Diff for /imach/src/imach.c between versions 1.30 and 1.110

version 1.30, 2002/03/08 16:17:18 version 1.110, 2006/01/25 00:51:50
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.110  2006/01/25 00:51:50  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.109  2006/01/24 19:37:15  brouard
   first survey ("cross") where individuals from different ages are    (Module): Comments (lines starting with a #) are allowed in data.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.108  2006/01/19 18:05:42  lievre
   second wave of interviews ("longitudinal") which measure each change    Gnuplot problem appeared...
   (if any) in individual health status.  Health expectancies are    To be fixed
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.107  2006/01/19 16:20:37  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Test existence of gnuplot in imach path
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.106  2006/01/19 13:24:36  brouard
   conditional to be observed in state i at the first wave. Therefore    Some cleaning and links added in html output
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.105  2006/01/05 20:23:19  lievre
   complex model than "constant and age", you should modify the program    *** empty log message ***
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.104  2005/09/30 16:11:43  lievre
   convergence.    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
   The advantage of this computer programme, compared to a simple    that the person is alive, then we can code his/her status as -2
   multinomial logistic model, is clear when the delay between waves is not    (instead of missing=-1 in earlier versions) and his/her
   identical for each individual. Also, if a individual missed an    contributions to the likelihood is 1 - Prob of dying from last
   intermediate interview, the information is lost, but taken into    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   account using an interpolation or extrapolation.      the healthy state at last known wave). Version is 0.98
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.103  2005/09/30 15:54:49  lievre
   conditional to the observed state i at age x. The delay 'h' can be    (Module): sump fixed, loop imx fixed, and simplifications.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.102  2004/09/15 17:31:30  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Add the possibility to read data file including tab characters.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.101  2004/09/15 10:38:38  brouard
   hPijx.    Fix on curr_time
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.100  2004/07/12 18:29:06  brouard
   of the life expectancies. It also computes the prevalence limits.    Add version for Mac OS X. Just define UNIX in Makefile
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.99  2004/06/05 08:57:40  brouard
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.98  2004/05/16 15:05:56  brouard
   It is copyrighted identically to a GNU software product, ie programme and    New version 0.97 . First attempt to estimate force of mortality
   software can be distributed freely for non commercial use. Latest version    directly from the data i.e. without the need of knowing the health
   can be accessed at http://euroreves.ined.fr/imach .    state at each age, but using a Gompertz model: log u =a + b*age .
   **********************************************************************/    This is the basic analysis of mortality and should be done before any
      other analysis, in order to test if the mortality estimated from the
 #include <math.h>    cross-longitudinal survey is different from the mortality estimated
 #include <stdio.h>    from other sources like vital statistic data.
 #include <stdlib.h>  
 #include <unistd.h>    The same imach parameter file can be used but the option for mle should be -3.
   
 #define MAXLINE 256    Agnès, who wrote this part of the code, tried to keep most of the
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    former routines in order to include the new code within the former code.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    The output is very simple: only an estimate of the intercept and of
 #define windows    the slope with 95% confident intervals.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Current limitations:
     A) Even if you enter covariates, i.e. with the
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    B) There is no computation of Life Expectancy nor Life Table.
   
 #define NINTERVMAX 8    Revision 1.97  2004/02/20 13:25:42  lievre
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Version 0.96d. Population forecasting command line is (temporarily)
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    suppressed.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.96  2003/07/15 15:38:55  brouard
 #define YEARM 12. /* Number of months per year */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define AGESUP 130    rewritten within the same printf. Workaround: many printfs.
 #define AGEBASE 40  
     Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 int erreur; /* Error number */    (Repository): Using imachwizard code to output a more meaningful covariance
 int nvar;    matrix (cov(a12,c31) instead of numbers.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.94  2003/06/27 13:00:02  brouard
 int nlstate=2; /* Number of live states */    Just cleaning
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.93  2003/06/25 16:33:55  brouard
 int popbased=0;    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Version 0.96b
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.92  2003/06/25 16:30:45  brouard
 int mle, weightopt;    (Module): On windows (cygwin) function asctime_r doesn't
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    exist so I changed back to asctime which exists.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.91  2003/06/25 15:30:29  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    * imach.c (Repository): Duplicated warning errors corrected.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Repository): Elapsed time after each iteration is now output. It
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    helps to forecast when convergence will be reached. Elapsed time
 FILE *ficgp,*ficresprob,*ficpop;    is stamped in powell.  We created a new html file for the graphs
 FILE *ficreseij;    concerning matrix of covariance. It has extension -cov.htm.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.90  2003/06/24 12:34:15  brouard
   char fileresv[FILENAMELENGTH];    (Module): Some bugs corrected for windows. Also, when
  FILE  *ficresvpl;    mle=-1 a template is output in file "or"mypar.txt with the design
   char fileresvpl[FILENAMELENGTH];    of the covariance matrix to be input.
   
 #define NR_END 1    Revision 1.89  2003/06/24 12:30:52  brouard
 #define FREE_ARG char*    (Module): Some bugs corrected for windows. Also, when
 #define FTOL 1.0e-10    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 #define NRANSI  
 #define ITMAX 200    Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 #define TOL 2.0e-4  
     Revision 1.87  2003/06/18 12:26:01  brouard
 #define CGOLD 0.3819660    Version 0.96
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 #define GOLD 1.618034    routine fileappend.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 static double maxarg1,maxarg2;    current date of interview. It may happen when the death was just
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    prior to the death. In this case, dh was negative and likelihood
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    was wrong (infinity). We still send an "Error" but patch by
      assuming that the date of death was just one stepm after the
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    interview.
 #define rint(a) floor(a+0.5)    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 static double sqrarg;    memory allocation. But we also truncated to 8 characters (left
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    truncation)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Repository): No more line truncation errors.
   
 int imx;    Revision 1.84  2003/06/13 21:44:43  brouard
 int stepm;    * imach.c (Repository): Replace "freqsummary" at a correct
 /* Stepm, step in month: minimum step interpolation*/    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 int m,nb;    parcimony.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.83  2003/06/10 13:39:11  lievre
 double dateintmean=0;    *** empty log message ***
   
 double *weight;    Revision 1.82  2003/06/05 15:57:20  brouard
 int **s; /* Status */    Add log in  imach.c and  fullversion number is now printed.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  */
   /*
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */     Interpolated Markov Chain
 double ftolhess; /* Tolerance for computing hessian */  
     Short summary of the programme:
 /**************** split *************************/    
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    char *s;                             /* pointer */    first survey ("cross") where individuals from different ages are
    int  l1, l2;                         /* length counters */    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
    l1 = strlen( path );                 /* length of path */    second wave of interviews ("longitudinal") which measure each change
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (if any) in individual health status.  Health expectancies are
 #ifdef windows    computed from the time spent in each health state according to a
    s = strrchr( path, '\\' );           /* find last / */    model. More health states you consider, more time is necessary to reach the
 #else    Maximum Likelihood of the parameters involved in the model.  The
    s = strrchr( path, '/' );            /* find last / */    simplest model is the multinomial logistic model where pij is the
 #endif    probability to be observed in state j at the second wave
    if ( s == NULL ) {                   /* no directory, so use current */    conditional to be observed in state i at the first wave. Therefore
 #if     defined(__bsd__)                /* get current working directory */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       extern char       *getwd( );    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
       if ( getwd( dirc ) == NULL ) {    where the markup *Covariates have to be included here again* invites
 #else    you to do it.  More covariates you add, slower the
       extern char       *getcwd( );    convergence.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    The advantage of this computer programme, compared to a simple
 #endif    multinomial logistic model, is clear when the delay between waves is not
          return( GLOCK_ERROR_GETCWD );    identical for each individual. Also, if a individual missed an
       }    intermediate interview, the information is lost, but taken into
       strcpy( name, path );             /* we've got it */    account using an interpolation or extrapolation.  
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    hPijx is the probability to be observed in state i at age x+h
       l2 = strlen( s );                 /* length of filename */    conditional to the observed state i at age x. The delay 'h' can be
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    split into an exact number (nh*stepm) of unobserved intermediate
       strcpy( name, s );                /* save file name */    states. This elementary transition (by month, quarter,
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    semester or year) is modelled as a multinomial logistic.  The hPx
       dirc[l1-l2] = 0;                  /* add zero */    matrix is simply the matrix product of nh*stepm elementary matrices
    }    and the contribution of each individual to the likelihood is simply
    l1 = strlen( dirc );                 /* length of directory */    hPijx.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Also this programme outputs the covariance matrix of the parameters but also
 #else    of the life expectancies. It also computes the stable prevalence. 
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    
 #endif    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    s = strrchr( name, '.' );            /* find last / */             Institut national d'études démographiques, Paris.
    s++;    This software have been partly granted by Euro-REVES, a concerted action
    strcpy(ext,s);                       /* save extension */    from the European Union.
    l1= strlen( name);    It is copyrighted identically to a GNU software product, ie programme and
    l2= strlen( s)+1;    software can be distributed freely for non commercial use. Latest version
    strncpy( finame, name, l1-l2);    can be accessed at http://euroreves.ined.fr/imach .
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 }    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
     **********************************************************************/
 /******************************************/  /*
     main
 void replace(char *s, char*t)    read parameterfile
 {    read datafile
   int i;    concatwav
   int lg=20;    freqsummary
   i=0;    if (mle >= 1)
   lg=strlen(t);      mlikeli
   for(i=0; i<= lg; i++) {    print results files
     (s[i] = t[i]);    if mle==1 
     if (t[i]== '\\') s[i]='/';       computes hessian
   }    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 int nbocc(char *s, char occ)    open html file
 {    stable prevalence
   int i,j=0;     for age prevalim()
   int lg=20;    h Pij x
   i=0;    variance of p varprob
   lg=strlen(s);    forecasting if prevfcast==1 prevforecast call prevalence()
   for(i=0; i<= lg; i++) {    health expectancies
   if  (s[i] == occ ) j++;    Variance-covariance of DFLE
   }    prevalence()
   return j;     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 void cutv(char *u,char *v, char*t, char occ)    total life expectancies
 {    Variance of stable prevalence
   int i,lg,j,p=0;   end
   i=0;  */
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  
    
   lg=strlen(t);  #include <math.h>
   for(j=0; j<p; j++) {  #include <stdio.h>
     (u[j] = t[j]);  #include <stdlib.h>
   }  #include <string.h>
      u[p]='\0';  #include <unistd.h>
   
    for(j=0; j<= lg; j++) {  #include <limits.h>
     if (j>=(p+1))(v[j-p-1] = t[j]);  #include <sys/types.h>
   }  #include <sys/stat.h>
 }  #include <errno.h>
   extern int errno;
 /********************** nrerror ********************/  
   /* #include <sys/time.h> */
 void nrerror(char error_text[])  #include <time.h>
 {  #include "timeval.h"
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  /* #include <libintl.h> */
   exit(1);  /* #define _(String) gettext (String) */
 }  
 /*********************** vector *******************/  #define MAXLINE 256
 double *vector(int nl, int nh)  
 {  #define GNUPLOTPROGRAM "gnuplot"
   double *v;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define FILENAMELENGTH 132
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 /************************ free vector ******************/  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 void free_vector(double*v, int nl, int nh)  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 {  
   free((FREE_ARG)(v+nl-NR_END));  #define NINTERVMAX 8
 }  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 /************************ivector *******************************/  #define NCOVMAX 8 /* Maximum number of covariates */
 int *ivector(long nl,long nh)  #define MAXN 20000
 {  #define YEARM 12. /* Number of months per year */
   int *v;  #define AGESUP 130
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define AGEBASE 40
   if (!v) nrerror("allocation failure in ivector");  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   return v-nl+NR_END;  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /******************free ivector **************************/  #define ODIRSEPARATOR '\\'
 void free_ivector(int *v, long nl, long nh)  #else
 {  #define DIRSEPARATOR '\\'
   free((FREE_ARG)(v+nl-NR_END));  #define CHARSEPARATOR "\\"
 }  #define ODIRSEPARATOR '/'
   #endif
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /* $Id$ */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /* $State$ */
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
   int **m;  char fullversion[]="$Revision$ $Date$"; 
    int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   /* allocate pointers to rows */  int nvar;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   if (!m) nrerror("allocation failure 1 in matrix()");  int npar=NPARMAX;
   m += NR_END;  int nlstate=2; /* Number of live states */
   m -= nrl;  int ndeath=1; /* Number of dead states */
    int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int *wav; /* Number of waves for this individuual 0 is possible */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int maxwav; /* Maxim number of waves */
   m[nrl] += NR_END;  int jmin, jmax; /* min, max spacing between 2 waves */
   m[nrl] -= ncl;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
    int gipmx, gsw; /* Global variables on the number of contributions 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;                     to the likelihood and the sum of weights (done by funcone)*/
    int mle, weightopt;
   /* return pointer to array of pointers to rows */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   return m;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
 /****************** free_imatrix *************************/  double jmean; /* Mean space between 2 waves */
 void free_imatrix(m,nrl,nrh,ncl,nch)  double **oldm, **newm, **savm; /* Working pointers to matrices */
       int **m;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       long nch,ncl,nrh,nrl;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
      /* free an int matrix allocated by imatrix() */  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  double fretone; /* Only one call to likelihood */
   free((FREE_ARG) (m+nrl-NR_END));  long ipmx; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /******************* matrix *******************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE *ficresilk;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  FILE *ficresprobmorprev;
   double **m;  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char filerese[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE  *ficresvij;
   m += NR_END;  char fileresv[FILENAMELENGTH];
   m -= nrl;  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char title[MAXLINE];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m[nrl] += NR_END;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   m[nrl] -= ncl;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int  outcmd=0;
   return m;  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
 /*************************free matrix ************************/  char filelog[FILENAMELENGTH]; /* Log file */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char popfile[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  
 }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 /******************* ma3x *******************************/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  struct timezone tzp;
 {  extern int gettimeofday();
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double ***m;  long time_value;
   extern long time();
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char strcurr[80], strfor[80];
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  char *endptr;
   m -= nrl;  long lval;
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define NR_END 1
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define FREE_ARG char*
   m[nrl] += NR_END;  #define FTOL 1.0e-10
   m[nrl] -= ncl;  
   #define NRANSI 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define ITMAX 200 
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define TOL 2.0e-4 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  #define CGOLD 0.3819660 
   m[nrl][ncl] -= nll;  #define ZEPS 1.0e-10 
   for (j=ncl+1; j<=nch; j++)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     m[nrl][j]=m[nrl][j-1]+nlay;  
    #define GOLD 1.618034 
   for (i=nrl+1; i<=nrh; i++) {  #define GLIMIT 100.0 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define TINY 1.0e-20 
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  static double maxarg1,maxarg2;
   }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   return m;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /*************************free ma3x ************************/  #define rint(a) floor(a+0.5)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  static double sqrarg;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   free((FREE_ARG)(m+nrl-NR_END));  int agegomp= AGEGOMP;
 }  
   int imx; 
 /***************** f1dim *************************/  int stepm=1;
 extern int ncom;  /* Stepm, step in month: minimum step interpolation*/
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 double f1dim(double x)  
 {  int m,nb;
   int j;  long *num;
   double f;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double *xt;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    double **pmmij, ***probs;
   xt=vector(1,ncom);  double *ageexmed,*agecens;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double dateintmean=0;
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  double *weight;
   return f;  int **s; /* Status */
 }  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 /*****************brent *************************/  double *lsurv, *lpop, *tpop;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   int iter;  double ftolhess; /* Tolerance for computing hessian */
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /**************** split *************************/
   double ftemp;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         the name of the file (name), its extension only (ext) and its first part of the name (finame)
   a=(ax < cx ? ax : cx);    */ 
   b=(ax > cx ? ax : cx);    char  *ss;                            /* pointer */
   x=w=v=bx;    int   l1, l2;                         /* length counters */
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    l1 = strlen(path );                   /* length of path */
     xm=0.5*(a+b);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     printf(".");fflush(stdout);      strcpy( name, path );               /* we got the fullname name because no directory */
 #ifdef DEBUG      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      /* get current working directory */
 #endif      /*    extern  char* getcwd ( char *buf , int len);*/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       *xmin=x;        return( GLOCK_ERROR_GETCWD );
       return fx;      }
     }      /* got dirc from getcwd*/
     ftemp=fu;      printf(" DIRC = %s \n",dirc);
     if (fabs(e) > tol1) {    } else {                              /* strip direcotry from path */
       r=(x-w)*(fx-fv);      ss++;                               /* after this, the filename */
       q=(x-v)*(fx-fw);      l2 = strlen( ss );                  /* length of filename */
       p=(x-v)*q-(x-w)*r;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       q=2.0*(q-r);      strcpy( name, ss );         /* save file name */
       if (q > 0.0) p = -p;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       q=fabs(q);      dirc[l1-l2] = 0;                    /* add zero */
       etemp=e;      printf(" DIRC2 = %s \n",dirc);
       e=d;    }
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    /* We add a separator at the end of dirc if not exists */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    l1 = strlen( dirc );                  /* length of directory */
       else {    if( dirc[l1-1] != DIRSEPARATOR ){
         d=p/q;      dirc[l1] =  DIRSEPARATOR;
         u=x+d;      dirc[l1+1] = 0; 
         if (u-a < tol2 || b-u < tol2)      printf(" DIRC3 = %s \n",dirc);
           d=SIGN(tol1,xm-x);    }
       }    ss = strrchr( name, '.' );            /* find last / */
     } else {    if (ss >0){
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      ss++;
     }      strcpy(ext,ss);                     /* save extension */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      l1= strlen( name);
     fu=(*f)(u);      l2= strlen(ss)+1;
     if (fu <= fx) {      strncpy( finame, name, l1-l2);
       if (u >= x) a=x; else b=x;      finame[l1-l2]= 0;
       SHFT(v,w,x,u)    }
         SHFT(fv,fw,fx,fu)  
         } else {    return( 0 );                          /* we're done */
           if (u < x) a=u; else b=u;  }
           if (fu <= fw || w == x) {  
             v=w;  
             w=u;  /******************************************/
             fv=fw;  
             fw=fu;  void replace_back_to_slash(char *s, char*t)
           } else if (fu <= fv || v == x || v == w) {  {
             v=u;    int i;
             fv=fu;    int lg=0;
           }    i=0;
         }    lg=strlen(t);
   }    for(i=0; i<= lg; i++) {
   nrerror("Too many iterations in brent");      (s[i] = t[i]);
   *xmin=x;      if (t[i]== '\\') s[i]='/';
   return fx;    }
 }  }
   
 /****************** mnbrak ***********************/  int nbocc(char *s, char occ)
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    int i,j=0;
             double (*func)(double))    int lg=20;
 {    i=0;
   double ulim,u,r,q, dum;    lg=strlen(s);
   double fu;    for(i=0; i<= lg; i++) {
      if  (s[i] == occ ) j++;
   *fa=(*func)(*ax);    }
   *fb=(*func)(*bx);    return j;
   if (*fb > *fa) {  }
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  void cutv(char *u,char *v, char*t, char occ)
       }  {
   *cx=(*bx)+GOLD*(*bx-*ax);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   *fc=(*func)(*cx);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   while (*fb > *fc) {       gives u="abcedf" and v="ghi2j" */
     r=(*bx-*ax)*(*fb-*fc);    int i,lg,j,p=0;
     q=(*bx-*cx)*(*fb-*fa);    i=0;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    for(j=0; j<=strlen(t)-1; j++) {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    lg=strlen(t);
     } else if ((*cx-u)*(u-ulim) > 0.0) {    for(j=0; j<p; j++) {
       fu=(*func)(u);      (u[j] = t[j]);
       if (fu < *fc) {    }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))       u[p]='\0';
           SHFT(*fb,*fc,fu,(*func)(u))  
           }     for(j=0; j<= lg; j++) {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      if (j>=(p+1))(v[j-p-1] = t[j]);
       u=ulim;    }
       fu=(*func)(u);  }
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  /********************** nrerror ********************/
       fu=(*func)(u);  
     }  void nrerror(char error_text[])
     SHFT(*ax,*bx,*cx,u)  {
       SHFT(*fa,*fb,*fc,fu)    fprintf(stderr,"ERREUR ...\n");
       }    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /*************** linmin ************************/  /*********************** vector *******************/
   double *vector(int nl, int nh)
 int ncom;  {
 double *pcom,*xicom;    double *v;
 double (*nrfunc)(double []);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      if (!v) nrerror("allocation failure in vector");
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    return v-nl+NR_END;
 {  }
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  /************************ free vector ******************/
   double f1dim(double x);  void free_vector(double*v, int nl, int nh)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  {
               double *fc, double (*func)(double));    free((FREE_ARG)(v+nl-NR_END));
   int j;  }
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /************************ivector *******************************/
    int *ivector(long nl,long nh)
   ncom=n;  {
   pcom=vector(1,n);    int *v;
   xicom=vector(1,n);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   nrfunc=func;    if (!v) nrerror("allocation failure in ivector");
   for (j=1;j<=n;j++) {    return v-nl+NR_END;
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  
   }  /******************free ivector **************************/
   ax=0.0;  void free_ivector(int *v, long nl, long nh)
   xx=1.0;  {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    free((FREE_ARG)(v+nl-NR_END));
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  }
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /************************lvector *******************************/
 #endif  long *lvector(long nl,long nh)
   for (j=1;j<=n;j++) {  {
     xi[j] *= xmin;    long *v;
     p[j] += xi[j];    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   }    if (!v) nrerror("allocation failure in ivector");
   free_vector(xicom,1,n);    return v-nl+NR_END;
   free_vector(pcom,1,n);  }
 }  
   /******************free lvector **************************/
 /*************** powell ************************/  void free_lvector(long *v, long nl, long nh)
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  {
             double (*func)(double []))    free((FREE_ARG)(v+nl-NR_END));
 {  }
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  /******************* imatrix *******************************/
   int i,ibig,j;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double del,t,*pt,*ptt,*xit;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double fp,fptt;  { 
   double *xits;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   pt=vector(1,n);    int **m; 
   ptt=vector(1,n);    
   xit=vector(1,n);    /* allocate pointers to rows */ 
   xits=vector(1,n);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   *fret=(*func)(p);    if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (j=1;j<=n;j++) pt[j]=p[j];    m += NR_END; 
   for (*iter=1;;++(*iter)) {    m -= nrl; 
     fp=(*fret);    
     ibig=0;    
     del=0.0;    /* allocate rows and set pointers to them */ 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for (i=1;i<=n;i++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       printf(" %d %.12f",i, p[i]);    m[nrl] += NR_END; 
     printf("\n");    m[nrl] -= ncl; 
     for (i=1;i<=n;i++) {    
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       fptt=(*fret);    
 #ifdef DEBUG    /* return pointer to array of pointers to rows */ 
       printf("fret=%lf \n",*fret);    return m; 
 #endif  } 
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  /****************** free_imatrix *************************/
       if (fabs(fptt-(*fret)) > del) {  void free_imatrix(m,nrl,nrh,ncl,nch)
         del=fabs(fptt-(*fret));        int **m;
         ibig=i;        long nch,ncl,nrh,nrl; 
       }       /* free an int matrix allocated by imatrix() */ 
 #ifdef DEBUG  { 
       printf("%d %.12e",i,(*fret));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for (j=1;j<=n;j++) {    free((FREE_ARG) (m+nrl-NR_END)); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  } 
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /******************* matrix *******************************/
       for(j=1;j<=n;j++)  double **matrix(long nrl, long nrh, long ncl, long nch)
         printf(" p=%.12e",p[j]);  {
       printf("\n");    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 #endif    double **m;
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()");
       int k[2],l;    m += NR_END;
       k[0]=1;    m -= nrl;
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for (j=1;j<=n;j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         printf(" %.12e",p[j]);    m[nrl] += NR_END;
       printf("\n");    m[nrl] -= ncl;
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    return m;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         }     */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  }
       }  
 #endif  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
       free_vector(xit,1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       free_vector(xits,1,n);    free((FREE_ARG)(m+nrl-NR_END));
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  
       return;  /******************* ma3x *******************************/
     }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  {
     for (j=1;j<=n;j++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       ptt[j]=2.0*p[j]-pt[j];    double ***m;
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     fptt=(*func)(ptt);    m += NR_END;
     if (fptt < fp) {    m -= nrl;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         linmin(p,xit,n,fret,func);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         for (j=1;j<=n;j++) {    m[nrl] += NR_END;
           xi[j][ibig]=xi[j][n];    m[nrl] -= ncl;
           xi[j][n]=xit[j];  
         }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         for(j=1;j<=n;j++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           printf(" %.12e",xit[j]);    m[nrl][ncl] += NR_END;
         printf("\n");    m[nrl][ncl] -= nll;
 #endif    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
     }    
   }    for (i=nrl+1; i<=nrh; i++) {
 }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
 /**** Prevalence limit ****************/        m[i][j]=m[i][j-1]+nlay;
     }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    return m; 
 {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      matrix by transitions matrix until convergence is reached */    */
   }
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  /*************************free ma3x ************************/
   double **matprod2();  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double **out, cov[NCOVMAX], **pmij();  {
   double **newm;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double agefin, delaymax=50 ; /* Max number of years to converge */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   for (ii=1;ii<=nlstate+ndeath;ii++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*************** function subdirf ***********/
     }  char *subdirf(char fileres[])
   {
    cov[1]=1.;    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,"/"); /* Add to the right */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    strcat(tmpout,fileres);
     newm=savm;    return tmpout;
     /* Covariates have to be included here again */  }
      cov[2]=agefin;  
    /*************** function subdirf2 ***********/
       for (k=1; k<=cptcovn;k++) {  char *subdirf2(char fileres[], char *preop)
         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]);*/    
       }    /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovage;k++)    strcpy(tmpout,optionfilefiname);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcat(tmpout,"/");
       for (k=1; k<=cptcovprod;k++)    strcat(tmpout,preop);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,fileres);
     return tmpout;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   /*************** function subdirf3 ***********/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  char *subdirf3(char fileres[], char *preop, char *preop2)
   {
     savm=oldm;    
     oldm=newm;    /* Caution optionfilefiname is hidden */
     maxmax=0.;    strcpy(tmpout,optionfilefiname);
     for(j=1;j<=nlstate;j++){    strcat(tmpout,"/");
       min=1.;    strcat(tmpout,preop);
       max=0.;    strcat(tmpout,preop2);
       for(i=1; i<=nlstate; i++) {    strcat(tmpout,fileres);
         sumnew=0;    return tmpout;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  }
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /***************** f1dim *************************/
         min=FMIN(min,prlim[i][j]);  extern int ncom; 
       }  extern double *pcom,*xicom;
       maxmin=max-min;  extern double (*nrfunc)(double []); 
       maxmax=FMAX(maxmax,maxmin);   
     }  double f1dim(double x) 
     if(maxmax < ftolpl){  { 
       return prlim;    int j; 
     }    double f;
   }    double *xt; 
 }   
     xt=vector(1,ncom); 
 /*************** transition probabilities ***************/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    free_vector(xt,1,ncom); 
 {    return f; 
   double s1, s2;  } 
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for(i=1; i<= nlstate; i++){  { 
     for(j=1; j<i;j++){    int iter; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double a,b,d,etemp;
         /*s2 += param[i][j][nc]*cov[nc];*/    double fu,fv,fw,fx;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double ftemp;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       }    double e=0.0; 
       ps[i][j]=s2;   
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    a=(ax < cx ? ax : cx); 
     }    b=(ax > cx ? ax : cx); 
     for(j=i+1; j<=nlstate+ndeath;j++){    x=w=v=bx; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    fw=fv=fx=(*f)(x); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    for (iter=1;iter<=ITMAX;iter++) { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      xm=0.5*(a+b); 
       }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       ps[i][j]=s2;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     }      printf(".");fflush(stdout);
   }      fprintf(ficlog,".");fflush(ficlog);
     /*ps[3][2]=1;*/  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for(i=1; i<= nlstate; i++){      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);
      s1=0;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(j=1; j<i; j++)  #endif
       s1+=exp(ps[i][j]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for(j=i+1; j<=nlstate+ndeath; j++)        *xmin=x; 
       s1+=exp(ps[i][j]);        return fx; 
     ps[i][i]=1./(s1+1.);      } 
     for(j=1; j<i; j++)      ftemp=fu;
       ps[i][j]= exp(ps[i][j])*ps[i][i];      if (fabs(e) > tol1) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        r=(x-w)*(fx-fv); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        q=(x-v)*(fx-fw); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        p=(x-v)*q-(x-w)*r; 
   } /* end i */        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        q=fabs(q); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        etemp=e; 
       ps[ii][jj]=0;        e=d; 
       ps[ii][ii]=1;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   }        else { 
           d=p/q; 
           u=x+d; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          if (u-a < tol2 || b-u < tol2) 
     for(jj=1; jj<= nlstate+ndeath; jj++){            d=SIGN(tol1,xm-x); 
      printf("%lf ",ps[ii][jj]);        } 
    }      } else { 
     printf("\n ");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
     printf("\n ");printf("%lf ",cov[2]);*/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 /*      fu=(*f)(u); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      if (fu <= fx) { 
   goto end;*/        if (u >= x) a=x; else b=x; 
     return ps;        SHFT(v,w,x,u) 
 }          SHFT(fv,fw,fx,fu) 
           } else { 
 /**************** Product of 2 matrices ******************/            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)              v=w; 
 {              w=u; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times              fv=fw; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */              fw=fu; 
   /* in, b, out are matrice of pointers which should have been initialized            } else if (fu <= fv || v == x || v == w) { 
      before: only the contents of out is modified. The function returns              v=u; 
      a pointer to pointers identical to out */              fv=fu; 
   long i, j, k;            } 
   for(i=nrl; i<= nrh; i++)          } 
     for(k=ncolol; k<=ncoloh; k++)    } 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    nrerror("Too many iterations in brent"); 
         out[i][k] +=in[i][j]*b[j][k];    *xmin=x; 
     return fx; 
   return out;  } 
 }  
   /****************** mnbrak ***********************/
   
 /************* Higher Matrix Product ***************/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  { 
 {    double ulim,u,r,q, dum;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    double fu; 
      duration (i.e. until   
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    *fa=(*func)(*ax); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    *fb=(*func)(*bx); 
      (typically every 2 years instead of every month which is too big).    if (*fb > *fa) { 
      Model is determined by parameters x and covariates have to be      SHFT(dum,*ax,*bx,dum) 
      included manually here.        SHFT(dum,*fb,*fa,dum) 
         } 
      */    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
   int i, j, d, h, k;    while (*fb > *fc) { 
   double **out, cov[NCOVMAX];      r=(*bx-*ax)*(*fb-*fc); 
   double **newm;      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   /* Hstepm could be zero and should return the unit matrix */        (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) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        fu=(*func)(u); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     }        fu=(*func)(u); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        if (fu < *fc) { 
   for(h=1; h <=nhstepm; h++){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for(d=1; d <=hstepm; d++){            SHFT(*fb,*fc,fu,(*func)(u)) 
       newm=savm;            } 
       /* Covariates have to be included here again */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       cov[1]=1.;        u=ulim; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        fu=(*func)(u); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      } else { 
       for (k=1; k<=cptcovage;k++)        u=(*cx)+GOLD*(*cx-*bx); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        fu=(*func)(u); 
       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]]];      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
         } 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  } 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /*************** linmin ************************/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  int ncom; 
       oldm=newm;  double *pcom,*xicom;
     }  double (*nrfunc)(double []); 
     for(i=1; i<=nlstate+ndeath; i++)   
       for(j=1;j<=nlstate+ndeath;j++) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         po[i][j][h]=newm[i][j];  { 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double brent(double ax, double bx, double cx, 
          */                 double (*f)(double), double tol, double *xmin); 
       }    double f1dim(double x); 
   } /* end h */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   return po;                double *fc, double (*func)(double)); 
 }    int j; 
     double xx,xmin,bx,ax; 
     double fx,fb,fa;
 /*************** log-likelihood *************/   
 double func( double *x)    ncom=n; 
 {    pcom=vector(1,n); 
   int i, ii, j, k, mi, d, kk;    xicom=vector(1,n); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    nrfunc=func; 
   double **out;    for (j=1;j<=n;j++) { 
   double sw; /* Sum of weights */      pcom[j]=p[j]; 
   double lli; /* Individual log likelihood */      xicom[j]=xi[j]; 
   long ipmx;    } 
   /*extern weight */    ax=0.0; 
   /* We are differentiating ll according to initial status */    xx=1.0; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   /*for(i=1;i<imx;i++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     printf(" %d\n",s[4][i]);  #ifdef DEBUG
   */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   cov[1]=1.;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for (j=1;j<=n;j++) { 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      xi[j] *= xmin; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      p[j] += xi[j]; 
     for(mi=1; mi<= wav[i]-1; mi++){    } 
       for (ii=1;ii<=nlstate+ndeath;ii++)    free_vector(xicom,1,n); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    free_vector(pcom,1,n); 
       for(d=0; d<dh[mi][i]; d++){  } 
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  char *asc_diff_time(long time_sec, char ascdiff[])
         for (kk=1; kk<=cptcovage;kk++) {  {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    long sec_left, days, hours, minutes;
         }    days = (time_sec) / (60*60*24);
            sec_left = (time_sec) % (60*60*24);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    hours = (sec_left) / (60*60) ;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    sec_left = (sec_left) %(60*60);
         savm=oldm;    minutes = (sec_left) /60;
         oldm=newm;    sec_left = (sec_left) % (60);
            sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
            return ascdiff;
       } /* end mult */  }
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /*************** powell ************************/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       ipmx +=1;              double (*func)(double [])) 
       sw += weight[i];  { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    void linmin(double p[], double xi[], int n, double *fret, 
     } /* end of wave */                double (*func)(double [])); 
   } /* end of individual */    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double fp,fptt;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    double *xits;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    int niterf, itmp;
   return -l;  
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
     xit=vector(1,n); 
 /*********** Maximum Likelihood Estimation ***************/    xits=vector(1,n); 
     *fret=(*func)(p); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    for (j=1;j<=n;j++) pt[j]=p[j]; 
 {    for (*iter=1;;++(*iter)) { 
   int i,j, iter;      fp=(*fret); 
   double **xi,*delti;      ibig=0; 
   double fret;      del=0.0; 
   xi=matrix(1,npar,1,npar);      last_time=curr_time;
   for (i=1;i<=npar;i++)      (void) gettimeofday(&curr_time,&tzp);
     for (j=1;j<=npar;j++)      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       xi[i][j]=(i==j ? 1.0 : 0.0);      /*    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("Powell\n");      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   powell(p,xi,npar,ftol,&iter,&fret,func);      */
      for (i=1;i<=n;i++) {
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        printf(" %d %.12f",i, p[i]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
 }      }
       printf("\n");
 /**** Computes Hessian and covariance matrix ***/      fprintf(ficlog,"\n");
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      fprintf(ficrespow,"\n");fflush(ficrespow);
 {      if(*iter <=3){
   double  **a,**y,*x,pd;        tm = *localtime(&curr_time.tv_sec);
   double **hess;        strcpy(strcurr,asctime(&tm));
   int i, j,jk;  /*       asctime_r(&tm,strcurr); */
   int *indx;        forecast_time=curr_time; 
         itmp = strlen(strcurr);
   double hessii(double p[], double delta, int theta, double delti[]);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double hessij(double p[], double delti[], int i, int j);          strcurr[itmp-1]='\0';
   void lubksb(double **a, int npar, int *indx, double b[]) ;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   hess=matrix(1,npar,1,npar);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*      asctime_r(&tmf,strfor); */
   for (i=1;i<=npar;i++){          strcpy(strfor,asctime(&tmf));
     printf("%d",i);fflush(stdout);          itmp = strlen(strfor);
     hess[i][i]=hessii(p,ftolhess,i,delti);          if(strfor[itmp-1]=='\n')
     /*printf(" %f ",p[i]);*/          strfor[itmp-1]='\0';
     /*printf(" %lf ",hess[i][i]);*/          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
          }
   for (i=1;i<=npar;i++) {      }
     for (j=1;j<=npar;j++)  {      for (i=1;i<=n;i++) { 
       if (j>i) {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         printf(".%d%d",i,j);fflush(stdout);        fptt=(*fret); 
         hess[i][j]=hessij(p,delti,i,j);  #ifdef DEBUG
         hess[j][i]=hess[i][j];            printf("fret=%lf \n",*fret);
         /*printf(" %lf ",hess[i][j]);*/        fprintf(ficlog,"fret=%lf \n",*fret);
       }  #endif
     }        printf("%d",i);fflush(stdout);
   }        fprintf(ficlog,"%d",i);fflush(ficlog);
   printf("\n");        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          del=fabs(fptt-(*fret)); 
            ibig=i; 
   a=matrix(1,npar,1,npar);        } 
   y=matrix(1,npar,1,npar);  #ifdef DEBUG
   x=vector(1,npar);        printf("%d %.12e",i,(*fret));
   indx=ivector(1,npar);        fprintf(ficlog,"%d %.12e",i,(*fret));
   for (i=1;i<=npar;i++)        for (j=1;j<=n;j++) {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   ludcmp(a,npar,indx,&pd);          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for (j=1;j<=npar;j++) {        }
     for (i=1;i<=npar;i++) x[i]=0;        for(j=1;j<=n;j++) {
     x[j]=1;          printf(" p=%.12e",p[j]);
     lubksb(a,npar,indx,x);          fprintf(ficlog," p=%.12e",p[j]);
     for (i=1;i<=npar;i++){        }
       matcov[i][j]=x[i];        printf("\n");
     }        fprintf(ficlog,"\n");
   }  #endif
       } 
   printf("\n#Hessian matrix#\n");      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for (i=1;i<=npar;i++) {  #ifdef DEBUG
     for (j=1;j<=npar;j++) {        int k[2],l;
       printf("%.3e ",hess[i][j]);        k[0]=1;
     }        k[1]=-1;
     printf("\n");        printf("Max: %.12e",(*func)(p));
   }        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   /* Recompute Inverse */          printf(" %.12e",p[j]);
   for (i=1;i<=npar;i++)          fprintf(ficlog," %.12e",p[j]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        }
   ludcmp(a,npar,indx,&pd);        printf("\n");
         fprintf(ficlog,"\n");
   /*  printf("\n#Hessian matrix recomputed#\n");        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   for (j=1;j<=npar;j++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for (i=1;i<=npar;i++) x[i]=0;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     x[j]=1;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     lubksb(a,npar,indx,x);          }
     for (i=1;i<=npar;i++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       y[i][j]=x[i];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       printf("%.3e ",y[i][j]);        }
     }  #endif
     printf("\n");  
   }  
   */        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   free_matrix(a,1,npar,1,npar);        free_vector(ptt,1,n); 
   free_matrix(y,1,npar,1,npar);        free_vector(pt,1,n); 
   free_vector(x,1,npar);        return; 
   free_ivector(indx,1,npar);      } 
   free_matrix(hess,1,npar,1,npar);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 }        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
 /*************** hessian matrix ****************/      } 
 double hessii( double x[], double delta, int theta, double delti[])      fptt=(*func)(ptt); 
 {      if (fptt < fp) { 
   int i;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   int l=1, lmax=20;        if (t < 0.0) { 
   double k1,k2;          linmin(p,xit,n,fret,func); 
   double p2[NPARMAX+1];          for (j=1;j<=n;j++) { 
   double res;            xi[j][ibig]=xi[j][n]; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            xi[j][n]=xit[j]; 
   double fx;          }
   int k=0,kmax=10;  #ifdef DEBUG
   double l1;          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);
   fx=func(x);          for(j=1;j<=n;j++){
   for (i=1;i<=npar;i++) p2[i]=x[i];            printf(" %.12e",xit[j]);
   for(l=0 ; l <=lmax; l++){            fprintf(ficlog," %.12e",xit[j]);
     l1=pow(10,l);          }
     delts=delt;          printf("\n");
     for(k=1 ; k <kmax; k=k+1){          fprintf(ficlog,"\n");
       delt = delta*(l1*k);  #endif
       p2[theta]=x[theta] +delt;        }
       k1=func(p2)-fx;      } 
       p2[theta]=x[theta]-delt;    } 
       k2=func(p2)-fx;  } 
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /**** Prevalence limit (stable prevalence)  ****************/
        
 #ifdef DEBUG  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  {
 #endif    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       matrix by transitions matrix until convergence is reached */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    double **matprod2();
         k=kmax; l=lmax*10.;    double **out, cov[NCOVMAX], **pmij();
       }    double **newm;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double agefin, delaymax=50 ; /* Max number of years to converge */
         delts=delt;  
       }    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   delti[theta]=delts;      }
   return res;  
       cov[1]=1.;
 }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 double hessij( double x[], double delti[], int thetai,int thetaj)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {      newm=savm;
   int i;      /* Covariates have to be included here again */
   int l=1, l1, lmax=20;       cov[2]=agefin;
   double k1,k2,k3,k4,res,fx;    
   double p2[NPARMAX+1];        for (k=1; k<=cptcovn;k++) {
   int k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   fx=func(x);        }
   for (k=1; k<=2; k++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovprod;k++)
     p2[thetai]=x[thetai]+delti[thetai]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
          /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetai]=x[thetai]+delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     k2=func(p2)-fx;  
        savm=oldm;
     p2[thetai]=x[thetai]-delti[thetai]/k;      oldm=newm;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      maxmax=0.;
     k3=func(p2)-fx;      for(j=1;j<=nlstate;j++){
          min=1.;
     p2[thetai]=x[thetai]-delti[thetai]/k;        max=0.;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(i=1; i<=nlstate; i++) {
     k4=func(p2)-fx;          sumnew=0;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 #ifdef DEBUG          prlim[i][j]= newm[i][j]/(1-sumnew);
     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);          max=FMAX(max,prlim[i][j]);
 #endif          min=FMIN(min,prlim[i][j]);
   }        }
   return res;        maxmin=max-min;
 }        maxmax=FMAX(maxmax,maxmin);
       }
 /************** Inverse of matrix **************/      if(maxmax < ftolpl){
 void ludcmp(double **a, int n, int *indx, double *d)        return prlim;
 {      }
   int i,imax,j,k;    }
   double big,dum,sum,temp;  }
   double *vv;  
    /*************** transition probabilities ***************/ 
   vv=vector(1,n);  
   *d=1.0;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   for (i=1;i<=n;i++) {  {
     big=0.0;    double s1, s2;
     for (j=1;j<=n;j++)    /*double t34;*/
       if ((temp=fabs(a[i][j])) > big) big=temp;    int i,j,j1, nc, ii, jj;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;      for(i=1; i<= nlstate; i++){
   }        for(j=1; j<i;j++){
   for (j=1;j<=n;j++) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for (i=1;i<j;i++) {            /*s2 += param[i][j][nc]*cov[nc];*/
       sum=a[i][j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       a[i][j]=sum;          }
     }          ps[i][j]=s2;
     big=0.0;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];        for(j=i+1; j<=nlstate+ndeath;j++){
       for (k=1;k<j;k++)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         sum -= a[i][k]*a[k][j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       a[i][j]=sum;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       if ( (dum=vv[i]*fabs(sum)) >= big) {          }
         big=dum;          ps[i][j]=s2;
         imax=i;        }
       }      }
     }      /*ps[3][2]=1;*/
     if (j != imax) {      
       for (k=1;k<=n;k++) {      for(i=1; i<= nlstate; i++){
         dum=a[imax][k];        s1=0;
         a[imax][k]=a[j][k];        for(j=1; j<i; j++)
         a[j][k]=dum;          s1+=exp(ps[i][j]);
       }        for(j=i+1; j<=nlstate+ndeath; j++)
       *d = -(*d);          s1+=exp(ps[i][j]);
       vv[imax]=vv[j];        ps[i][i]=1./(s1+1.);
     }        for(j=1; j<i; j++)
     indx[j]=imax;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     if (a[j][j] == 0.0) a[j][j]=TINY;        for(j=i+1; j<=nlstate+ndeath; j++)
     if (j != n) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
       dum=1.0/(a[j][j]);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      } /* end i */
     }      
   }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   free_vector(vv,1,n);  /* Doesn't work */        for(jj=1; jj<= nlstate+ndeath; jj++){
 ;          ps[ii][jj]=0;
 }          ps[ii][ii]=1;
         }
 void lubksb(double **a, int n, int *indx, double b[])      }
 {      
   int i,ii=0,ip,j;  
   double sum;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
    /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   for (i=1;i<=n;i++) {  /*         printf("ddd %lf ",ps[ii][jj]); */
     ip=indx[i];  /*       } */
     sum=b[ip];  /*       printf("\n "); */
     b[ip]=b[i];  /*        } */
     if (ii)  /*        printf("\n ");printf("%lf ",cov[2]); */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];         /*
     else if (sum) ii=i;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     b[i]=sum;        goto end;*/
   }      return ps;
   for (i=n;i>=1;i--) {  }
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /**************** Product of 2 matrices ******************/
     b[i]=sum/a[i][i];  
   }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 }  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 /************ Frequencies ********************/       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    /* in, b, out are matrice of pointers which should have been initialized 
 {  /* Some frequencies */       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    long i, j, k;
   double ***freq; /* Frequencies */    for(i=nrl; i<= nrh; i++)
   double *pp;      for(k=ncolol; k<=ncoloh; k++)
   double pos, k2, dateintsum=0,k2cpt=0;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   FILE *ficresp;          out[i][k] +=in[i][j]*b[j][k];
   char fileresp[FILENAMELENGTH];  
      return out;
   pp=vector(1,nlstate);  }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);  /************* Higher Matrix Product ***************/
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     exit(0);  {
   }    /* Computes the transition matrix starting at age 'age' over 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       'nhstepm*hstepm*stepm' months (i.e. until
   j1=0;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
   j=cptcoveff;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}       (typically every 2 years instead of every month which is too big 
        for the memory).
   for(k1=1; k1<=j;k1++){       Model is determined by parameters x and covariates have to be 
    for(i1=1; i1<=ncodemax[k1];i1++){       included manually here. 
        j1++;  
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);       */
          scanf("%d", i);*/  
         for (i=-1; i<=nlstate+ndeath; i++)      int i, j, d, h, k;
          for (jk=-1; jk<=nlstate+ndeath; jk++)      double **out, cov[NCOVMAX];
            for(m=agemin; m <= agemax+3; m++)    double **newm;
              freq[i][jk][m]=0;  
     /* Hstepm could be zero and should return the unit matrix */
         dateintsum=0;    for (i=1;i<=nlstate+ndeath;i++)
         k2cpt=0;      for (j=1;j<=nlstate+ndeath;j++){
        for (i=1; i<=imx; i++) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
          bool=1;        po[i][j][0]=(i==j ? 1.0 : 0.0);
          if  (cptcovn>0) {      }
            for (z1=1; z1<=cptcoveff; z1++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for(h=1; h <=nhstepm; h++){
                bool=0;      for(d=1; d <=hstepm; d++){
          }        newm=savm;
          if (bool==1) {        /* Covariates have to be included here again */
            for(m=firstpass; m<=lastpass; m++){        cov[1]=1.;
              k2=anint[m][i]+(mint[m][i]/12.);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                if(agev[m][i]==0) agev[m][i]=agemax+1;        for (k=1; k<=cptcovage;k++)
                if(agev[m][i]==1) agev[m][i]=agemax+2;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for (k=1; k<=cptcovprod;k++)
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  
                  dateintsum=dateintsum+k2;  
                  k2cpt++;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
              }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
            }        savm=oldm;
          }        oldm=newm;
        }      }
              for(i=1; i<=nlstate+ndeath; i++)
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(j=1;j<=nlstate+ndeath;j++) {
           po[i][j][h]=newm[i][j];
         if  (cptcovn>0) {          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
          fprintf(ficresp, "\n#********** Variable ");           */
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
        fprintf(ficresp, "**********\n#");    } /* end h */
         }    return po;
        for(i=1; i<=nlstate;i++)  }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");  
          /*************** log-likelihood *************/
   for(i=(int)agemin; i <= (int)agemax+3; i++){  double func( double *x)
     if(i==(int)agemax+3)  {
       printf("Total");    int i, ii, j, k, mi, d, kk;
     else    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       printf("Age %d", i);    double **out;
     for(jk=1; jk <=nlstate ; jk++){    double sw; /* Sum of weights */
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double lli; /* Individual log likelihood */
         pp[jk] += freq[jk][m][i];    int s1, s2;
     }    double bbh, survp;
     for(jk=1; jk <=nlstate ; jk++){    long ipmx;
       for(m=-1, pos=0; m <=0 ; m++)    /*extern weight */
         pos += freq[jk][m][i];    /* We are differentiating ll according to initial status */
       if(pp[jk]>=1.e-10)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /*for(i=1;i<imx;i++) 
       else      printf(" %d\n",s[4][i]);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    */
     }    cov[1]=1.;
   
      for(jk=1; jk <=nlstate ; jk++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
         pp[jk] += freq[jk][m][i];    if(mle==1){
      }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(jk=1,pos=0; jk <=nlstate ; jk++)        for(mi=1; mi<= wav[i]-1; mi++){
       pos += pp[jk];          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
       if(pos>=1.e-5)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else            }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          for(d=0; d<dh[mi][i]; d++){
       if( i <= (int) agemax){            newm=savm;
         if(pos>=1.e-5){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for (kk=1; kk<=cptcovage;kk++) {
           probs[i][jk][j1]= pp[jk]/pos;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            savm=oldm;
       }            oldm=newm;
     }          } /* end mult */
     for(jk=-1; jk <=nlstate+ndeath; jk++)        
       for(m=-1; m <=nlstate+ndeath; m++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          /* But now since version 0.9 we anticipate for bias at large stepm.
     if(i <= (int) agemax)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       fprintf(ficresp,"\n");           * (in months) between two waves is not a multiple of stepm, we rounded to 
     printf("\n");           * the nearest (and in case of equal distance, to the lowest) interval but now
     }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }           * (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
   dateintmean=dateintsum/k2cpt;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
             * -stepm/2 to stepm/2 .
   fclose(ficresp);           * For stepm=1 the results are the same as for previous versions of Imach.
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * For stepm > 1 the results are less biased than in previous versions. 
   free_vector(pp,1,nlstate);           */
           s1=s[mw[mi][i]][i];
   /* End of Freq */          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
 /************ Prevalence ********************/           * is higher than the multiple of stepm and negative otherwise.
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)           */
 {  /* Some frequencies */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            if( s2 > nlstate){ 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            /* i.e. if s2 is a death state and if the date of death is known 
   double ***freq; /* Frequencies */               then the contribution to the likelihood is the probability to 
   double *pp;               die between last step unit time and current  step unit time, 
   double pos, k2;               which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
   pp=vector(1,nlstate);               In version up to 0.92 likelihood was computed
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          as if date of death was unknown. Death was treated as any other
            health state: the date of the interview describes the actual state
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          and not the date of a change in health state. The former idea was
   j1=0;          to consider that at each interview the state was recorded
            (healthy, disable or death) and IMaCh was corrected; but when we
   j=cptcoveff;          introduced the exact date of death then we should have modified
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          the contribution of an exact death to the likelihood. This new
            contribution is smaller and very dependent of the step unit
  for(k1=1; k1<=j;k1++){          stepm. It is no more the probability to die between last interview
     for(i1=1; i1<=ncodemax[k1];i1++){          and month of death but the probability to survive from last
       j1++;          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
       for (i=-1; i<=nlstate+ndeath; i++)            Jackson for correcting this bug.  Former versions increased
         for (jk=-1; jk<=nlstate+ndeath; jk++)            mortality artificially. The bad side is that we add another loop
           for(m=agemin; m <= agemax+3; m++)          which slows down the processing. The difference can be up to 10%
             freq[i][jk][m]=0;          lower mortality.
                  */
       for (i=1; i<=imx; i++) {            lli=log(out[s1][s2] - savm[s1][s2]);
         bool=1;  
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)          } else if  (s2==-2) {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            for (j=1,survp=0. ; j<=nlstate; j++) 
               bool=0;              survp += out[s1][j];
         }            lli= survp;
         if (bool==1) {          }
           for(m=firstpass; m<=lastpass; m++){          
             k2=anint[m][i]+(mint[m][i]/12.);          else if  (s2==-4) {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (j=3,survp=0. ; j<=nlstate; j++) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;              survp += out[s1][j];
               if(agev[m][i]==1) agev[m][i]=agemax+2;            lli= survp;
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          }
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          
             }          else if  (s2==-5) {
           }            for (j=1,survp=0. ; j<=2; j++) 
         }              survp += out[s1][j];
       }            lli= survp;
         for(i=(int)agemin; i <= (int)agemax+3; i++){          }
           for(jk=1; jk <=nlstate ; jk++){  
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
               pp[jk] += freq[jk][m][i];          else{
           }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for(jk=1; jk <=nlstate ; jk++){            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
             for(m=-1, pos=0; m <=0 ; m++)          } 
             pos += freq[jk][m][i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         }          /*if(lli ==000.0)*/
                  /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          sw += weight[i];
              pp[jk] += freq[jk][m][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          }        } /* end of wave */
                } /* end of individual */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for(jk=1; jk <=nlstate ; jk++){                  for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            if( i <= (int) agemax){        for(mi=1; mi<= wav[i]-1; mi++){
              if(pos>=1.e-5){          for (ii=1;ii<=nlstate+ndeath;ii++)
                probs[i][jk][j1]= pp[jk]/pos;            for (j=1;j<=nlstate+ndeath;j++){
              }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          }            }
                    for(d=0; d<=dh[mi][i]; d++){
         }            newm=savm;
     }            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];
              }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(pp,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
 }  /* End of Freq */            oldm=newm;
           } /* end mult */
 /************* Waves Concatenation ***************/        
           s1=s[mw[mi][i]][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)          s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual 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 */
      Death is a valid wave (if date is known).          ipmx +=1;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          sw += weight[i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      and mw[mi+1][i]. dh depends on stepm.        } /* end of wave */
      */      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
   int i, mi, m;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      double sum=0., jmean=0.;*/        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   int j, k=0,jk, ju, jl;            for (j=1;j<=nlstate+ndeath;j++){
   double sum=0.;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmin=1e+5;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmax=-1;            }
   jmean=0.;          for(d=0; d<dh[mi][i]; d++){
   for(i=1; i<=imx; i++){            newm=savm;
     mi=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     m=firstpass;            for (kk=1; kk<=cptcovage;kk++) {
     while(s[m][i] <= nlstate){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if(s[m][i]>=1)            }
         mw[++mi][i]=m;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(m >=lastpass)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         break;            savm=oldm;
       else            oldm=newm;
         m++;          } /* end mult */
     }/* end while */        
     if (s[m][i] > nlstate){          s1=s[mw[mi][i]][i];
       mi++;     /* Death is another wave */          s2=s[mw[mi+1][i]][i];
       /* if(mi==0)  never been interviewed correctly before death */          bbh=(double)bh[mi][i]/(double)stepm; 
          /* Only death is a correct wave */          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 */
       mw[mi][i]=m;          ipmx +=1;
     }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     wav[i]=mi;        } /* end of wave */
     if(mi==0)      } /* end of individual */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    }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];
   for(i=1; i<=imx; i++){        for(mi=1; mi<= wav[i]-1; mi++){
     for(mi=1; mi<wav[i];mi++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       if (stepm <=0)            for (j=1;j<=nlstate+ndeath;j++){
         dh[mi][i]=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else{              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (s[mw[mi+1][i]][i] > nlstate) {            }
           if (agedc[i] < 2*AGESUP) {          for(d=0; d<dh[mi][i]; d++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            newm=savm;
           if(j==0) j=1;  /* Survives at least one month after exam */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           k=k+1;            for (kk=1; kk<=cptcovage;kk++) {
           if (j >= jmax) jmax=j;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if (j <= jmin) jmin=j;            }
           sum=sum+j;          
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
         else{            oldm=newm;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          } /* end mult */
           k=k+1;        
           if (j >= jmax) jmax=j;          s1=s[mw[mi][i]][i];
           else if (j <= jmin)jmin=j;          s2=s[mw[mi+1][i]][i];
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          if( s2 > nlstate){ 
           sum=sum+j;            lli=log(out[s1][s2] - savm[s1][s2]);
         }          }else{
         jk= j/stepm;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         jl= j -jk*stepm;          }
         ju= j -(jk+1)*stepm;          ipmx +=1;
         if(jl <= -ju)          sw += weight[i];
           dh[mi][i]=jk;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         else  /*      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]); */
           dh[mi][i]=jk+1;        } /* end of wave */
         if(dh[mi][i]==0)      } /* end of individual */
           dh[mi][i]=1; /* At least one step */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   jmean=sum/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            for (j=1;j<=nlstate+ndeath;j++){
  }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /*********** Tricode ****************************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void tricode(int *Tvar, int **nbcode, int imx)            }
 {          for(d=0; d<dh[mi][i]; d++){
   int Ndum[20],ij=1, k, j, i;            newm=savm;
   int cptcode=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   cptcoveff=0;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (k=0; k<19; k++) Ndum[k]=0;            }
   for (k=1; k<=7; k++) ncodemax[k]=0;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1; i<=imx; i++) {            savm=oldm;
       ij=(int)(covar[Tvar[j]][i]);            oldm=newm;
       Ndum[ij]++;          } /* end mult */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        
       if (ij > cptcode) cptcode=ij;          s1=s[mw[mi][i]][i];
     }          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for (i=0; i<=cptcode; i++) {          ipmx +=1;
       if(Ndum[i]!=0) ncodemax[j]++;          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     ij=1;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
       } /* end of individual */
     for (i=1; i<=ncodemax[j]; i++) {    } /* End of if */
       for (k=0; k<=19; k++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         if (Ndum[k] != 0) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           nbcode[Tvar[j]][ij]=k;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           ij++;    return -l;
         }  }
         if (ij > ncodemax[j]) break;  
       }    /*************** log-likelihood *************/
     }  double funcone( double *x)
   }    {
     /* Same as likeli but slower because of a lot of printf and if */
  for (k=0; k<19; k++) Ndum[k]=0;    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
  for (i=1; i<=ncovmodel-2; i++) {    double **out;
       ij=Tvar[i];    double lli; /* Individual log likelihood */
       Ndum[ij]++;    double llt;
     }    int s1, s2;
     double bbh, survp;
  ij=1;    /*extern weight */
  for (i=1; i<=10; i++) {    /* We are differentiating ll according to initial status */
    if((Ndum[i]!=0) && (i<=ncov)){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      Tvaraff[ij]=i;    /*for(i=1;i<imx;i++) 
      ij++;      printf(" %d\n",s[4][i]);
    }    */
  }    cov[1]=1.;
    
     cptcoveff=ij-1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
 }  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /*********** Health Expectancies ****************/      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        for (ii=1;ii<=nlstate+ndeath;ii++)
 {          for (j=1;j<=nlstate+ndeath;j++){
   /* Health expectancies */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm, h;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age, agelim,hf;          }
   double ***p3mat;        for(d=0; d<dh[mi][i]; d++){
            newm=savm;
   fprintf(ficreseij,"# Health expectancies\n");          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficreseij,"# Age");          for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=nlstate;j++)          }
       fprintf(ficreseij," %1d-%1d",i,j);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficreseij,"\n");                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
   hstepm=1*YEARM; /*  Every j years of age (in month) */          oldm=newm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } /* end mult */
         
   agelim=AGESUP;        s1=s[mw[mi][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        s2=s[mw[mi+1][i]][i];
     /* nhstepm age range expressed in number of stepm */        bbh=(double)bh[mi][i]/(double)stepm; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        /* bias is positive if real duration
     /* Typically if 20 years = 20*12/6=40 stepm */         * is higher than the multiple of stepm and negative otherwise.
     /*if (stepm >= YEARM) hstepm=1;*/         */
 hstepm=1;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          lli=log(out[s1][s2] - savm[s1][s2]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } else if (mle==1){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        } else if(mle==2){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            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 */
 hf=stepm/YEARM;        } else if(mle==3){  /* exponential inter-extrapolation */
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for(i=1; i<=nlstate;i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       for(j=1; j<=nlstate;j++)          lli=log(out[s1][s2]); /* Original formula */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;          lli=log(out[s1][s2]); /* Original formula */
         }        } /* End of if */
            ipmx +=1;
     /* hf=1;        sw += weight[i];
        if (stepm >= YEARM) hf=stepm/YEARM;*/        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 hf=stepm/YEARM;  /*       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(ficreseij,"%3.0f",age );          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     for(i=1; i<=nlstate;i++)   %10.6f %10.6f %10.6f ", \
       for(j=1; j<=nlstate;j++){                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     fprintf(ficreseij,"\n");            llt +=ll[k]*gipmx/gsw;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   }          }
 }          fprintf(ficresilk," %10.6f\n", -llt);
         }
 /************ Variance ******************/      } /* end of wave */
 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)    } /* end of individual */
 {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* Variance of health expectancies */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double **newm;    if(globpr==0){ /* First time we count the contributions and weights */
   double **dnewm,**doldm;      gipmx=ipmx;
   int i, j, nhstepm, hstepm, h;      gsw=sw;
   int k, cptcode;    }
   double *xp;    return -l;
   double **gp, **gm;  }
   double ***gradg, ***trgradg;  
   double ***p3mat;  
   double age,agelim;  /*************** function likelione ***********/
   int theta;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /* This routine should help understanding what is done with 
   fprintf(ficresvij,"# Age");       the selection of individuals/waves and
   for(i=1; i<=nlstate;i++)       to check the exact contribution to the likelihood.
     for(j=1; j<=nlstate;j++)       Plotting could be done.
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);     */
   fprintf(ficresvij,"\n");    int k;
   
   xp=vector(1,npar);    if(*globpri !=0){ /* Just counts and sums, no printings */
   dnewm=matrix(1,nlstate,1,npar);      strcpy(fileresilk,"ilk"); 
   doldm=matrix(1,nlstate,1,nlstate);      strcat(fileresilk,fileres);
        if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   hstepm=1*YEARM; /* Every year of age */        printf("Problem with resultfile: %s\n", fileresilk);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   agelim = AGESUP;      }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      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");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     if (stepm >= YEARM) hstepm=1;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for(k=1; k<=nlstate; k++) 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     gp=matrix(0,nhstepm,1,nlstate);    }
     gm=matrix(0,nhstepm,1,nlstate);  
     *fretone=(*funcone)(p);
     for(theta=1; theta <=npar; theta++){    if(*globpri !=0){
       for(i=1; i<=npar; i++){ /* Computes gradient */      fclose(ficresilk);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       }      fflush(fichtm); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return;
   }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  /*********** Maximum Likelihood Estimation ***************/
       }  
    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       for(j=1; j<= nlstate; j++){  {
         for(h=0; h<=nhstepm; h++){    int i,j, iter;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double **xi;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double fret;
         }    double fretone; /* Only one call to likelihood */
       }    /*  char filerespow[FILENAMELENGTH];*/
        xi=matrix(1,npar,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=1;i<=npar;i++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          xi[i][j]=(i==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      strcpy(filerespow,"pow"); 
       if (popbased==1) {    strcat(filerespow,fileres);
         for(i=1; i<=nlstate;i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           prlim[i][i]=probs[(int)age][i][ij];      printf("Problem with resultfile: %s\n", filerespow);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
       for(j=1; j<= nlstate; j++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         for(h=0; h<=nhstepm; h++){    for (i=1;i<=nlstate;i++)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(j=1;j<=nlstate+ndeath;j++)
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         }    fprintf(ficrespow,"\n");
       }  
     powell(p,xi,npar,ftol,&iter,&fret,func);
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; h++){    fclose(ficrespow);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     } /* End theta */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  }
   
     for(h=0; h<=nhstepm; h++)  /**** Computes Hessian and covariance matrix ***/
       for(j=1; j<=nlstate;j++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         for(theta=1; theta <=npar; theta++)  {
           trgradg[h][j][theta]=gradg[h][theta][j];    double  **a,**y,*x,pd;
     double **hess;
     for(i=1;i<=nlstate;i++)    int i, j,jk;
       for(j=1;j<=nlstate;j++)    int *indx;
         vareij[i][j][(int)age] =0.;  
     for(h=0;h<=nhstepm;h++){    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(k=0;k<=nhstepm;k++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    void lubksb(double **a, int npar, int *indx, double b[]) ;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
         for(i=1;i<=nlstate;i++)    double gompertz(double p[]);
           for(j=1;j<=nlstate;j++)    hess=matrix(1,npar,1,npar);
             vareij[i][j][(int)age] += doldm[i][j];  
       }    printf("\nCalculation of the hessian matrix. Wait...\n");
     }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     h=1;    for (i=1;i<=npar;i++){
     if (stepm >= YEARM) h=stepm/YEARM;      printf("%d",i);fflush(stdout);
     fprintf(ficresvij,"%.0f ",age );      fprintf(ficlog,"%d",i);fflush(ficlog);
     for(i=1; i<=nlstate;i++)     
       for(j=1; j<=nlstate;j++){       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      
       }      /*  printf(" %f ",p[i]);
     fprintf(ficresvij,"\n");          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     free_matrix(gp,0,nhstepm,1,nlstate);    }
     free_matrix(gm,0,nhstepm,1,nlstate);    
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    for (i=1;i<=npar;i++) {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for (j=1;j<=npar;j++)  {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (j>i) { 
   } /* End age */          printf(".%d%d",i,j);fflush(stdout);
            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   free_vector(xp,1,npar);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   free_matrix(doldm,1,nlstate,1,npar);          
   free_matrix(dnewm,1,nlstate,1,nlstate);          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
 }        }
       }
 /************ 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)    printf("\n");
 {    fprintf(ficlog,"\n");
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **newm;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm;    a=matrix(1,npar,1,npar);
   int k, cptcode;    y=matrix(1,npar,1,npar);
   double *xp;    x=vector(1,npar);
   double *gp, *gm;    indx=ivector(1,npar);
   double **gradg, **trgradg;    for (i=1;i<=npar;i++)
   double age,agelim;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   int theta;    ludcmp(a,npar,indx,&pd);
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (j=1;j<=npar;j++) {
   fprintf(ficresvpl,"# Age");      for (i=1;i<=npar;i++) x[i]=0;
   for(i=1; i<=nlstate;i++)      x[j]=1;
       fprintf(ficresvpl," %1d-%1d",i,i);      lubksb(a,npar,indx,x);
   fprintf(ficresvpl,"\n");      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);  
      printf("\n#Hessian matrix#\n");
   hstepm=1*YEARM; /* Every year of age */    fprintf(ficlog,"\n#Hessian matrix#\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=1;i<=npar;i++) { 
   agelim = AGESUP;      for (j=1;j<=npar;j++) { 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        printf("%.3e ",hess[i][j]);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        fprintf(ficlog,"%.3e ",hess[i][j]);
     if (stepm >= YEARM) hstepm=1;      }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      printf("\n");
     gradg=matrix(1,npar,1,nlstate);      fprintf(ficlog,"\n");
     gp=vector(1,nlstate);    }
     gm=vector(1,nlstate);  
     /* Recompute Inverse */
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++)
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    ludcmp(a,npar,indx,&pd);
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*  printf("\n#Hessian matrix recomputed#\n");
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];    for (j=1;j<=npar;j++) {
          for (i=1;i<=npar;i++) x[i]=0;
       for(i=1; i<=npar; i++) /* Computes gradient */      x[j]=1;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      lubksb(a,npar,indx,x);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (i=1;i<=npar;i++){ 
       for(i=1;i<=nlstate;i++)        y[i][j]=x[i];
         gm[i] = prlim[i][i];        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
       for(i=1;i<=nlstate;i++)      }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      printf("\n");
     } /* End theta */      fprintf(ficlog,"\n");
     }
     trgradg =matrix(1,nlstate,1,npar);    */
   
     for(j=1; j<=nlstate;j++)    free_matrix(a,1,npar,1,npar);
       for(theta=1; theta <=npar; theta++)    free_matrix(y,1,npar,1,npar);
         trgradg[j][theta]=gradg[theta][j];    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     for(i=1;i<=nlstate;i++)    free_matrix(hess,1,npar,1,npar);
       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 */  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     fprintf(ficresvpl,"%.0f ",age );  {
     for(i=1; i<=nlstate;i++)    int i;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    int l=1, lmax=20;
     fprintf(ficresvpl,"\n");    double k1,k2;
     free_vector(gp,1,nlstate);    double p2[NPARMAX+1];
     free_vector(gm,1,nlstate);    double res;
     free_matrix(gradg,1,npar,1,nlstate);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     free_matrix(trgradg,1,nlstate,1,npar);    double fx;
   } /* End age */    int k=0,kmax=10;
     double l1;
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    fx=func(x);
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
 }      l1=pow(10,l);
       delts=delt;
 /************ Variance of one-step probabilities  ******************/      for(k=1 ; k <kmax; k=k+1){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        delt = delta*(l1*k);
 {        p2[theta]=x[theta] +delt;
   int i, j;        k1=func(p2)-fx;
   int k=0, cptcode;        p2[theta]=x[theta]-delt;
   double **dnewm,**doldm;        k2=func(p2)-fx;
   double *xp;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double *gp, *gm;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double **gradg, **trgradg;        
   double age,agelim, cov[NCOVMAX];  #ifdef DEBUG
   int theta;        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);
   char fileresprob[FILENAMELENGTH];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
   strcpy(fileresprob,"prob");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   strcat(fileresprob,fileres);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          k=kmax;
     printf("Problem with resultfile: %s\n", fileresprob);        }
   }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          k=kmax; l=lmax*10.;
          }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   xp=vector(1,npar);          delts=delt;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      }
      }
   cov[1]=1;    delti[theta]=delts;
   for (age=bage; age<=fage; age ++){    return res; 
     cov[2]=age;    
     gradg=matrix(1,npar,1,9);  }
     trgradg=matrix(1,9,1,npar);  
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  {
        int i;
     for(theta=1; theta <=npar; theta++){    int l=1, l1, lmax=20;
       for(i=1; i<=npar; i++)    double k1,k2,k3,k4,res,fx;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double p2[NPARMAX+1];
          int k;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
        fx=func(x);
       k=0;    for (k=1; k<=2; k++) {
       for(i=1; i<= (nlstate+ndeath); i++){      for (i=1;i<=npar;i++) p2[i]=x[i];
         for(j=1; j<=(nlstate+ndeath);j++){      p2[thetai]=x[thetai]+delti[thetai]/k;
            k=k+1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           gp[k]=pmmij[i][j];      k1=func(p2)-fx;
         }    
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(i=1; i<=npar; i++)      k2=func(p2)-fx;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    
          p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      k3=func(p2)-fx;
       k=0;    
       for(i=1; i<=(nlstate+ndeath); i++){      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(j=1; j<=(nlstate+ndeath);j++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           k=k+1;      k4=func(p2)-fx;
           gm[k]=pmmij[i][j];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         }  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
            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);
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  #endif
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      }
     }    return res;
   }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)  /************** Inverse of matrix **************/
       trgradg[j][theta]=gradg[theta][j];  void ludcmp(double **a, int n, int *indx, double *d) 
    { 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    int i,imax,j,k; 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double big,dum,sum,temp; 
     double *vv; 
      pmij(pmmij,cov,ncovmodel,x,nlstate);   
     vv=vector(1,n); 
      k=0;    *d=1.0; 
      for(i=1; i<=(nlstate+ndeath); i++){    for (i=1;i<=n;i++) { 
        for(j=1; j<=(nlstate+ndeath);j++){      big=0.0; 
          k=k+1;      for (j=1;j<=n;j++) 
          gm[k]=pmmij[i][j];        if ((temp=fabs(a[i][j])) > big) big=temp; 
         }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      }      vv[i]=1.0/big; 
          } 
      /*printf("\n%d ",(int)age);    for (j=1;j<=n;j++) { 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for (i=1;i<j;i++) { 
                sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        a[i][j]=sum; 
      }*/      } 
       big=0.0; 
   fprintf(ficresprob,"\n%d ",(int)age);      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        for (k=1;k<j;k++) 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          sum -= a[i][k]*a[k][j]; 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        a[i][j]=sum; 
   }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          imax=i; 
     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);      if (j != imax) { 
 }        for (k=1;k<=n;k++) { 
  free_vector(xp,1,npar);          dum=a[imax][k]; 
 fclose(ficresprob);          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
 }        } 
         *d = -(*d); 
 /******************* Printing html file ***********/        vv[imax]=vv[j]; 
 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 optionfile[],char optionfilehtm[],char rfileres[] ){      } 
   int jj1, k1, i1, cpt;      indx[j]=imax; 
   FILE *fichtm;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   /*char optionfilehtm[FILENAMELENGTH];*/      if (j != n) { 
         dum=1.0/(a[j][j]); 
   strcpy(optionfilehtm,optionfile);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   strcat(optionfilehtm,".htm");      } 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    } 
     printf("Problem with %s \n",optionfilehtm), exit(0);    free_vector(vv,1,n);  /* Doesn't work */
   }  ;
   } 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
 Total number of observations=%d <br>    int i,ii=0,ip,j; 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    double sum; 
 <hr  size=\"2\" color=\"#EC5E5E\">   
 <li>Outputs files<br><br>\n    for (i=1;i<=n;i++) { 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      ip=indx[i]; 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      sum=b[ip]; 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      b[ip]=b[i]; 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      if (ii) 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      else if (sum) ii=i; 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      b[i]=sum; 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    } 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    for (i=n;i>=1;i--) { 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>      sum=b[i]; 
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      b[i]=sum/a[i][i]; 
      } 
 fprintf(fichtm," <li>Graphs</li><p>");  } 
   
  m=cptcoveff;  /************ Frequencies ********************/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   {  /* Some frequencies */
  jj1=0;    
  for(k1=1; k1<=m;k1++){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
    for(i1=1; i1<=ncodemax[k1];i1++){    int first;
        jj1++;    double ***freq; /* Frequencies */
        if (cptcovn > 0) {    double *pp, **prop;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
          for (cpt=1; cpt<=cptcoveff;cpt++)    FILE *ficresp;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    char fileresp[FILENAMELENGTH];
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    
        }    pp=vector(1,nlstate);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    prop=matrix(1,nlstate,iagemin,iagemax+3);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        strcpy(fileresp,"p");
        for(cpt=1; cpt<nlstate;cpt++){    strcat(fileresp,fileres);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    if((ficresp=fopen(fileresp,"w"))==NULL) {
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      printf("Problem with prevalence resultfile: %s\n", fileresp);
        }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     for(cpt=1; cpt<=nlstate;cpt++) {      exit(0);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    }
 interval) in state (%d): v%s%d%d.gif <br>    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      j1=0;
      }    
      for(cpt=1; cpt<=nlstate;cpt++) {    j=cptcoveff;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }    first=1;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>    for(k1=1; k1<=j;k1++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      for(i1=1; i1<=ncodemax[k1];i1++){
 fprintf(fichtm,"\n</body>");        j1++;
    }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
    }          scanf("%d", i);*/
 fclose(fichtm);        for (i=-5; i<=nlstate+ndeath; i++)  
 }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
 /******************* Gnuplot file **************/              freq[i][jk][m]=0;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){  
       for (i=1; i<=nlstate; i++)  
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
   strcpy(optionfilegnuplot,optionfilefiname);        
   strcat(optionfilegnuplot,".plt");        dateintsum=0;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        k2cpt=0;
     printf("Problem with file %s",optionfilegnuplot);        for (i=1; i<=imx; i++) {
   }          bool=1;
           if  (cptcovn>0) {
 #ifdef windows            for (z1=1; z1<=cptcoveff; z1++) 
     fprintf(ficgp,"cd \"%s\" \n",pathc);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 #endif                bool=0;
 m=pow(2,cptcoveff);          }
            if (bool==1){
  /* 1eme*/            for(m=firstpass; m<=lastpass; m++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {              k2=anint[m][i]+(mint[m][i]/12.);
    for (k1=1; k1<= m ; k1 ++) {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
 #ifdef windows                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 #endif                if (m<lastpass) {
 #ifdef unix                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 #endif                }
                 
 for (i=1; i<= nlstate ; i ++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  dateintsum=dateintsum+k2;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  k2cpt++;
 }                }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                /*}*/
     for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }         
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      for (i=1; i<= nlstate ; i ++) {  fprintf(ficresp, "#Local time at start: %s", strstart);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if  (cptcovn>0) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficresp, "\n#********** Variable "); 
 }            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          fprintf(ficresp, "**********\n#");
 #ifdef unix        }
 fprintf(ficgp,"\nset ter gif small size 400,300");        for(i=1; i<=nlstate;i++) 
 #endif          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        fprintf(ficresp, "\n");
    }        
   }        for(i=iagemin; i <= iagemax+3; i++){
   /*2 eme*/          if(i==iagemax+3){
             fprintf(ficlog,"Total");
   for (k1=1; k1<= m ; k1 ++) {          }else{
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            if(first==1){
                  first=0;
     for (i=1; i<= nlstate+1 ; i ++) {              printf("See log file for details...\n");
       k=2*i;            }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            fprintf(ficlog,"Age %d", i);
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 }                pp[jk] += freq[jk][m][i]; 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(m=-1, pos=0; m <=0 ; m++)
       for (j=1; j<= nlstate+1 ; j ++) {              pos += freq[jk][m][i];
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            if(pp[jk]>=1.e-10){
         else fprintf(ficgp," \%%*lf (\%%*lf)");              if(first==1){
 }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficgp,"\" t\"\" w l 0,");              }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for (j=1; j<= nlstate+1 ; j ++) {            }else{
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if(first==1)
   else fprintf(ficgp," \%%*lf (\%%*lf)");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            }
       else fprintf(ficgp,"\" t\"\" w l 0,");          }
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                pp[jk] += freq[jk][m][i];
   /*3eme*/          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   for (k1=1; k1<= m ; k1 ++) {            pos += pp[jk];
     for (cpt=1; cpt<= nlstate ; cpt ++) {            posprop += prop[jk][i];
       k=2+nlstate*(cpt-1);          }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i< nlstate ; i ++) {            if(pos>=1.e-5){
         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(first==1)
       }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     }            }else{
     }              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /* CV preval stat */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for (k1=1; k1<= m ; k1 ++) {            }
     for (cpt=1; cpt<nlstate ; cpt ++) {            if( i <= iagemax){
       k=3;              if(pos>=1.e-5){
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
       for (i=1; i< nlstate ; i ++)                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         fprintf(ficgp,"+$%d",k+i+1);              }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              else
                      fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       l=3+(nlstate+ndeath)*cpt;            }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          }
       for (i=1; i< nlstate ; i ++) {          
         l=3+(nlstate+ndeath)*cpt;          for(jk=-1; jk <=nlstate+ndeath; jk++)
         fprintf(ficgp,"+$%d",l+i+1);            for(m=-1; m <=nlstate+ndeath; m++)
       }              if(freq[jk][m][i] !=0 ) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                if(first==1)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                }
            if(i <= iagemax)
   /* proba elementaires */            fprintf(ficresp,"\n");
    for(i=1,jk=1; i <=nlstate; i++){          if(first==1)
     for(k=1; k <=(nlstate+ndeath); k++){            printf("Others in log...\n");
       if (k != i) {          fprintf(ficlog,"\n");
         for(j=1; j <=ncovmodel; j++){        }
              }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    }
           jk++;    dateintmean=dateintsum/k2cpt; 
           fprintf(ficgp,"\n");   
         }    fclose(ficresp);
       }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     }    free_vector(pp,1,nlstate);
     }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     for(jk=1; jk <=m; jk++) {  }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);  
    i=1;  /************ Prevalence ********************/
    for(k2=1; k2<=nlstate; k2++) {  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)
      k3=i;  {  
      for(k=1; k<=(nlstate+ndeath); k++) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        if (k != k2){       in each health status at the date of interview (if between dateprev1 and dateprev2).
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       We still use firstpass and lastpass as another selection.
 ij=1;    */
         for(j=3; j <=ncovmodel; j++) {   
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double ***freq; /* Frequencies */
             ij++;    double *pp, **prop;
           }    double pos,posprop; 
           else    double  y2; /* in fractional years */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int iagemin, iagemax;
         }  
           fprintf(ficgp,")/(1");    iagemin= (int) agemin;
            iagemax= (int) agemax;
         for(k1=1; k1 <=nlstate; k1++){      /*pp=vector(1,nlstate);*/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
 ij=1;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           for(j=3; j <=ncovmodel; j++){    j1=0;
           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]]]);    j=cptcoveff;
             ij++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           }    
           else    for(k1=1; k1<=j;k1++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(i1=1; i1<=ncodemax[k1];i1++){
           }        j1++;
           fprintf(ficgp,")");        
         }        for (i=1; i<=nlstate; i++)  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          for(m=iagemin; m <= iagemax+3; m++)
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            prop[i][m]=0.0;
         i=i+ncovmodel;       
        }        for (i=1; i<=imx; i++) { /* Each individual */
      }          bool=1;
    }          if  (cptcovn>0) {
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            for (z1=1; z1<=cptcoveff; z1++) 
    }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
   fclose(ficgp);          } 
 }  /* end gnuplot */          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 /*************** Moving average **************/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   int i, cpt, cptcod;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     for (agedeb=agemin; agedeb<=fage; agedeb++)                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for (i=1; i<=nlstate;i++)                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           mobaverage[(int)agedeb][i][cptcod]=0.;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                    } 
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){              }
       for (i=1; i<=nlstate;i++){            } /* end selection of waves */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
           for (cpt=0;cpt<=4;cpt++){        }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for(i=iagemin; i <= iagemax+3; i++){  
           }          
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         }            posprop += prop[jk][i]; 
       }          } 
     }  
              for(jk=1; jk <=nlstate ; jk++){     
 }            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
 /************** Forecasting ******************/              } 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            } 
            }/* end jk */ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }/* end i */ 
   int *popage;      } /* end i1 */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    } /* end k1 */
   double *popeffectif,*popcount;    
   double ***p3mat;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   char fileresf[FILENAMELENGTH];    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
  agelim=AGESUP;  }  /* End of prevalence */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
   /************* Waves Concatenation ***************/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
    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)
    {
   strcpy(fileresf,"f");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   strcat(fileresf,fileres);       Death is a valid wave (if date is known).
   if((ficresf=fopen(fileresf,"w"))==NULL) {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     printf("Problem with forecast resultfile: %s\n", fileresf);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   }       and mw[mi+1][i]. dh depends on stepm.
   printf("Computing forecasting: result on file '%s' \n", fileresf);       */
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   if (mobilav==1) {       double sum=0., jmean=0.;*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int first;
     movingaverage(agedeb, fage, agemin, mobaverage);    int j, k=0,jk, ju, jl;
   }    double sum=0.;
     first=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    jmin=1e+5;
   if (stepm<=12) stepsize=1;    jmax=-1;
      jmean=0.;
   agelim=AGESUP;    for(i=1; i<=imx; i++){
        mi=0;
   hstepm=1;      m=firstpass;
   hstepm=hstepm/stepm;      while(s[m][i] <= nlstate){
   yp1=modf(dateintmean,&yp);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   anprojmean=yp;          mw[++mi][i]=m;
   yp2=modf((yp1*12),&yp);        if(m >=lastpass)
   mprojmean=yp;          break;
   yp1=modf((yp2*30.5),&yp);        else
   jprojmean=yp;          m++;
   if(jprojmean==0) jprojmean=1;      }/* end while */
   if(mprojmean==0) jprojmean=1;      if (s[m][i] > nlstate){
          mi++;     /* Death is another wave */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        /* if(mi==0)  never been interviewed correctly before death */
             /* Only death is a correct wave */
   for(cptcov=1;cptcov<=i2;cptcov++){        mw[mi][i]=m;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      }
       k=k+1;  
       fprintf(ficresf,"\n#******");      wav[i]=mi;
       for(j=1;j<=cptcoveff;j++) {      if(mi==0){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        nbwarn++;
       }        if(first==0){
       fprintf(ficresf,"******\n");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fprintf(ficresf,"# StartingAge FinalAge");          first=1;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }
              if(first==1){
                fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        }
         fprintf(ficresf,"\n");      } /* end mi==0 */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      } /* End individuals */
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    for(i=1; i<=imx; i++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(mi=1; mi<wav[i];mi++){
           nhstepm = nhstepm/hstepm;        if (stepm <=0)
                    dh[mi][i]=1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        else{
           oldm=oldms;savm=savms;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              if (agedc[i] < 2*AGESUP) {
                      j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           for (h=0; h<=nhstepm; h++){              if(j==0) j=1;  /* Survives at least one month after exam */
             if (h==(int) (calagedate+YEARM*cpt)) {              else if(j<0){
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);                nberr++;
             }                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]);
             for(j=1; j<=nlstate+ndeath;j++) {                j=1; /* Temporary Dangerous patch */
               kk1=0.;kk2=0;                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               for(i=1; i<=nlstate;i++) {                              fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 if (mobilav==1)                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);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              }
                 else {              k=k+1;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              if (j >= jmax){
                 }                jmax=j;
                                ijmax=i;
               }              }
               if (h==(int)(calagedate+12*cpt)){              if (j <= jmin){
                 fprintf(ficresf," %.3f", kk1);                jmin=j;
                                        ijmin=i;
               }              }
             }              sum=sum+j;
           }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         }            }
       }          }
     }          else{
   }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
          /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
             k=k+1;
   fclose(ficresf);            if (j >= jmax) {
 }              jmax=j;
 /************** Forecasting ******************/              ijmax=i;
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){            }
              else if (j <= jmin){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              jmin=j;
   int *popage;              ijmin=i;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }
   double *popeffectif,*popcount;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   double ***p3mat,***tabpop,***tabpopprev;            /*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]);*/
   char filerespop[FILENAMELENGTH];            if(j<0){
               nberr++;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              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]);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              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]);
   agelim=AGESUP;            }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            sum=sum+j;
            }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          jk= j/stepm;
            jl= j -jk*stepm;
            ju= j -(jk+1)*stepm;
   strcpy(filerespop,"pop");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   strcat(filerespop,fileres);            if(jl==0){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              dh[mi][i]=jk;
     printf("Problem with forecast resultfile: %s\n", filerespop);              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
   printf("Computing forecasting: result on file '%s' \n", filerespop);                    * at the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              bh[mi][i]=ju;
             }
   if (mobilav==1) {          }else{
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(jl <= -ju){
     movingaverage(agedeb, fage, agemin, mobaverage);              dh[mi][i]=jk;
   }              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   stepsize=(int) (stepm+YEARM-1)/YEARM;                                   */
   if (stepm<=12) stepsize=1;            }
              else{
   agelim=AGESUP;              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   hstepm=1;            }
   hstepm=hstepm/stepm;            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   if (popforecast==1) {              bh[mi][i]=ju; /* At least one step */
     if((ficpop=fopen(popfile,"r"))==NULL) {              /*  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);*/
       printf("Problem with population file : %s\n",popfile);exit(0);            }
     }          } /* end if mle */
     popage=ivector(0,AGESUP);        }
     popeffectif=vector(0,AGESUP);      } /* end wave */
     popcount=vector(0,AGESUP);    }
        jmean=sum/k;
     i=1;      printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
       }
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  /*********** Tricode ****************************/
   }  void tricode(int *Tvar, int **nbcode, int imx)
   {
   for(cptcov=1;cptcov<=i2;cptcov++){    
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
       k=k+1;    int cptcode=0;
       fprintf(ficrespop,"\n#******");    cptcoveff=0; 
       for(j=1;j<=cptcoveff;j++) {   
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (k=0; k<maxncov; k++) Ndum[k]=0;
       }    for (k=1; k<=7; k++) ncodemax[k]=0;
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       if (popforecast==1)  fprintf(ficrespop," [Population]");                                 modality*/ 
              ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for (cpt=0; cpt<=0;cpt++) {        Ndum[ij]++; /*store the modality */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){                                         Tvar[j]. If V=sex and male is 0 and 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                                         female is 1, then  cptcode=1.*/
           nhstepm = nhstepm/hstepm;      }
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=0; i<=cptcode; i++) {
           oldm=oldms;savm=savms;        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 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        }
          
           for (h=0; h<=nhstepm; h++){      ij=1; 
             if (h==(int) (calagedate+YEARM*cpt)) {      for (i=1; i<=ncodemax[j]; i++) {
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for (k=0; k<= maxncov; k++) {
             }          if (Ndum[k] != 0) {
             for(j=1; j<=nlstate+ndeath;j++) {            nbcode[Tvar[j]][ij]=k; 
               kk1=0.;kk2=0;            /* 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; */
               for(i=1; i<=nlstate;i++) {                          
                 if (mobilav==1)            ij++;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          }
                 else {          if (ij > ncodemax[j]) break; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }  
                 }      } 
               }    }  
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;   for (k=0; k< maxncov; k++) Ndum[k]=0;
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/   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];
             for(i=1; i<=nlstate;i++){     Ndum[ij]++;
               kk1=0.;   }
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];   ij=1;
                 }   for (i=1; i<= maxncov; i++) {
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];     if((Ndum[i]!=0) && (i<=ncovcol)){
             }       Tvaraff[ij]=i; /*For printing */
        ij++;
             if (h==(int)(calagedate+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);   cptcoveff=ij-1; /*Number of simple covariates*/
         }  }
       }  
    /*********** Health Expectancies ****************/
   /******/  
   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[] )
       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)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    /* Health expectancies */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
           nhstepm = nhstepm/hstepm;    double age, agelim, hf;
              double ***p3mat,***varhe;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewm,**doldm;
           oldm=oldms;savm=savms;    double *xp;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **gp, **gm;
           for (h=0; h<=nhstepm; h++){    double ***gradg, ***trgradg;
             if (h==(int) (calagedate+YEARM*cpt)) {    int theta;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
             for(j=1; j<=nlstate+ndeath;j++) {    xp=vector(1,npar);
               kk1=0.;kk2=0;    dnewm=matrix(1,nlstate*nlstate,1,npar);
               for(i=1; i<=nlstate;i++) {                  doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        
               }    fprintf(ficreseij,"# Local time at start: %s", strstart);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    fprintf(ficreseij,"# Health expectancies\n");
             }    fprintf(ficreseij,"# Age");
           }    for(i=1; i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=1; j<=nlstate;j++)
         }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       }    fprintf(ficreseij,"\n");
    }  
   }    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     else  hstepm=estepm;   
   if (popforecast==1) {    /* We compute the life expectancy from trapezoids spaced every estepm months
     free_ivector(popage,0,AGESUP);     * This is mainly to measure the difference between two models: for example
     free_vector(popeffectif,0,AGESUP);     * if stepm=24 months pijx are given only every 2 years and by summing them
     free_vector(popcount,0,AGESUP);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }     * progression in between and thus overestimating or underestimating according
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * to the curvature of the survival function. If, for the same date, we 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   fclose(ficrespop);     * to compare the new estimate of Life expectancy with the same linear 
 }     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
 /***********************************************/  
 /**************** Main Program *****************/    /* For example we decided to compute the life expectancy with the smallest unit */
 /***********************************************/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
 int main(int argc, char *argv[])       nstepm is the number of stepm from age to agelin. 
 {       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double agedeb, agefin,hf;       survival function given by stepm (the optimization length). Unfortunately it
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double fret;       results. So we changed our mind and took the option of the best precision.
   double **xi,tmp,delta;    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double dum; /* Dummy variable */  
   double ***p3mat;    agelim=AGESUP;
   int *indx;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char line[MAXLINE], linepar[MAXLINE];      /* nhstepm age range expressed in number of stepm */
   char title[MAXLINE];      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   char filerest[FILENAMELENGTH];      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   char fileregp[FILENAMELENGTH];      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   int firstobs=1, lastobs=10;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   int sdeb, sfin; /* Status at beginning and end */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   int c,  h , cpt,l;   
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;      /* Computing  Variances of health expectancies */
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
   double bage, fage, age, agelim, agebase;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double ftolpl=FTOL;        }
   double **prlim;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double *severity;    
   double ***param; /* Matrix of parameters */        cptj=0;
   double  *p;        for(j=1; j<= nlstate; j++){
   double **matcov; /* Matrix of covariance */          for(i=1; i<=nlstate; i++){
   double ***delti3; /* Scale */            cptj=cptj+1;
   double *delti; /* Scale */            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   double ***eij, ***vareij;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double **varpl; /* Variances of prevalence limits by age */            }
   double *epj, vepp;          }
   double kk1, kk2;        }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;       
         
         for(i=1; i<=npar; i++) 
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   char *alph[]={"a","a","b","c","d","e"}, str[4];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         
         cptj=0;
   char z[1]="c", occ;        for(j=1; j<= nlstate; j++){
 #include <sys/time.h>          for(i=1;i<=nlstate;i++){
 #include <time.h>            cptj=cptj+1;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
    
   /* long total_usecs;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   struct timeval start_time, end_time;            }
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        }
         for(j=1; j<= nlstate*nlstate; j++)
           for(h=0; h<=nhstepm-1; h++){
   printf("\n%s",version);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if(argc <=1){          }
     printf("\nEnter the parameter file name: ");       } 
     scanf("%s",pathtot);     
   }  /* End theta */
   else{  
     strcpy(pathtot,argv[1]);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/       for(h=0; h<=nhstepm-1; h++)
   /*cygwin_split_path(pathtot,path,optionfile);        for(j=1; j<=nlstate*nlstate;j++)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for(theta=1; theta <=npar; theta++)
   /* cutv(path,optionfile,pathtot,'\\');*/            trgradg[h][j][theta]=gradg[h][theta][j];
        
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);       for(i=1;i<=nlstate*nlstate;i++)
   chdir(path);        for(j=1;j<=nlstate*nlstate;j++)
   replace(pathc,path);          varhe[i][j][(int)age] =0.;
   
 /*-------- arguments in the command line --------*/       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   strcpy(fileres,"r");       for(h=0;h<=nhstepm-1;h++){
   strcat(fileres, optionfilefiname);        for(k=0;k<=nhstepm-1;k++){
   strcat(fileres,".txt");    /* Other files have txt extension */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   /*---------arguments file --------*/          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1;j<=nlstate*nlstate;j++)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     printf("Problem with optionfile %s\n",optionfile);        }
     goto end;      }
   }      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   strcpy(filereso,"o");        for(j=1; j<=nlstate;j++)
   strcat(filereso,fileres);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   if((ficparo=fopen(filereso,"w"))==NULL) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            
   }  /* 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]);*/
   
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(ficreseij,"%3.0f",age );
     fgets(line, MAXLINE, ficpar);      cptj=0;
     puts(line);      for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);        for(j=1; j<=nlstate;j++){
   }          cptj++;
   ungetc(c,ficpar);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         }
   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);      fprintf(ficreseij,"\n");
   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);     
   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);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 while((c=getc(ficpar))=='#' && c!= EOF){      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     ungetc(c,ficpar);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     fgets(line, MAXLINE, ficpar);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     puts(line);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);    }
   }    printf("\n");
   ungetc(c,ficpar);    fprintf(ficlog,"\n");
    
        free_vector(xp,1,npar);
   covar=matrix(0,NCOVMAX,1,n);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   cptcovn=0;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  /************ 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[])
   /* Read guess parameters */  {
   /* Reads comments: lines beginning with '#' */    /* Variance of health expectancies */
   while((c=getc(ficpar))=='#' && c!= EOF){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     ungetc(c,ficpar);    /* double **newm;*/
     fgets(line, MAXLINE, ficpar);    double **dnewm,**doldm;
     puts(line);    double **dnewmp,**doldmp;
     fputs(line,ficparo);    int i, j, nhstepm, hstepm, h, nstepm ;
   }    int k, cptcode;
   ungetc(c,ficpar);    double *xp;
      double **gp, **gm;  /* for var eij */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double ***gradg, ***trgradg; /*for var eij */
     for(i=1; i <=nlstate; i++)    double **gradgp, **trgradgp; /* for var p point j */
     for(j=1; j <=nlstate+ndeath-1; j++){    double *gpp, *gmp; /* for var p point j */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       fprintf(ficparo,"%1d%1d",i1,j1);    double ***p3mat;
       printf("%1d%1d",i,j);    double age,agelim, hf;
       for(k=1; k<=ncovmodel;k++){    double ***mobaverage;
         fscanf(ficpar," %lf",&param[i][j][k]);    int theta;
         printf(" %lf",param[i][j][k]);    char digit[4];
         fprintf(ficparo," %lf",param[i][j][k]);    char digitp[25];
       }  
       fscanf(ficpar,"\n");    char fileresprobmorprev[FILENAMELENGTH];
       printf("\n");  
       fprintf(ficparo,"\n");    if(popbased==1){
     }      if(mobilav!=0)
          strcpy(digitp,"-populbased-mobilav-");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      else strcpy(digitp,"-populbased-nomobil-");
     }
   p=param[1][1];    else 
        strcpy(digitp,"-stablbased-");
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    if (mobilav!=0) {
     ungetc(c,ficpar);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fgets(line, MAXLINE, ficpar);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     puts(line);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     fputs(line,ficparo);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   }      }
   ungetc(c,ficpar);    }
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    strcpy(fileresprobmorprev,"prmorprev"); 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    sprintf(digit,"%-d",ij);
   for(i=1; i <=nlstate; i++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     for(j=1; j <=nlstate+ndeath-1; j++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       printf("%1d%1d",i,j);    strcat(fileresprobmorprev,fileres);
       fprintf(ficparo,"%1d%1d",i1,j1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       for(k=1; k<=ncovmodel;k++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         printf(" %le",delti3[i][j][k]);    }
         fprintf(ficparo," %le",delti3[i][j][k]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }   
       fscanf(ficpar,"\n");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       printf("\n");    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
       fprintf(ficparo,"\n");    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   delti=delti3[1][1];      fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   while((c=getc(ficpar))=='#' && c!= EOF){    }  
     ungetc(c,ficpar);    fprintf(ficresprobmorprev,"\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficgp,"\n# Routine varevsij");
     puts(line);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fputs(line,ficparo);    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   ungetc(c,ficpar);  /*   } */
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   matcov=matrix(1,npar,1,npar);   fprintf(ficresvij, "#Local time at start: %s", strstart);
   for(i=1; i <=npar; i++){    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");
     fscanf(ficpar,"%s",&str);    fprintf(ficresvij,"# Age");
     printf("%s",str);    for(i=1; i<=nlstate;i++)
     fprintf(ficparo,"%s",str);      for(j=1; j<=nlstate;j++)
     for(j=1; j <=i; j++){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
       fscanf(ficpar," %le",&matcov[i][j]);    fprintf(ficresvij,"\n");
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
     fscanf(ficpar,"\n");    doldm=matrix(1,nlstate,1,nlstate);
     printf("\n");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     fprintf(ficparo,"\n");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
   for(i=1; i <=npar; i++)    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     for(j=i+1;j<=npar;j++)    gpp=vector(nlstate+1,nlstate+ndeath);
       matcov[i][j]=matcov[j][i];    gmp=vector(nlstate+1,nlstate+ndeath);
        trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   printf("\n");    
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     /*-------- Rewriting paramater file ----------*/    }
      strcpy(rfileres,"r");    /* "Rparameterfile */    else  hstepm=estepm;   
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    /* For example we decided to compute the life expectancy with the smallest unit */
      strcat(rfileres,".");    /* */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */       nhstepm is the number of hstepm from age to agelim 
     if((ficres =fopen(rfileres,"w"))==NULL) {       nstepm is the number of stepm from age to agelin. 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;       Look at hpijx to understand the reason of that which relies in memory size
     }       and note for a fixed period like k years */
     fprintf(ficres,"#%s\n",version);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
     /*-------- data file ----------*/       means that if the survival funtion is printed every two years of age and if
     if((fic=fopen(datafile,"r"))==NULL)    {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("Problem with datafile: %s\n", datafile);goto end;       results. So we changed our mind and took the option of the best precision.
     }    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     n= lastobs;    agelim = AGESUP;
     severity = vector(1,maxwav);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     outcome=imatrix(1,maxwav+1,1,n);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     num=ivector(1,n);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     moisnais=vector(1,n);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     annais=vector(1,n);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     moisdc=vector(1,n);      gp=matrix(0,nhstepm,1,nlstate);
     andc=vector(1,n);      gm=matrix(0,nhstepm,1,nlstate);
     agedc=vector(1,n);  
     cod=ivector(1,n);  
     weight=vector(1,n);      for(theta=1; theta <=npar; theta++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     mint=matrix(1,maxwav,1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     anint=matrix(1,maxwav,1,n);        }
     s=imatrix(1,maxwav+1,1,n);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     adl=imatrix(1,maxwav+1,1,n);            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);        if (popbased==1) {
           if(mobilav ==0){
     i=1;            for(i=1; i<=nlstate;i++)
     while (fgets(line, MAXLINE, fic) != NULL)    {              prlim[i][i]=probs[(int)age][i][ij];
       if ((i >= firstobs) && (i <=lastobs)) {          }else{ /* mobilav */ 
                    for(i=1; i<=nlstate;i++)
         for (j=maxwav;j>=1;j--){              prlim[i][i]=mobaverage[(int)age][i][ij];
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          }
           strcpy(line,stra);        }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<= nlstate; j++){
         }          for(h=0; h<=nhstepm; h++){
                    for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        /* This for computing probability of death (h=1 means
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        */
         for (j=ncov;j>=1;j--){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         num[i]=atol(stra);        }    
                /* end probability of death */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         i=i+1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }   
     /* printf("ii=%d", ij);        if (popbased==1) {
        scanf("%d",i);*/          if(mobilav ==0){
   imx=i-1; /* Number of individuals */            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   /* for (i=1; i<=imx; i++){          }else{ /* mobilav */ 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            for(i=1; i<=nlstate;i++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              prlim[i][i]=mobaverage[(int)age][i][ij];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          }
     }        }
   
     for (i=1; i<=imx; i++)        for(j=1; j<= nlstate; j++){
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   /* Calculation of the number of parameter from char model*/              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   Tvar=ivector(1,15);          }
   Tprod=ivector(1,15);        }
   Tvaraff=ivector(1,15);        /* This for computing probability of death (h=1 means
   Tvard=imatrix(1,15,1,2);           computed over hstepm matrices product = hstepm*stepm months) 
   Tage=ivector(1,15);                 as a weighted average of prlim.
            */
   if (strlen(model) >1){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     j=0, j1=0, k1=1, k2=1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     j=nbocc(model,'+');           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     j1=nbocc(model,'*');        }    
     cptcovn=j+1;        /* end probability of death */
     cptcovprod=j1;  
            for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
     strcpy(modelsav,model);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          }
       printf("Error. Non available option model=%s ",model);  
       goto end;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
            }
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');      } /* End theta */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {      for(h=0; h<=nhstepm; h++) /* veij */
         cutv(strd,strc,strb,'*');        for(j=1; j<=nlstate;j++)
         if (strcmp(strc,"age")==0) {          for(theta=1; theta <=npar; theta++)
           cptcovprod--;            trgradg[h][j][theta]=gradg[h][theta][j];
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           cptcovage++;        for(theta=1; theta <=npar; theta++)
             Tage[cptcovage]=i;          trgradgp[j][theta]=gradgp[theta][j];
             /*printf("stre=%s ", stre);*/    
         }  
         else if (strcmp(strd,"age")==0) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           cptcovprod--;      for(i=1;i<=nlstate;i++)
           cutv(strb,stre,strc,'V');        for(j=1;j<=nlstate;j++)
           Tvar[i]=atoi(stre);          vareij[i][j][(int)age] =0.;
           cptcovage++;  
           Tage[cptcovage]=i;      for(h=0;h<=nhstepm;h++){
         }        for(k=0;k<=nhstepm;k++){
         else {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           cutv(strb,stre,strc,'V');          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           Tvar[i]=ncov+k1;          for(i=1;i<=nlstate;i++)
           cutv(strb,strc,strd,'V');            for(j=1;j<=nlstate;j++)
           Tprod[k1]=i;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           Tvard[k1][1]=atoi(strc);        }
           Tvard[k1][2]=atoi(stre);      }
           Tvar[cptcovn+k2]=Tvard[k1][1];    
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      /* pptj */
           for (k=1; k<=lastobs;k++)      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           k1++;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           k2=k2+2;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         }          varppt[j][i]=doldmp[j][i];
       }      /* end ppptj */
       else {      /*  x centered again */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        /*  scanf("%d",i);*/      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       cutv(strd,strc,strb,'V');   
       Tvar[i]=atoi(strc);      if (popbased==1) {
       }        if(mobilav ==0){
       strcpy(modelsav,stra);            for(i=1; i<=nlstate;i++)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            prlim[i][i]=probs[(int)age][i][ij];
         scanf("%d",i);*/        }else{ /* mobilav */ 
     }          for(i=1; i<=nlstate;i++)
 }            prlim[i][i]=mobaverage[(int)age][i][ij];
          }
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      }
   printf("cptcovprod=%d ", cptcovprod);               
   scanf("%d ",i);*/      /* This for computing probability of death (h=1 means
     fclose(fic);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
     /*  if(mle==1){*/      */
     if (weightopt != 1) { /* Maximisation without weights*/      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       for(i=1;i<=n;i++) weight[i]=1.0;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     /*-calculation of age at interview from date of interview and age at death -*/      }    
     agev=matrix(1,maxwav,1,imx);      /* end probability of death */
   
    for (i=1; i<=imx; i++)      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
      for(m=2; (m<= maxwav); m++)      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          anint[m][i]=9999;        for(i=1; i<=nlstate;i++){
          s[m][i]=-1;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
        }        }
          } 
     for (i=1; i<=imx; i++)  {      fprintf(ficresprobmorprev,"\n");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){      fprintf(ficresvij,"%.0f ",age );
         if(s[m][i] >0){      for(i=1; i<=nlstate;i++)
           if (s[m][i] == nlstate+1) {        for(j=1; j<=nlstate;j++){
             if(agedc[i]>0)          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
               if(moisdc[i]!=99 && andc[i]!=9999)        }
               agev[m][i]=agedc[i];      fprintf(ficresvij,"\n");
             else {      free_matrix(gp,0,nhstepm,1,nlstate);
               if (andc[i]!=9999){      free_matrix(gm,0,nhstepm,1,nlstate);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
               agev[m][i]=-1;      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);
           else if(s[m][i] !=9){ /* Should no more exist */    free_vector(gmp,nlstate+1,nlstate+ndeath);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             if(mint[m][i]==99 || anint[m][i]==9999)    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
               agev[m][i]=1;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
             else if(agev[m][i] <agemin){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
               agemin=agev[m][i];    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  /*   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); */
             else if(agev[m][i] >agemax){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
               agemax=agev[m][i];    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    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));
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
             /*   agev[m][i] = age[i]+2*m;*/    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);
           else { /* =9 */  */
             agev[m][i]=1;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
             s[m][i]=-1;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           }  
         }    free_vector(xp,1,npar);
         else /*= 0 Unknown */    free_matrix(doldm,1,nlstate,1,nlstate);
           agev[m][i]=1;    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);
     for (i=1; i<=imx; i++)  {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(m=1; (m<= maxwav); m++){    fclose(ficresprobmorprev);
         if (s[m][i] > (nlstate+ndeath)) {    fflush(ficgp);
           printf("Error: Wrong value in nlstate or ndeath\n");      fflush(fichtm); 
           goto end;  }  /* 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[])
   {
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     free_vector(severity,1,maxwav);    double **newm;
     free_imatrix(outcome,1,maxwav+1,1,n);    double **dnewm,**doldm;
     free_vector(moisnais,1,n);    int i, j, nhstepm, hstepm;
     free_vector(annais,1,n);    int k, cptcode;
     /* free_matrix(mint,1,maxwav,1,n);    double *xp;
        free_matrix(anint,1,maxwav,1,n);*/    double *gp, *gm;
     free_vector(moisdc,1,n);    double **gradg, **trgradg;
     free_vector(andc,1,n);    double age,agelim;
     int theta;
        fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     wav=ivector(1,imx);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(ficresvpl,"# Age");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    for(i=1; i<=nlstate;i++)
            fprintf(ficresvpl," %1d-%1d",i,i);
     /* Concatenates waves */    fprintf(ficresvpl,"\n");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
       Tcode=ivector(1,100);    doldm=matrix(1,nlstate,1,nlstate);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    
       ncodemax[1]=1;    hstepm=1*YEARM; /* Every year of age */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
          agelim = AGESUP;
    codtab=imatrix(1,100,1,10);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    h=0;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    m=pow(2,cptcoveff);      if (stepm >= YEARM) hstepm=1;
        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
    for(k=1;k<=cptcoveff; k++){      gradg=matrix(1,npar,1,nlstate);
      for(i=1; i <=(m/pow(2,k));i++){      gp=vector(1,nlstate);
        for(j=1; j <= ncodemax[k]; j++){      gm=vector(1,nlstate);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;      for(theta=1; theta <=npar; theta++){
            if (h>m) h=1;codtab[h][k]=j;        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 <=m ;i++){        for(i=1; i<=npar; i++) /* Computes gradient */
      for(k=1; k <=cptcovn; k++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      }        for(i=1;i<=nlstate;i++)
      printf("\n");          gm[i] = prlim[i][i];
    }  
    scanf("%d",i);*/        for(i=1;i<=nlstate;i++)
              gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
    /* Calculates basic frequencies. Computes observed prevalence at single age      } /* End theta */
        and prints on file fileres'p'. */  
       trgradg =matrix(1,nlstate,1,npar);
      
          for(j=1; j<=nlstate;j++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(theta=1; theta <=npar; theta++)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          trgradg[j][theta]=gradg[theta][j];
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1;i<=nlstate;i++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        varpl[i][(int)age] =0.;
            matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     /* For Powell, parameters are in a vector p[] starting at p[1]      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(i=1;i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
     if(mle==1){      fprintf(ficresvpl,"%.0f ",age );
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      for(i=1; i<=nlstate;i++)
     }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
          fprintf(ficresvpl,"\n");
     /*--------- results files --------------*/      free_vector(gp,1,nlstate);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);      free_vector(gm,1,nlstate);
        free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
    jk=1;    } /* End age */
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");    free_vector(xp,1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    free_matrix(doldm,1,nlstate,1,npar);
      for(k=1; k <=(nlstate+ndeath); k++){    free_matrix(dnewm,1,nlstate,1,nlstate);
        if (k != i)  
          {  }
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);  /************ Variance of one-step probabilities  ******************/
            for(j=1; j <=ncovmodel; j++){  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
              printf("%f ",p[jk]);  {
              fprintf(ficres,"%f ",p[jk]);    int i, j=0,  i1, k1, l1, t, tj;
              jk++;    int k2, l2, j1,  z1;
            }    int k=0,l, cptcode;
            printf("\n");    int first=1, first1;
            fprintf(ficres,"\n");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
          }    double **dnewm,**doldm;
      }    double *xp;
    }    double *gp, *gm;
  if(mle==1){    double **gradg, **trgradg;
     /* Computing hessian and covariance matrix */    double **mu;
     ftolhess=ftol; /* Usually correct */    double age,agelim, cov[NCOVMAX];
     hesscov(matcov, p, npar, delti, ftolhess, func);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
  }    int theta;
     fprintf(ficres,"# Scales\n");    char fileresprob[FILENAMELENGTH];
     printf("# Scales\n");    char fileresprobcov[FILENAMELENGTH];
      for(i=1,jk=1; i <=nlstate; i++){    char fileresprobcor[FILENAMELENGTH];
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {    double ***varpij;
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);    strcpy(fileresprob,"prob"); 
           for(k=1; k<=ncovmodel;k++){    strcat(fileresprob,fileres);
             printf(" %.5e",delti[jk]);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
             fprintf(ficres," %.5e",delti[jk]);      printf("Problem with resultfile: %s\n", fileresprob);
             jk++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           }    }
           printf("\n");    strcpy(fileresprobcov,"probcov"); 
           fprintf(ficres,"\n");    strcat(fileresprobcov,fileres);
         }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobcov);
      }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
        }
     k=1;    strcpy(fileresprobcor,"probcor"); 
     fprintf(ficres,"# Covariance\n");    strcat(fileresprobcor,fileres);
     printf("# Covariance\n");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     for(i=1;i<=npar;i++){      printf("Problem with resultfile: %s\n", fileresprobcor);
       /*  if (k>nlstate) k=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       i1=(i-1)/(ncovmodel*nlstate)+1;    }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       fprintf(ficres,"%3d",i);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       printf("%3d",i);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       for(j=1; j<=i;j++){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         fprintf(ficres," %.5e",matcov[i][j]);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         printf(" %.5e",matcov[i][j]);    fprintf(ficresprob, "#Local time at start: %s", strstart);
       }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       fprintf(ficres,"\n");    fprintf(ficresprob,"# Age");
       printf("\n");    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
       k++;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     }    fprintf(ficresprobcov,"# Age");
        fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       ungetc(c,ficpar);    fprintf(ficresprobcov,"# Age");
       fgets(line, MAXLINE, ficpar);  
       puts(line);  
       fputs(line,ficparo);    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=(nlstate+ndeath);j++){
     ungetc(c,ficpar);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
          }  
     if (fage <= 2) {   /* fprintf(ficresprob,"\n");
       bage = agemin;    fprintf(ficresprobcov,"\n");
       fage = agemaxpar;    fprintf(ficresprobcor,"\n");
     }   */
       xp=vector(1,npar);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     while((c=getc(ficpar))=='#' && c!= EOF){    first=1;
     ungetc(c,ficpar);    fprintf(ficgp,"\n# Routine varprob");
     fgets(line, MAXLINE, ficpar);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     puts(line);    fprintf(fichtm,"\n");
     fputs(line,ficparo);  
   }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   ungetc(c,ficpar);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
      file %s<br>\n",optionfilehtmcov);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  and drawn. It helps understanding how is the covariance between two incidences.\
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   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. \
   while((c=getc(ficpar))=='#' && c!= EOF){  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     ungetc(c,ficpar);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     fgets(line, MAXLINE, ficpar);  standard deviations wide on each axis. <br>\
     puts(line);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     fputs(line,ficparo);   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");
   ungetc(c,ficpar);  
      cov[1]=1;
     tj=cptcoveff;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    j1=0;
     for(t=1; t<=tj;t++){
   fscanf(ficpar,"pop_based=%d\n",&popbased);      for(i1=1; i1<=ncodemax[t];i1++){ 
   fprintf(ficparo,"pop_based=%d\n",popbased);          j1++;
   fprintf(ficres,"pop_based=%d\n",popbased);          if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
   while((c=getc(ficpar))=='#' && c!= EOF){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     ungetc(c,ficpar);          fprintf(ficresprob, "**********\n#\n");
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov, "\n#********** Variable "); 
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficresprobcov, "**********\n#\n");
   }          
   ungetc(c,ficpar);          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          fprintf(ficgp, "**********\n#\n");
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          
           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]]);
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcor, "\n#********** Variable ");    
     puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fputs(line,ficparo);          fprintf(ficresprobcor, "**********\n#");    
   }        }
   ungetc(c,ficpar);        
         for (age=bage; age<=fage; age ++){ 
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          cov[2]=age;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          for (k=1; k<=cptcovn;k++) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
 /*------------ gnuplot -------------*/            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
 /*------------ free_vector  -------------*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
  chdir(path);          gp=vector(1,(nlstate)*(nlstate+ndeath));
            gm=vector(1,(nlstate)*(nlstate+ndeath));
  free_ivector(wav,1,imx);      
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          for(theta=1; theta <=npar; theta++){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              for(i=1; i<=npar; i++)
  free_ivector(num,1,n);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
  free_vector(agedc,1,n);            
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
  fclose(ficparo);            
  fclose(ficres);            k=0;
             for(i=1; i<= (nlstate); i++){
 /*--------- index.htm --------*/              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);                gp[k]=pmmij[i][j];
               }
              }
   /*--------------- Prevalence limit --------------*/            
              for(i=1; i<=npar; i++)
   strcpy(filerespl,"pl");              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   strcat(filerespl,fileres);      
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            k=0;
   }            for(i=1; i<=(nlstate); i++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(ficrespl,"#Prevalence limit\n");                k=k+1;
   fprintf(ficrespl,"#Age ");                gm[k]=pmmij[i][j];
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              }
   fprintf(ficrespl,"\n");            }
         
   prlim=matrix(1,nlstate,1,nlstate);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   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 */          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(theta=1; theta <=npar; theta++)
   k=0;              trgradg[j][theta]=gradg[theta][j];
   agebase=agemin;          
   agelim=agemaxpar;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   ftolpl=1.e-10;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   i1=cptcoveff;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   if (cptcovn < 1){i1=1;}          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;          pmij(pmmij,cov,ncovmodel,x,nlstate);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          
         fprintf(ficrespl,"\n#******");          k=0;
         for(j=1;j<=cptcoveff;j++)          for(i=1; i<=(nlstate); i++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrespl,"******\n");              k=k+1;
                      mu[k][(int) age]=pmmij[i][j];
         for (age=agebase; age<=agelim; age++){            }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          }
           fprintf(ficrespl,"%.0f",age );          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
           for(i=1; i<=nlstate;i++)            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           fprintf(ficrespl," %.5f", prlim[i][i]);              varpij[i][j][(int)age] = doldm[i][j];
           fprintf(ficrespl,"\n");  
         }          /*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]));
   fclose(ficrespl);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   /*------------- h Pij x at various ages ------------*/  
            fprintf(ficresprob,"\n%d ",(int)age);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          fprintf(ficresprobcov,"\n%d ",(int)age);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          fprintf(ficresprobcor,"\n%d ",(int)age);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   printf("Computing pij: result on file '%s' \n", filerespij);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   /*if (stepm<=24) stepsize=2;*/            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
   agelim=AGESUP;          i=0;
   hstepm=stepsize*YEARM; /* Every year of age */          for (k=1; k<=(nlstate);k++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            for (l=1; l<=(nlstate+ndeath);l++){ 
                i=i++;
   k=0;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   for(cptcov=1;cptcov<=i1;cptcov++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              for (j=1; j<=i;j++){
       k=k+1;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         fprintf(ficrespij,"\n#****** ");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
         for(j=1;j<=cptcoveff;j++)              }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
         fprintf(ficrespij,"******\n");          }/* end of loop for state */
                } /* end of loop for age */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        /* Confidence intervalle of pij  */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        /*
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp,"\nset noparametric;unset label");
           oldm=oldms;savm=savms;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(ficrespij,"# Age");          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           for(i=1; i<=nlstate;i++)          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
               fprintf(ficrespij," %1d-%1d",i,j);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           fprintf(ficrespij,"\n");        */
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
             for(i=1; i<=nlstate;i++)        first1=1;
               for(j=1; j<=nlstate+ndeath;j++)        for (k2=1; k2<=(nlstate);k2++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             fprintf(ficrespij,"\n");            if(l2==k2) continue;
           }            j=(k2-1)*(nlstate+ndeath)+l2;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (k1=1; k1<=(nlstate);k1++){
           fprintf(ficrespij,"\n");              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 ++){ 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                  if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   fclose(ficrespij);                    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 ;
   /*---------- Forecasting ------------------*/                    mu2=mu[j][(int) age]/stepm*YEARM;
   if((stepm == 1) && (model==".")){                    c12=cv12/sqrt(v1*v2);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                    /* Computing eigen value of matrix of covariance */
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     free_matrix(mint,1,maxwav,1,n);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                    /* Eigen vectors */
     free_vector(weight,1,n);}                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   else{                    /*v21=sqrt(1.-v11*v11); *//* error */
     erreur=108;                    v21=(lc1-v1)/cv12*v11;
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);                    v12=-v21;
   }                    v22=v11;
                      tnalp=v21/v11;
                     if(first1==1){
   /*---------- Health expectancies and variances ------------*/                      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);
   strcpy(filerest,"t");                    }
   strcat(filerest,fileres);                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   if((ficrest=fopen(filerest,"w"))==NULL) {                    /*printf(fignu*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                    if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
   strcpy(filerese,"e");                      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);
   strcat(filerese,fileres);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if((ficreseij=fopen(filerese,"w"))==NULL) {                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   }  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  strcpy(fileresv,"v");                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   strcat(fileresv,fileres);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                      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);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                      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),\
   k=0;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   for(cptcov=1;cptcov<=i1;cptcov++){                    }else{
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      first=0;
       k=k+1;                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       fprintf(ficrest,"\n#****** ");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      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",\
       fprintf(ficrest,"******\n");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       fprintf(ficreseij,"\n#****** ");                    }/* if first */
       for(j=1;j<=cptcoveff;j++)                  } /* age mod 5 */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                } /* end loop age */
       fprintf(ficreseij,"******\n");                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
       fprintf(ficresvij,"\n#****** ");              } /*l12 */
       for(j=1;j<=cptcoveff;j++)            } /* k12 */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          } /*l1 */
       fprintf(ficresvij,"******\n");        }/* k1 */
       } /* loop covariates */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    }
       oldm=oldms;savm=savms;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_vector(xp,1,npar);
       oldm=oldms;savm=savms;    fclose(ficresprob);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fclose(ficresprobcov);
        fclose(ficresprobcor);
     fflush(ficgp);
      fflush(fichtmcov);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");  
   /******************* Printing html file ***********/
       hf=1;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       if (stepm >= YEARM) hf=stepm/YEARM;                    int lastpass, int stepm, int weightopt, char model[],\
       epj=vector(1,nlstate+1);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       for(age=bage; age <=fage ;age++){                    int popforecast, int estepm ,\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    double jprev1, double mprev1,double anprev1, \
         if (popbased==1) {                    double jprev2, double mprev2,double anprev2){
           for(i=1; i<=nlstate;i++)    int jj1, k1, i1, cpt;
             prlim[i][i]=probs[(int)age][i][k];  
         }     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 \
         fprintf(ficrest," %.0f",age);  </ul>");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
           }     fprintf(fichtm,"\
           epj[nlstate+1] +=epj[j];   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
         }             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
         for(i=1, vepp=0.;i <=nlstate;i++)     fprintf(fichtm,"\
           for(j=1;j <=nlstate;j++)   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             vepp += vareij[i][j][(int)age];             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));     fprintf(fichtm,"\
         for(j=1;j <=nlstate;j++){   - Life expectancies by age and initial health status (estepm=%2d months): \
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));     <a href=\"%s\">%s</a> <br>\n</li>",
         }             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
         fprintf(ficrest,"\n");  
       }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     }  
   }   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   fclose(ficreseij);  
   fclose(ficresvij);   jj1=0;
   fclose(ficrest);   for(k1=1; k1<=m;k1++){
   fclose(ficpar);     for(i1=1; i1<=ncodemax[k1];i1++){
   free_vector(epj,1,nlstate+1);       jj1++;
         if (cptcovn > 0) {
   /*------- Variance limit prevalence------*/           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   strcpy(fileresvpl,"vpl");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   strcat(fileresvpl,fileres);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {       }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       /* Pij */
     exit(0);       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);     
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);       /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   k=0;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   for(cptcov=1;cptcov<=i1;cptcov++){  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         /* Stable prevalence in each health state */
       k=k+1;         for(cpt=1; cpt<nlstate;cpt++){
       fprintf(ficresvpl,"\n#****** ");           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       for(j=1;j<=cptcoveff;j++)  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         }
       fprintf(ficresvpl,"******\n");       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> \
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       oldm=oldms;savm=savms;       }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     } /* end i1 */
     }   }/* End k1 */
  }   fprintf(fichtm,"</ul>");
   
   fclose(ficresvpl);  
    fprintf(fichtm,"\
   /*---------- End : free ----------------*/  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
     fprintf(fichtm,"\
     - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);   fprintf(fichtm,"\
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   free_matrix(matcov,1,npar,1,npar);   fprintf(fichtm,"\
   free_vector(delti,1,npar);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   free_matrix(agev,1,maxwav,1,imx);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);   fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   if(erreur >0)           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     printf("End of Imach with error %d\n",erreur);   fprintf(fichtm,"\
   else   printf("End of Imach\n");   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    
   /* 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);*/  /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*printf("Total time was %d uSec.\n", total_usecs);*/  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*------ End -----------*/  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
  end:  /*    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); */
 #ifdef windows   fflush(fichtm);
   /* chdir(pathcd);*/   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
 #endif  
  /*system("wgnuplot graph.plt");*/   m=cptcoveff;
  /*system("../gp37mgw/wgnuplot graph.plt");*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/   jj1=0;
  strcpy(plotcmd,GNUPLOTPROGRAM);   for(k1=1; k1<=m;k1++){
  strcat(plotcmd," ");     for(i1=1; i1<=ncodemax[k1];i1++){
  strcat(plotcmd,optionfilegnuplot);       jj1++;
  system(plotcmd);       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 #ifdef windows         for (cpt=1; cpt<=cptcoveff;cpt++) 
   while (z[0] != 'q') {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     chdir(path);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       }
     scanf("%s",z);       for(cpt=1; cpt<=nlstate;cpt++) {
     if (z[0] == 'c') system("./imach");         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
     else if (z[0] == 'e') {  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
       chdir(path);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
       system(optionfilehtm);       }
     }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     else if (z[0] == 'q') exit(0);  health expectancies in states (1) and (2): %s%d.png<br>\
   }  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
 #endif     } /* 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) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs)))    {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
           ;
         };
         line[j+1]=0;  /* Trims blanks at end of line */
         if(line[0]=='#'){
           fprintf(ficlog,"Comment line\n%s\n",line);
           printf("Comment line\n%s\n",line);
           continue;
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %d %s for individual %d\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n",lval, i,line,linei,j,maxwav);
             exit(1);
           }
           s[j][i]=lval;
   
           strcpy(line,stra);
           cutv(stra, strb,line,' ');
           if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
           }
           else  if(iout=sscanf(strb,".") != 0){
             month=99;
             year=9999;
           }else{
             printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,j);
             exit(1);
           }
           anint[j][i]= (double) year; 
           mint[j][i]= (double)month; 
           strcpy(line,stra);
         } /* ENd Waves */
           
         cutv(stra, strb,line,' '); 
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,".") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,j);
           exit(1);
         }
         andc[i]=(double) year; 
         moisdc[i]=(double) month; 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,".") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,j);
           exit(1);
         }
         annais[i]=(double)(year);
         moisnais[i]=(double)(month); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         weight[i]=(double)(lval); 
         strcpy(line,stra);
   
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, i,line,linei);
             exit(1);
           }
           if(lval <-1 || lval >1){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,i,line,linei,j);
             exit(1);
           }
           covar[j][i]=(double)(lval);
           strcpy(line,stra);
         } 
         lstra=strlen(stra);
   
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
     } /* End loop reading  data */
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.1; p[NDIM]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
   #ifndef UNIX
     /*  strcpy(plotcmd,"\""); */
   #endif
     strcpy(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     /*  strcat(plotcmd,"\"");*/
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
   
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     strcat(plotcmd,"\"");
   #endif
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

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  Added in v.1.110


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