2==-5) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for (j=1,survp=0. ; j<=2; j++) 
     for (i=1; i<=imx; i++) {              survp += out[s1][j];
       ij=(int)(covar[Tvar[j]][i]);            lli= survp;
       Ndum[ij]++;          }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;  
     }          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for (i=0; i<=cptcode; i++) {            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       if(Ndum[i]!=0) ncodemax[j]++;          } 
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     ij=1;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
     for (i=1; i<=ncodemax[j]; i++) {          sw += weight[i];
       for (k=0; k<=19; k++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if (Ndum[k] != 0) {        } /* end of wave */
           nbcode[Tvar[j]][ij]=k;      } /* end of individual */
           ij++;    }  else if(mle==2){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if (ij > ncodemax[j]) break;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }          for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
   }              for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (k=0; k<19; k++) Ndum[k]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
  for (i=1; i<=ncovmodel; i++) {          for(d=0; d<=dh[mi][i]; d++){
       ij=Tvar[i];            newm=savm;
       Ndum[ij]++;            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];
  ij=1;            }
  for (i=1; i<=10; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    if((Ndum[i]!=0) && (i<=ncov)){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      Tvaraff[ij]=i;            savm=oldm;
      ij++;            oldm=newm;
    }          } /* end mult */
  }        
            s1=s[mw[mi][i]][i];
     cptcoveff=ij-1;          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 /*********** Health Expectancies ****************/          ipmx +=1;
           sw += weight[i];
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 {        } /* end of wave */
   /* Health expectancies */      } /* end of individual */
   int i, j, nhstepm, hstepm, h;    }  else if(mle==3){  /* exponential inter-extrapolation */
   double age, agelim,hf;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double ***p3mat;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficreseij,"# Health expectancies\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficreseij,"# Age");            for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<=nlstate;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficreseij," %1d-%1d",i,j);            }
   fprintf(ficreseij,"\n");          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   hstepm=1*YEARM; /*  Every j years of age (in month) */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   agelim=AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* nhstepm age range expressed in number of stepm */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            savm=oldm;
     /* Typically if 20 years = 20*12/6=40 stepm */            oldm=newm;
     if (stepm >= YEARM) hstepm=1;          } /* end mult */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s1=s[mw[mi][i]][i];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          s2=s[mw[mi+1][i]][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          bbh=(double)bh[mi][i]/(double)stepm; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            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 */
           ipmx +=1;
           sw += weight[i];
     for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<=nlstate;j++)        } /* end of wave */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      } /* end of individual */
           eij[i][j][(int)age] +=p3mat[i][j][h];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     hf=1;        for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) hf=stepm/YEARM;          for (ii=1;ii<=nlstate+ndeath;ii++)
     fprintf(ficreseij,"%.0f",age );            for (j=1;j<=nlstate+ndeath;j++){
     for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            }
       }          for(d=0; d<dh[mi][i]; d++){
     fprintf(ficreseij,"\n");            newm=savm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            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 ******************/          
 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)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Variance of health expectancies */            savm=oldm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            oldm=newm;
   double **newm;          } /* end mult */
   double **dnewm,**doldm;        
   int i, j, nhstepm, hstepm, h;          s1=s[mw[mi][i]][i];
   int k, cptcode;          s2=s[mw[mi+1][i]][i];
    double *xp;          if( s2 > nlstate){ 
   double **gp, **gm;            lli=log(out[s1][s2] - savm[s1][s2]);
   double ***gradg, ***trgradg;          }else{
   double ***p3mat;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double age,agelim;          }
   int theta;          ipmx +=1;
           sw += weight[i];
    fprintf(ficresvij,"# Covariances of life expectancies\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficresvij,"# Age");  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   for(i=1; i<=nlstate;i++)        } /* end of wave */
     for(j=1; j<=nlstate;j++)      } /* end of individual */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   fprintf(ficresvij,"\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   xp=vector(1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   dnewm=matrix(1,nlstate,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   doldm=matrix(1,nlstate,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=1*YEARM; /* Every year of age */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }
   agelim = AGESUP;          for(d=0; d<dh[mi][i]; d++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            newm=savm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (stepm >= YEARM) hstepm=1;            for (kk=1; kk<=cptcovage;kk++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          
     gp=matrix(0,nhstepm,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gm=matrix(0,nhstepm,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(theta=1; theta <=npar; theta++){            oldm=newm;
       for(i=1; i<=npar; i++){ /* Computes gradient */          } /* end mult */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        
       }          s1=s[mw[mi][i]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            s2=s[mw[mi+1][i]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(j=1; j<= nlstate; j++){          ipmx +=1;
         for(h=0; h<=nhstepm; h++){          sw += weight[i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             gp[h][j] += prlim[i][i]*p3mat[i][j][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]);*/
         }        } /* end of wave */
       }      } /* end of individual */
        } /* End of if */
       for(i=1; i<=npar; i++) /* Computes gradient */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return -l;
       for(j=1; j<= nlstate; j++){  }
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  /*************** log-likelihood *************/
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  double funcone( double *x)
         }  {
       }    /* Same as likeli but slower because of a lot of printf and if */
       for(j=1; j<= nlstate; j++)    int i, ii, j, k, mi, d, kk;
         for(h=0; h<=nhstepm; h++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double **out;
         }    double lli; /* Individual log likelihood */
     } /* End theta */    double llt;
     int s1, s2;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    double bbh, survp;
     /*extern weight */
     for(h=0; h<=nhstepm; h++)    /* We are differentiating ll according to initial status */
       for(j=1; j<=nlstate;j++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         for(theta=1; theta <=npar; theta++)    /*for(i=1;i<imx;i++) 
           trgradg[h][j][theta]=gradg[h][theta][j];      printf(" %d\n",s[4][i]);
     */
     for(i=1;i<=nlstate;i++)    cov[1]=1.;
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for(mi=1; mi<= wav[i]-1; mi++){
         for(i=1;i<=nlstate;i++)        for (ii=1;ii<=nlstate+ndeath;ii++)
           for(j=1;j<=nlstate;j++)          for (j=1;j<=nlstate+ndeath;j++){
             vareij[i][j][(int)age] += doldm[i][j];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }          }
     h=1;        for(d=0; d<dh[mi][i]; d++){
     if (stepm >= YEARM) h=stepm/YEARM;          newm=savm;
     fprintf(ficresvij,"%.0f ",age );          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];
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          }
       }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficresvij,"\n");                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_matrix(gp,0,nhstepm,1,nlstate);          savm=oldm;
     free_matrix(gm,0,nhstepm,1,nlstate);          oldm=newm;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        } /* end mult */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        s1=s[mw[mi][i]][i];
   } /* End age */        s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm; 
   free_vector(xp,1,npar);        /* bias is positive if real duration
   free_matrix(doldm,1,nlstate,1,npar);         * is higher than the multiple of stepm and negative otherwise.
   free_matrix(dnewm,1,nlstate,1,nlstate);         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
 }          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if (mle==1){
 /************ Variance of prevlim ******************/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        } else if(mle==2){
 {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   /* Variance of prevalence limit */        } else if(mle==3){  /* exponential inter-extrapolation */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          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 */
   double **newm;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **dnewm,**doldm;          lli=log(out[s1][s2]); /* Original formula */
   int i, j, nhstepm, hstepm;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   int k, cptcode;          lli=log(out[s1][s2]); /* Original formula */
   double *xp;        } /* End of if */
   double *gp, *gm;        ipmx +=1;
   double **gradg, **trgradg;        sw += weight[i];
   double age,agelim;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int theta;  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
            if(globpr){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   fprintf(ficresvpl,"# Age");   %10.6f %10.6f %10.6f ", \
   for(i=1; i<=nlstate;i++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       fprintf(ficresvpl," %1d-%1d",i,i);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   fprintf(ficresvpl,"\n");          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
   xp=vector(1,npar);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   dnewm=matrix(1,nlstate,1,npar);          }
   doldm=matrix(1,nlstate,1,nlstate);          fprintf(ficresilk," %10.6f\n", -llt);
          }
   hstepm=1*YEARM; /* Every year of age */      } /* end of wave */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    } /* end of individual */
   agelim = AGESUP;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if (stepm >= YEARM) hstepm=1;    if(globpr==0){ /* First time we count the contributions and weights */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      gipmx=ipmx;
     gradg=matrix(1,npar,1,nlstate);      gsw=sw;
     gp=vector(1,nlstate);    }
     gm=vector(1,nlstate);    return -l;
   }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*************** function likelione ***********/
       }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    /* This routine should help understanding what is done with 
         gp[i] = prlim[i][i];       the selection of individuals/waves and
           to check the exact contribution to the likelihood.
       for(i=1; i<=npar; i++) /* Computes gradient */       Plotting could be done.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);     */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int k;
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
       for(i=1;i<=nlstate;i++)      strcat(fileresilk,fileres);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     } /* End theta */        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     trgradg =matrix(1,nlstate,1,npar);      }
       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");
     for(j=1; j<=nlstate;j++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       for(theta=1; theta <=npar; theta++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         trgradg[j][theta]=gradg[theta][j];      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     for(i=1;i<=nlstate;i++)      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       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);    *fretone=(*funcone)(p);
     for(i=1;i<=nlstate;i++)    if(*globpri !=0){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fprintf(ficresvpl,"%.0f ",age );      fflush(fichtm); 
     for(i=1; i<=nlstate;i++)    } 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    return;
     fprintf(ficresvpl,"\n");  }
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);  /*********** Maximum Likelihood Estimation ***************/
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   free_vector(xp,1,npar);    int i,j, iter;
   free_matrix(doldm,1,nlstate,1,npar);    double **xi;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double fret;
     double fretone; /* Only one call to likelihood */
 }    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
 /***********************************************/        xi[i][j]=(i==j ? 1.0 : 0.0);
 /**************** Main Program *****************/    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 /***********************************************/    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
 /*int main(int argc, char *argv[])*/    if((ficrespow=fopen(filerespow,"w"))==NULL) {
 int main()      printf("Problem with resultfile: %s\n", filerespow);
 {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double agedeb, agefin,hf;    for (i=1;i<=nlstate;i++)
   double agemin=1.e20, agemax=-1.e20;      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double fret;    fprintf(ficrespow,"\n");
   double **xi,tmp,delta;  
     powell(p,xi,npar,ftol,&iter,&fret,func);
   double dum; /* Dummy variable */  
   double ***p3mat;    fclose(ficrespow);
   int *indx;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   char line[MAXLINE], linepar[MAXLINE];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   char title[MAXLINE];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];  }
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];  /**** Computes Hessian and covariance matrix ***/
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   int firstobs=1, lastobs=10;  {
   int sdeb, sfin; /* Status at beginning and end */    double  **a,**y,*x,pd;
   int c,  h , cpt,l;    double **hess;
   int ju,jl, mi;    int i, j,jk;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int *indx;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
      double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int hstepm, nhstepm;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   double bage, fage, age, agelim, agebase;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double ftolpl=FTOL;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double **prlim;    double gompertz(double p[]);
   double *severity;    hess=matrix(1,npar,1,npar);
   double ***param; /* Matrix of parameters */  
   double  *p;    printf("\nCalculation of the hessian matrix. Wait...\n");
   double **matcov; /* Matrix of covariance */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double ***delti3; /* Scale */    for (i=1;i<=npar;i++){
   double *delti; /* Scale */      printf("%d",i);fflush(stdout);
   double ***eij, ***vareij;      fprintf(ficlog,"%d",i);fflush(ficlog);
   double **varpl; /* Variances of prevalence limits by age */     
   double *epj, vepp;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";      
   char *alph[]={"a","a","b","c","d","e"}, str[4];      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   char z[1]="c", occ;    }
 #include <sys/time.h>    
 #include <time.h>    for (i=1;i<=npar;i++) {
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      for (j=1;j<=npar;j++)  {
   /* long total_usecs;        if (j>i) { 
   struct timeval start_time, end_time;          printf(".%d%d",i,j);fflush(stdout);
            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
           hess[j][i]=hess[i][j];    
   printf("\nIMACH, Version 0.64a");          /*printf(" %lf ",hess[i][j]);*/
   printf("\nEnter the parameter file name: ");        }
       }
 #ifdef windows    }
   scanf("%s",pathtot);    printf("\n");
   getcwd(pathcd, size);    fprintf(ficlog,"\n");
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /* cutv(path,optionfile,pathtot,'\\');*/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
 split(pathtot, path,optionfile);    a=matrix(1,npar,1,npar);
   chdir(path);    y=matrix(1,npar,1,npar);
   replace(pathc,path);    x=vector(1,npar);
 #endif    indx=ivector(1,npar);
 #ifdef unix    for (i=1;i<=npar;i++)
   scanf("%s",optionfile);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 #endif    ludcmp(a,npar,indx,&pd);
   
 /*-------- arguments in the command line --------*/    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   strcpy(fileres,"r");      x[j]=1;
   strcat(fileres, optionfile);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   /*---------arguments file --------*/        matcov[i][j]=x[i];
       }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    printf("\n#Hessian matrix#\n");
   }    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   strcpy(filereso,"o");      for (j=1;j<=npar;j++) { 
   strcat(filereso,fileres);        printf("%.3e ",hess[i][j]);
   if((ficparo=fopen(filereso,"w"))==NULL) {        fprintf(ficlog,"%.3e ",hess[i][j]);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      }
   }      printf("\n");
       fprintf(ficlog,"\n");
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /* Recompute Inverse */
     fgets(line, MAXLINE, ficpar);    for (i=1;i<=npar;i++)
     puts(line);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fputs(line,ficparo);    ludcmp(a,npar,indx,&pd);
   }  
   ungetc(c,ficpar);    /*  printf("\n#Hessian matrix recomputed#\n");
   
   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);      for (i=1;i<=npar;i++) x[i]=0;
   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);      x[j]=1;
       lubksb(a,npar,indx,x);
   covar=matrix(0,NCOVMAX,1,n);      for (i=1;i<=npar;i++){ 
   cptcovn=0;        y[i][j]=x[i];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
   ncovmodel=2+cptcovn;      }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      printf("\n");
        fprintf(ficlog,"\n");
   /* Read guess parameters */    }
   /* Reads comments: lines beginning with '#' */    */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    free_matrix(a,1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);    free_matrix(y,1,npar,1,npar);
     puts(line);    free_vector(x,1,npar);
     fputs(line,ficparo);    free_ivector(indx,1,npar);
   }    free_matrix(hess,1,npar,1,npar);
   ungetc(c,ficpar);  
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  }
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){  /*************** hessian matrix ****************/
       fscanf(ficpar,"%1d%1d",&i1,&j1);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       fprintf(ficparo,"%1d%1d",i1,j1);  {
       printf("%1d%1d",i,j);    int i;
       for(k=1; k<=ncovmodel;k++){    int l=1, lmax=20;
         fscanf(ficpar," %lf",&param[i][j][k]);    double k1,k2;
         printf(" %lf",param[i][j][k]);    double p2[NPARMAX+1];
         fprintf(ficparo," %lf",param[i][j][k]);    double res;
       }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       fscanf(ficpar,"\n");    double fx;
       printf("\n");    int k=0,kmax=10;
       fprintf(ficparo,"\n");    double l1;
     }  
      fx=func(x);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    for (i=1;i<=npar;i++) p2[i]=x[i];
   p=param[1][1];    for(l=0 ; l <=lmax; l++){
        l1=pow(10,l);
   /* Reads comments: lines beginning with '#' */      delts=delt;
   while((c=getc(ficpar))=='#' && c!= EOF){      for(k=1 ; k <kmax; k=k+1){
     ungetc(c,ficpar);        delt = delta*(l1*k);
     fgets(line, MAXLINE, ficpar);        p2[theta]=x[theta] +delt;
     puts(line);        k1=func(p2)-fx;
     fputs(line,ficparo);        p2[theta]=x[theta]-delt;
   }        k2=func(p2)-fx;
   ungetc(c,ficpar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  #ifdef DEBUG
   for(i=1; i <=nlstate; i++){        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     for(j=1; j <=nlstate+ndeath-1; j++){        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  #endif
       printf("%1d%1d",i,j);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       fprintf(ficparo,"%1d%1d",i1,j1);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for(k=1; k<=ncovmodel;k++){          k=kmax;
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }
         printf(" %le",delti3[i][j][k]);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         fprintf(ficparo," %le",delti3[i][j][k]);          k=kmax; l=lmax*10.;
       }        }
       fscanf(ficpar,"\n");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       printf("\n");          delts=delt;
       fprintf(ficparo,"\n");        }
     }      }
   }    }
   delti=delti3[1][1];    delti[theta]=delts;
      return res; 
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){  }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     puts(line);  {
     fputs(line,ficparo);    int i;
   }    int l=1, l1, lmax=20;
   ungetc(c,ficpar);    double k1,k2,k3,k4,res,fx;
      double p2[NPARMAX+1];
   matcov=matrix(1,npar,1,npar);    int k;
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);    fx=func(x);
     printf("%s",str);    for (k=1; k<=2; k++) {
     fprintf(ficparo,"%s",str);      for (i=1;i<=npar;i++) p2[i]=x[i];
     for(j=1; j <=i; j++){      p2[thetai]=x[thetai]+delti[thetai]/k;
       fscanf(ficpar," %le",&matcov[i][j]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       printf(" %.5le",matcov[i][j]);      k1=func(p2)-fx;
       fprintf(ficparo," %.5le",matcov[i][j]);    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
     fscanf(ficpar,"\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     printf("\n");      k2=func(p2)-fx;
     fprintf(ficparo,"\n");    
   }      p2[thetai]=x[thetai]-delti[thetai]/k;
   for(i=1; i <=npar; i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(j=i+1;j<=npar;j++)      k3=func(p2)-fx;
       matcov[i][j]=matcov[j][i];    
          p2[thetai]=x[thetai]-delti[thetai]/k;
   printf("\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     /*-------- data file ----------*/  #ifdef DEBUG
     if((ficres =fopen(fileres,"w"))==NULL) {      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       printf("Problem with resultfile: %s\n", fileres);goto end;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }  #endif
     fprintf(ficres,"#%s\n",version);    }
        return res;
     if((fic=fopen(datafile,"r"))==NULL)    {  }
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
     n= lastobs;  { 
     severity = vector(1,maxwav);    int i,imax,j,k; 
     outcome=imatrix(1,maxwav+1,1,n);    double big,dum,sum,temp; 
     num=ivector(1,n);    double *vv; 
     moisnais=vector(1,n);   
     annais=vector(1,n);    vv=vector(1,n); 
     moisdc=vector(1,n);    *d=1.0; 
     andc=vector(1,n);    for (i=1;i<=n;i++) { 
     agedc=vector(1,n);      big=0.0; 
     cod=ivector(1,n);      for (j=1;j<=n;j++) 
     weight=vector(1,n);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     mint=matrix(1,maxwav,1,n);      vv[i]=1.0/big; 
     anint=matrix(1,maxwav,1,n);    } 
     s=imatrix(1,maxwav+1,1,n);    for (j=1;j<=n;j++) { 
     adl=imatrix(1,maxwav+1,1,n);          for (i=1;i<j;i++) { 
     tab=ivector(1,NCOVMAX);        sum=a[i][j]; 
     ncodemax=ivector(1,8);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
     i=1;      } 
     while (fgets(line, MAXLINE, fic) != NULL)    {      big=0.0; 
       if ((i >= firstobs) && (i <=lastobs)) {      for (i=j;i<=n;i++) { 
                sum=a[i][j]; 
         for (j=maxwav;j>=1;j--){        for (k=1;k<j;k++) 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          sum -= a[i][k]*a[k][j]; 
           strcpy(line,stra);        a[i][j]=sum; 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          big=dum; 
         }          imax=i; 
                } 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      if (j != imax) { 
         for (k=1;k<=n;k++) { 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          dum=a[imax][k]; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        } 
         for (j=ncov;j>=1;j--){        *d = -(*d); 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        vv[imax]=vv[j]; 
         }      } 
         num[i]=atol(stra);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
         /*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 != n) { 
         dum=1.0/(a[j][j]); 
         i=i+1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       }      } 
     }    } 
     free_vector(vv,1,n);  /* Doesn't work */
     /*scanf("%d",i);*/  ;
   imx=i-1; /* Number of individuals */  } 
   
   /* Calculation of the number of parameter from char model*/  void lubksb(double **a, int n, int *indx, double b[]) 
   Tvar=ivector(1,15);  { 
   Tprod=ivector(1,15);    int i,ii=0,ip,j; 
   Tvaraff=ivector(1,15);    double sum; 
   Tvard=imatrix(1,15,1,2);   
   Tage=ivector(1,15);          for (i=1;i<=n;i++) { 
          ip=indx[i]; 
   if (strlen(model) >1){      sum=b[ip]; 
     j=0, j1=0, k1=1, k2=1;      b[ip]=b[i]; 
     j=nbocc(model,'+');      if (ii) 
     j1=nbocc(model,'*');        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     cptcovn=j+1;      else if (sum) ii=i; 
     cptcovprod=j1;      b[i]=sum; 
        } 
        for (i=n;i>=1;i--) { 
     strcpy(modelsav,model);      sum=b[i]; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       printf("Error. Non available option model=%s ",model);      b[i]=sum/a[i][i]; 
       goto end;    } 
     }  } 
      
     for(i=(j+1); 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[])
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  {  /* Some frequencies */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    
       /*scanf("%d",i);*/    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       if (strchr(strb,'*')) {    int first;
         cutv(strd,strc,strb,'*');    double ***freq; /* Frequencies */
         if (strcmp(strc,"age")==0) {    double *pp, **prop;
           cptcovprod--;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           cutv(strb,stre,strd,'V');    FILE *ficresp;
           Tvar[i]=atoi(stre);    char fileresp[FILENAMELENGTH];
           cptcovage++;    
             Tage[cptcovage]=i;    pp=vector(1,nlstate);
             /*printf("stre=%s ", stre);*/    prop=matrix(1,nlstate,iagemin,iagemax+3);
         }    strcpy(fileresp,"p");
         else if (strcmp(strd,"age")==0) {    strcat(fileresp,fileres);
           cptcovprod--;    if((ficresp=fopen(fileresp,"w"))==NULL) {
           cutv(strb,stre,strc,'V');      printf("Problem with prevalence resultfile: %s\n", fileresp);
           Tvar[i]=atoi(stre);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           cptcovage++;      exit(0);
           Tage[cptcovage]=i;    }
         }    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         else {    j1=0;
           cutv(strb,stre,strc,'V');    
           Tvar[i]=ncov+k1;    j=cptcoveff;
           cutv(strb,strc,strd,'V');    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    first=1;
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];    for(k1=1; k1<=j;k1++){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for(i1=1; i1<=ncodemax[k1];i1++){
           for (k=1; k<=lastobs;k++)        j1++;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           k1++;          scanf("%d", i);*/
           k2=k2+2;        for (i=-5; i<=nlstate+ndeath; i++)  
         }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       }            for(m=iagemin; m <= iagemax+3; m++)
       else {              freq[i][jk][m]=0;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/      for (i=1; i<=nlstate; i++)  
       cutv(strd,strc,strb,'V');        for(m=iagemin; m <= iagemax+3; m++)
       Tvar[i]=atoi(strc);          prop[i][m]=0;
       }        
       strcpy(modelsav,stra);          dateintsum=0;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        k2cpt=0;
         scanf("%d",i);*/        for (i=1; i<=imx; i++) {
     }          bool=1;
 }          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   printf("cptcovprod=%d ", cptcovprod);                bool=0;
   scanf("%d ",i);*/          }
     fclose(fic);          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
     /*  if(mle==1){*/              k2=anint[m][i]+(mint[m][i]/12.);
     if (weightopt != 1) { /* Maximisation without weights*/              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       for(i=1;i<=n;i++) weight[i]=1.0;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     /*-calculation of age at interview from date of interview and age at death -*/                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     agev=matrix(1,maxwav,1,imx);                if (m<lastpass) {
                      freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for (i=1; i<=imx; i++)  {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                }
       for(m=1; (m<= maxwav); m++){                
         if(s[m][i] >0){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           if (s[m][i] == nlstate+1) {                  dateintsum=dateintsum+k2;
             if(agedc[i]>0)                  k2cpt++;
               if(moisdc[i]!=99 && andc[i]!=9999)                }
               agev[m][i]=agedc[i];                /*}*/
             else {            }
               if (andc[i]!=9999){          }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        }
               agev[m][i]=-1;         
               }        /*      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);
           }        if  (cptcovn>0) {
           else if(s[m][i] !=9){ /* Should no more exist */          fprintf(ficresp, "\n#********** Variable "); 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if(mint[m][i]==99 || anint[m][i]==9999)          fprintf(ficresp, "**********\n#");
               agev[m][i]=1;        }
             else if(agev[m][i] <agemin){        for(i=1; i<=nlstate;i++) 
               agemin=agev[m][i];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        fprintf(ficresp, "\n");
             }        
             else if(agev[m][i] >agemax){        for(i=iagemin; i <= iagemax+3; i++){
               agemax=agev[m][i];          if(i==iagemax+3){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            fprintf(ficlog,"Total");
             }          }else{
             /*agev[m][i]=anint[m][i]-annais[i];*/            if(first==1){
             /*   agev[m][i] = age[i]+2*m;*/              first=0;
           }              printf("See log file for details...\n");
           else { /* =9 */            }
             agev[m][i]=1;            fprintf(ficlog,"Age %d", i);
             s[m][i]=-1;          }
           }          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         else /*= 0 Unknown */              pp[jk] += freq[jk][m][i]; 
           agev[m][i]=1;          }
       }          for(jk=1; jk <=nlstate ; jk++){
                for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
     for (i=1; i<=imx; i++)  {            if(pp[jk]>=1.e-10){
       for(m=1; (m<= maxwav); m++){              if(first==1){
         if (s[m][i] > (nlstate+ndeath)) {              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           printf("Error: Wrong value in nlstate or ndeath\n");                }
           goto end;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }            }else{
       }              if(first==1)
     }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            }
           }
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);          for(jk=1; jk <=nlstate ; jk++){
     free_vector(moisnais,1,n);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     free_vector(annais,1,n);              pp[jk] += freq[jk][m][i];
     free_matrix(mint,1,maxwav,1,n);          }       
     free_matrix(anint,1,maxwav,1,n);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     free_vector(moisdc,1,n);            pos += pp[jk];
     free_vector(andc,1,n);            posprop += prop[jk][i];
           }
              for(jk=1; jk <=nlstate ; jk++){
     wav=ivector(1,imx);            if(pos>=1.e-5){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              if(first==1)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                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);
     /* Concatenates waves */            }else{
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       Tcode=ivector(1,100);            }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            if( i <= iagemax){
       ncodemax[1]=1;              if(pos>=1.e-5){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                      /*probs[i][jk][j1]= pp[jk]/pos;*/
    codtab=imatrix(1,100,1,10);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
    h=0;              }
    m=pow(2,cptcoveff);              else
                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
    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++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
            h++;            for(m=-1; m <=nlstate+ndeath; m++)
            if (h>m) h=1;codtab[h][k]=j;              if(freq[jk][m][i] !=0 ) {
          }              if(first==1)
        }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
    }              }
           if(i <= iagemax)
             fprintf(ficresp,"\n");
    /*for(i=1; i <=m ;i++){          if(first==1)
      for(k=1; k <=cptcovn; k++){            printf("Others in log...\n");
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          fprintf(ficlog,"\n");
      }        }
      printf("\n");      }
    }    }
    scanf("%d",i);*/    dateintmean=dateintsum/k2cpt; 
       
    /* Calculates basic frequencies. Computes observed prevalence at single age    fclose(ficresp);
        and prints on file fileres'p'. */    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* End of Freq */
     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 */  /************ Prevalence ********************/
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  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 Powell, parameters are in a vector p[] starting at p[1]    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       in each health status at the date of interview (if between dateprev1 and dateprev2).
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */       We still use firstpass and lastpass as another selection.
     */
     if(mle==1){   
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     }    double ***freq; /* Frequencies */
        double *pp, **prop;
     /*--------- results files --------------*/    double pos,posprop; 
     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);    double  y2; /* in fractional years */
        int iagemin, iagemax;
    jk=1;  
    fprintf(ficres,"# Parameters\n");    iagemin= (int) agemin;
    printf("# Parameters\n");    iagemax= (int) agemax;
    for(i=1,jk=1; i <=nlstate; i++){    /*pp=vector(1,nlstate);*/
      for(k=1; k <=(nlstate+ndeath); k++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
        if (k != i)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          {    j1=0;
            printf("%d%d ",i,k);    
            fprintf(ficres,"%1d%1d ",i,k);    j=cptcoveff;
            for(j=1; j <=ncovmodel; j++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
              printf("%f ",p[jk]);    
              fprintf(ficres,"%f ",p[jk]);    for(k1=1; k1<=j;k1++){
              jk++;      for(i1=1; i1<=ncodemax[k1];i1++){
            }        j1++;
            printf("\n");        
            fprintf(ficres,"\n");        for (i=1; i<=nlstate; i++)  
          }          for(m=iagemin; m <= iagemax+3; m++)
      }            prop[i][m]=0.0;
    }       
  if(mle==1){        for (i=1; i<=imx; i++) { /* Each individual */
     /* Computing hessian and covariance matrix */          bool=1;
     ftolhess=ftol; /* Usually correct */          if  (cptcovn>0) {
     hesscov(matcov, p, npar, delti, ftolhess, func);            for (z1=1; z1<=cptcoveff; z1++) 
  }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fprintf(ficres,"# Scales\n");                bool=0;
     printf("# Scales\n");          } 
      for(i=1,jk=1; i <=nlstate; i++){          if (bool==1) { 
       for(j=1; j <=nlstate+ndeath; j++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         if (j!=i) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           fprintf(ficres,"%1d%1d",i,j);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           printf("%1d%1d",i,j);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           for(k=1; k<=ncovmodel;k++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             printf(" %.5e",delti[jk]);                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); 
             fprintf(ficres," %.5e",delti[jk]);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             jk++;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
           }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           printf("\n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
           fprintf(ficres,"\n");                } 
         }              }
       }            } /* end selection of waves */
       }          }
            }
     k=1;        for(i=iagemin; i <= iagemax+3; i++){  
     fprintf(ficres,"# Covariance\n");          
     printf("# Covariance\n");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     for(i=1;i<=npar;i++){            posprop += prop[jk][i]; 
       /*  if (k>nlstate) k=1;          } 
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          for(jk=1; jk <=nlstate ; jk++){     
       printf("%s%d%d",alph[k],i1,tab[i]);*/            if( i <=  iagemax){ 
       fprintf(ficres,"%3d",i);              if(posprop>=1.e-5){ 
       printf("%3d",i);                probs[i][jk][j1]= prop[jk][i]/posprop;
       for(j=1; j<=i;j++){              } 
         fprintf(ficres," %.5e",matcov[i][j]);            } 
         printf(" %.5e",matcov[i][j]);          }/* end jk */ 
       }        }/* end i */ 
       fprintf(ficres,"\n");      } /* end i1 */
       printf("\n");    } /* end k1 */
       k++;    
     }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
        /*free_vector(pp,1,nlstate);*/
     while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       ungetc(c,ficpar);  }  /* End of prevalence */
       fgets(line, MAXLINE, ficpar);  
       puts(line);  /************* Waves Concatenation ***************/
       fputs(line,ficparo);  
     }  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)
     ungetc(c,ficpar);  {
      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       Death is a valid wave (if date is known).
           mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     if (fage <= 2) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       bage = agemin;       and mw[mi+1][i]. dh depends on stepm.
       fage = agemax;       */
     }  
     int i, mi, m;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       double sum=0., jmean=0.;*/
     int first;
        int j, k=0,jk, ju, jl;
 /*------------ gnuplot -------------*/    double sum=0.;
 chdir(pathcd);    first=0;
   if((ficgp=fopen("graph.plt","w"))==NULL) {    jmin=1e+5;
     printf("Problem with file graph.gp");goto end;    jmax=-1;
   }    jmean=0.;
 #ifdef windows    for(i=1; i<=imx; i++){
   fprintf(ficgp,"cd \"%s\" \n",pathc);      mi=0;
 #endif      m=firstpass;
 m=pow(2,cptcoveff);      while(s[m][i] <= nlstate){
          if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
  /* 1eme*/          mw[++mi][i]=m;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        if(m >=lastpass)
    for (k1=1; k1<= m ; k1 ++) {          break;
         else
 #ifdef windows          m++;
     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);      }/* end while */
 #endif      if (s[m][i] > nlstate){
 #ifdef unix        mi++;     /* Death is another wave */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        /* if(mi==0)  never been interviewed correctly before death */
 #endif           /* Only death is a correct wave */
         mw[mi][i]=m;
 for (i=1; i<= nlstate ; i ++) {      }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      wav[i]=mi;
 }      if(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);        nbwarn++;
     for (i=1; i<= nlstate ; i ++) {        if(first==0){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          first=1;
 }        }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        if(first==1){
      for (i=1; i<= nlstate ; i ++) {          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* end mi==0 */
 }      } /* End individuals */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    for(i=1; i<=imx; i++){
 fprintf(ficgp,"\nset ter gif small size 400,300");      for(mi=1; mi<wav[i];mi++){
 #endif        if (stepm <=0)
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          dh[mi][i]=1;
    }        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   /*2 eme*/            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   for (k1=1; k1<= m ; k1 ++) {              if(j==0) j=1;  /* Survives at least one month after exam */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              else if(j<0){
                    nberr++;
     for (i=1; i<= nlstate+1 ; i ++) {                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]);
       k=2*i;                j=1; /* Temporary Dangerous patch */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for (j=1; j<= nlstate+1 ; j ++) {                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              }
 }                k=k+1;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              if (j >= jmax) jmax=j;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              if (j <= jmin) jmin=j;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              sum=sum+j;
       for (j=1; j<= nlstate+1 ; j ++) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }            }
       fprintf(ficgp,"\" t\"\" w l 0,");          else{
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       for (j=1; j<= nlstate+1 ; j ++) {  /*        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]); */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");            k=k+1;
 }              if (j >= jmax) jmax=j;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            else if (j <= jmin)jmin=j;
       else fprintf(ficgp,"\" t\"\" w l 0,");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            if(j<0){
   }              nberr++;
                printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   /*3eme*/              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]);
             }
   for (k1=1; k1<= m ; k1 ++) {            sum=sum+j;
     for (cpt=1; cpt<= nlstate ; cpt ++) {          }
       k=2+nlstate*(cpt-1);          jk= j/stepm;
       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);          jl= j -jk*stepm;
       for (i=1; i< nlstate ; i ++) {          ju= j -(jk+1)*stepm;
         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);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       }            if(jl==0){
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              dh[mi][i]=jk;
     }              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
                      * at the price of an extra matrix product in likelihood */
   /* CV preval stat */              dh[mi][i]=jk+1;
   for (k1=1; k1<= m ; k1 ++) {              bh[mi][i]=ju;
     for (cpt=1; cpt<nlstate ; cpt ++) {            }
       k=3;          }else{
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);            if(jl <= -ju){
       for (i=1; i< nlstate ; i ++)              dh[mi][i]=jk;
         fprintf(ficgp,"+$%d",k+i+1);              bh[mi][i]=jl;       /* bias is positive if real duration
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                                   * is higher than the multiple of stepm and negative otherwise.
                                         */
       l=3+(nlstate+ndeath)*cpt;            }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            else{
       for (i=1; i< nlstate ; i ++) {              dh[mi][i]=jk+1;
         l=3+(nlstate+ndeath)*cpt;              bh[mi][i]=ju;
         fprintf(ficgp,"+$%d",l+i+1);            }
       }            if(dh[mi][i]==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                dh[mi][i]=1; /* At least one step */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              bh[mi][i]=ju; /* At least one step */
     }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   }            }
           } /* end if mle */
   /* proba elementaires */        }
    for(i=1,jk=1; i <=nlstate; i++){      } /* end wave */
     for(k=1; k <=(nlstate+ndeath); k++){    }
       if (k != i) {    jmean=sum/k;
         for(j=1; j <=ncovmodel; j++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           /*fprintf(ficgp,"%s",alph[1]);*/   }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;  /*********** Tricode ****************************/
           fprintf(ficgp,"\n");  void tricode(int *Tvar, int **nbcode, int imx)
         }  {
       }    
     }    int Ndum[20],ij=1, k, j, i, maxncov=19;
     }    int cptcode=0;
     cptcoveff=0; 
   for(jk=1; jk <=m; jk++) {   
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    for (k=0; k<maxncov; k++) Ndum[k]=0;
    i=1;    for (k=1; k<=7; k++) ncodemax[k]=0;
    for(k2=1; k2<=nlstate; k2++) {  
      k3=i;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
      for(k=1; k<=(nlstate+ndeath); k++) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
        if (k != k2){                                 modality*/ 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 ij=1;        Ndum[ij]++; /*store the modality */
         for(j=3; j <=ncovmodel; j++) {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                                         Tvar[j]. If V=sex and male is 0 and 
             ij++;                                         female is 1, then  cptcode=1.*/
           }      }
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for (i=0; i<=cptcode; i++) {
         }        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 */
           fprintf(ficgp,")/(1");      }
          
         for(k1=1; k1 <=nlstate; k1++){        ij=1; 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      for (i=1; i<=ncodemax[j]; i++) {
 ij=1;        for (k=0; k<= maxncov; k++) {
           for(j=3; j <=ncovmodel; j++){          if (Ndum[k] != 0) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            nbcode[Tvar[j]][ij]=k; 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             ij++;            
           }            ij++;
           else          }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          if (ij > ncodemax[j]) break; 
           }        }  
           fprintf(ficgp,")");      } 
         }    }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");   for (k=0; k< maxncov; k++) Ndum[k]=0;
         i=i+ncovmodel;  
        }   for (i=1; i<=ncovmodel-2; i++) { 
      }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    }     ij=Tvar[i];
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);     Ndum[ij]++;
   }   }
      
   fclose(ficgp);   ij=1;
       for (i=1; i<= maxncov; i++) {
 chdir(path);     if((Ndum[i]!=0) && (i<=ncovcol)){
     free_matrix(agev,1,maxwav,1,imx);       Tvaraff[ij]=i; /*For printing */
     free_ivector(wav,1,imx);       ij++;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);     }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   }
       
     free_imatrix(s,1,maxwav+1,1,n);   cptcoveff=ij-1; /*Number of simple covariates*/
      }
      
     free_ivector(num,1,n);  /*********** Health Expectancies ****************/
     free_vector(agedc,1,n);  
     free_vector(weight,1,n);  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[] )
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);  {
     fclose(ficres);    /* Health expectancies */
     /*  }*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
        double age, agelim, hf;
    /*________fin mle=1_________*/    double ***p3mat,***varhe;
        double **dnewm,**doldm;
     double *xp;
      double **gp, **gm;
     /* No more information from the sample is required now */    double ***gradg, ***trgradg;
   /* Reads comments: lines beginning with '#' */    int theta;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     fgets(line, MAXLINE, ficpar);    xp=vector(1,npar);
     puts(line);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     fputs(line,ficparo);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   }    
   ungetc(c,ficpar);    fprintf(ficreseij,"# Local time at start: %s", strstart);
      fprintf(ficreseij,"# Health expectancies\n");
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    fprintf(ficreseij,"# Age");
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    for(i=1; i<=nlstate;i++)
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      for(j=1; j<=nlstate;j++)
 /*--------- index.htm --------*/        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
   if((fichtm=fopen("index.htm","w"))==NULL)    {  
     printf("Problem with index.htm \n");goto end;    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64a </font> <hr size=\"2\" color=\"#EC5E5E\">    else  hstepm=estepm;   
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    /* We compute the life expectancy from trapezoids spaced every estepm months
 Total number of observations=%d <br>     * This is mainly to measure the difference between two models: for example
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>     * if stepm=24 months pijx are given only every 2 years and by summing them
 <hr  size=\"2\" color=\"#EC5E5E\">     * we are calculating an estimate of the Life Expectancy assuming a linear 
 <li>Outputs files<br><br>\n     * progression in between and thus overestimating or underestimating according
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n     * to the curvature of the survival function. If, for the same date, we 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>     * to compare the new estimate of Life expectancy with the same linear 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>     * hypothesis. A more precise result, taking into account a more precise
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>     * curvature will be obtained if estepm is as small as stepm. */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    /* For example we decided to compute the life expectancy with the smallest unit */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
  fprintf(fichtm," <li>Graphs</li><p>");       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
  m=cptcoveff;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
  j1=0;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  for(k1=1; k1<=m;k1++){       results. So we changed our mind and took the option of the best precision.
    for(i1=1; i1<=ncodemax[k1];i1++){    */
        j1++;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        if (cptcovn > 0) {  
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    agelim=AGESUP;
          for (cpt=1; cpt<=cptcoveff;cpt++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      /* nhstepm age range expressed in number of stepm */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
        }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      /* if (stepm >= YEARM) hstepm=1;*/
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        for(cpt=1; cpt<nlstate;cpt++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
        }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 interval) in state (%d): v%s%d%d.gif <br>         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
      }   
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }      /* Computing  Variances of health expectancies */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>       for(theta=1; theta <=npar; theta++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        for(i=1; i<=npar; i++){ 
 fprintf(fichtm,"\n</body>");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    }        }
  }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 fclose(fichtm);    
         cptj=0;
   /*--------------- Prevalence limit --------------*/        for(j=1; j<= nlstate; j++){
            for(i=1; i<=nlstate; i++){
   strcpy(filerespl,"pl");            cptj=cptj+1;
   strcat(filerespl,fileres);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            }
   }          }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        }
   fprintf(ficrespl,"#Prevalence limit\n");       
   fprintf(ficrespl,"#Age ");       
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(i=1; i<=npar; i++) 
   fprintf(ficrespl,"\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   prlim=matrix(1,nlstate,1,nlstate);        
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        cptj=0;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<= nlstate; j++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1;i<=nlstate;i++){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            cptj=cptj+1;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   k=0;  
   agebase=agemin;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   agelim=agemax;            }
   ftolpl=1.e-10;          }
   i1=cptcoveff;        }
   if (cptcovn < 1){i1=1;}        for(j=1; j<= nlstate*nlstate; j++)
           for(h=0; h<=nhstepm-1; h++){
   for(cptcov=1;cptcov<=i1;cptcov++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     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#******");  /* End theta */
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         fprintf(ficrespl,"******\n");  
               for(h=0; h<=nhstepm-1; h++)
         for (age=agebase; age<=agelim; age++){        for(j=1; j<=nlstate*nlstate;j++)
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for(theta=1; theta <=npar; theta++)
           fprintf(ficrespl,"%.0f",age );            trgradg[h][j][theta]=gradg[h][theta][j];
           for(i=1; i<=nlstate;i++)       
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");       for(i=1;i<=nlstate*nlstate;i++)
         }        for(j=1;j<=nlstate*nlstate;j++)
       }          varhe[i][j][(int)age] =0.;
     }  
   fclose(ficrespl);       printf("%d|",(int)age);fflush(stdout);
   /*------------- h Pij x at various ages ------------*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        for(k=0;k<=nhstepm-1;k++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   }          for(i=1;i<=nlstate*nlstate;i++)
   printf("Computing pij: result on file '%s' \n", filerespij);            for(j=1;j<=nlstate*nlstate;j++)
                varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   if (stepm<=24) stepsize=2;      }
       /* Computing expectancies */
   agelim=AGESUP;      for(i=1; i<=nlstate;i++)
   hstepm=stepsize*YEARM; /* Every year of age */        for(j=1; j<=nlstate;j++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
              eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   k=0;            
   for(cptcov=1;cptcov<=i1;cptcov++){  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;          }
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)      fprintf(ficreseij,"%3.0f",age );
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      cptj=0;
         fprintf(ficrespij,"******\n");      for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          cptj++;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficreseij,"\n");
           oldm=oldms;savm=savms;     
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficrespij,"# Age");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           for(i=1; i<=nlstate;i++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             for(j=1; j<=nlstate+ndeath;j++)      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
               fprintf(ficrespij," %1d-%1d",i,j);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");    }
           for (h=0; h<=nhstepm; h++){    printf("\n");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficlog,"\n");
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)    free_vector(xp,1,npar);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             fprintf(ficrespij,"\n");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
           fprintf(ficrespij,"\n");  
         }  /************ Variance ******************/
     }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   }  {
     /* Variance of health expectancies */
   fclose(ficrespij);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
   /*---------- Health expectancies and variances ------------*/    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
   strcpy(filerest,"t");    int i, j, nhstepm, hstepm, h, nstepm ;
   strcat(filerest,fileres);    int k, cptcode;
   if((ficrest=fopen(filerest,"w"))==NULL) {    double *xp;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   strcpy(filerese,"e");    double ***p3mat;
   strcat(filerese,fileres);    double age,agelim, hf;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double ***mobaverage;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    int theta;
   }    char digit[4];
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    char digitp[25];
   
  strcpy(fileresv,"v");    char fileresprobmorprev[FILENAMELENGTH];
   strcat(fileresv,fileres);  
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if(popbased==1){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      if(mobilav!=0)
   }        strcpy(digitp,"-populbased-mobilav-");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      else strcpy(digitp,"-populbased-nomobil-");
     }
   k=0;    else 
   for(cptcov=1;cptcov<=i1;cptcov++){      strcpy(digitp,"-stablbased-");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    if (mobilav!=0) {
       fprintf(ficrest,"\n#****** ");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(j=1;j<=cptcoveff;j++)      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficrest,"******\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
       fprintf(ficreseij,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    strcpy(fileresprobmorprev,"prmorprev"); 
       fprintf(ficreseij,"******\n");    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       fprintf(ficresvij,"\n#****** ");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for(j=1;j<=cptcoveff;j++)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    strcat(fileresprobmorprev,fileres);
       fprintf(ficresvij,"******\n");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       oldm=oldms;savm=savms;    }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   
       oldm=oldms;savm=savms;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
          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(ficrest,"#Total LEs with variances: e.. (std) ");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficrest,"\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
              for(i=1; i<=nlstate;i++)
       hf=1;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       if (stepm >= YEARM) hf=stepm/YEARM;    }  
       epj=vector(1,nlstate+1);    fprintf(ficresprobmorprev,"\n");
       for(age=bage; age <=fage ;age++){    fprintf(ficgp,"\n# Routine varevsij");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         fprintf(ficrest," %.0f",age);    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(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  /*   } */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }   fprintf(ficresvij, "#Local time at start: %s", strstart);
           epj[nlstate+1] +=epj[j];    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
         }    fprintf(ficresvij,"# Age");
         for(i=1, vepp=0.;i <=nlstate;i++)    for(i=1; i<=nlstate;i++)
           for(j=1;j <=nlstate;j++)      for(j=1; j<=nlstate;j++)
             vepp += vareij[i][j][(int)age];        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    fprintf(ficresvij,"\n");
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficrest,"\n");    doldm=matrix(1,nlstate,1,nlstate);
       }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
            gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  fclose(ficreseij);    gpp=vector(nlstate+1,nlstate+ndeath);
  fclose(ficresvij);    gmp=vector(nlstate+1,nlstate+ndeath);
   fclose(ficrest);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   fclose(ficpar);    
   free_vector(epj,1,nlstate+1);    if(estepm < stepm){
   /*  scanf("%d ",i); */      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   /*------- Variance limit prevalence------*/      else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
 strcpy(fileresvpl,"vpl");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(fileresvpl,fileres);       nhstepm is the number of hstepm from age to agelim 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       Look at hpijx to understand the reason of that which relies in memory size
     exit(0);       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("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
  k=0;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  for(cptcov=1;cptcov<=i1;cptcov++){       results. So we changed our mind and took the option of the best precision.
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    */
      k=k+1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      fprintf(ficresvpl,"\n#****** ");    agelim = AGESUP;
      for(j=1;j<=cptcoveff;j++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
      fprintf(ficresvpl,"******\n");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
      oldm=oldms;savm=savms;      gp=matrix(0,nhstepm,1,nlstate);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      gm=matrix(0,nhstepm,1,nlstate);
    }  
  }  
       for(theta=1; theta <=npar; theta++){
   fclose(ficresvpl);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*---------- End : free ----------------*/        }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        if (popbased==1) {
            if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);              prlim[i][i]=probs[(int)age][i][ij];
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          }else{ /* mobilav */ 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            for(i=1; i<=nlstate;i++)
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   free_matrix(matcov,1,npar,1,npar);        }
   free_vector(delti,1,npar);    
          for(j=1; j<= nlstate; j++){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   printf("End of Imach\n");              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          }
          }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        /* This for computing probability of death (h=1 means
   /*printf("Total time was %d uSec.\n", total_usecs);*/           computed over hstepm matrices product = hstepm*stepm months) 
   /*------ End -----------*/           as a weighted average of prlim.
         */
  end:        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 #ifdef windows          for(i=1,gpp[j]=0.; i<= nlstate; i++)
  chdir(pathcd);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 #endif        }    
  /*system("wgnuplot graph.plt");*/        /* end probability of death */
  system("../gp37mgw/wgnuplot graph.plt");  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
 #ifdef windows          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   while (z[0] != 'q') {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     chdir(pathcd);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");   
     scanf("%s",z);        if (popbased==1) {
     if (z[0] == 'c') system("./imach");          if(mobilav ==0){
     else if (z[0] == 'e') {            for(i=1; i<=nlstate;i++)
       chdir(path);              prlim[i][i]=probs[(int)age][i][ij];
       system("index.htm");          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     else if (z[0] == 'q') exit(0);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
 #endif        }
 }  
         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 linei;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) ||((i >= firstobs) && (i <=lastobs)))    {
       linei=linei+1;
       printf("IIIII= %d linei=%d\n",i,linei);
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10);j--){;};line[j+1]=0;  /* Trims blanks at end of line */
         if(line[0]=='#'){
           fprintf(ficlog,"Comment line\n%s\n",line);
           printf("Comment line\n%s\n",line);
           continue;
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %d %s for individual %d\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n",lval, i,line,linei,j,maxwav);
             exit(1);
           }
           s[j][i]=lval;
   
           strcpy(line,stra);
           cutv(stra, strb,line,'/');
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",lval, i,line,linei,j);
             exit(1);
           }
           anint[j][i]=(double)(lval); 
   
           strcpy(line,stra);
           cutv(stra, strb,line,' ');
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of exam at wave %d.  Exiting.\n",lval, i,line, linei,j);
             exit(1);
           }
           mint[j][i]=(double)(lval); 
           strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of death.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         andc[i]=(double)(lval); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of death.  Exiting.\n",lval,i,line, linei);
           exit(1);
         }
         moisdc[i]=(double)(lval); 
   
         strcpy(line,stra);
         cutv(stra, strb,line,'/'); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of birth.  Exiting.\n",lval, i,line, linei);
           exit(1);
         }
         annais[i]=(double)(lval);
   
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of birth.  Exiting.\n",lval,i,line,linei);
           exit(1);
         }
         moisnais[i]=(double)(lval); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         weight[i]=(double)(lval); 
         strcpy(line,stra);
   
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, i,line,linei);
             exit(1);
           }
           if(lval <0 || lval >1){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,i,line,linei,j);
             exit(1);
           }
           covar[j][i]=(double)(lval);
           strcpy(line,stra);
         } 
         lstra=strlen(stra);
   
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
         printf ("num [i] %ld %d\n",i, num[i]);fflush(stdout);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
     } /* End loop reading  data */
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
      
        for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
      
         for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
    tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
          }
      
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
   #ifndef UNIX
     /*  strcpy(plotcmd,"\""); */
   #endif
     strcpy(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     /*  strcat(plotcmd,"\"");*/
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
   
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     strcat(plotcmd,"\"");
   #endif
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.8  
changed lines
  Added in v.1.109


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