Diff for /imach/src/imach.c between versions 1.30 and 1.117

version 1.30, 2002/03/08 16:17:18 version 1.117, 2006/03/14 17:16:22
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.117  2006/03/14 17:16:22  brouard
      (Module): varevsij Comments added explaining the second
   This program computes Healthy Life Expectancies from    table of variances if popbased=1 .
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   first survey ("cross") where individuals from different ages are    (Module): Function pstamp added
   interviewed on their health status or degree of disability (in the    (Module): Version 0.98d
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.116  2006/03/06 10:29:27  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Variance-covariance wrong links and
   computed from the time spent in each health state according to a    varian-covariance of ej. is needed (Saito).
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.115  2006/02/27 12:17:45  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): One freematrix added in mlikeli! 0.98c
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.114  2006/02/26 12:57:58  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): Some improvements in processing parameter
   'age' is age and 'sex' is a covariate. If you want to have a more    filename with strsep.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.113  2006/02/24 14:20:24  brouard
   you to do it.  More covariates you add, slower the    (Module): Memory leaks checks with valgrind and:
   convergence.    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.112  2006/01/30 09:55:26  brouard
   identical for each individual. Also, if a individual missed an    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
   hPijx is the probability to be observed in state i at age x+h    (Module): Comments can be added in data file. Missing date values
   conditional to the observed state i at age x. The delay 'h' can be    can be a simple dot '.'.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.110  2006/01/25 00:51:50  brouard
   semester or year) is model as a multinomial logistic.  The hPx    (Module): Lots of cleaning and bugs added (Gompertz)
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.109  2006/01/24 19:37:15  brouard
   hPijx.    (Module): Comments (lines starting with a #) are allowed in data.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.108  2006/01/19 18:05:42  lievre
   of the life expectancies. It also computes the prevalence limits.    Gnuplot problem appeared...
      To be fixed
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.107  2006/01/19 16:20:37  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Test existence of gnuplot in imach path
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.106  2006/01/19 13:24:36  brouard
   software can be distributed freely for non commercial use. Latest version    Some cleaning and links added in html output
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.105  2006/01/05 20:23:19  lievre
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.104  2005/09/30 16:11:43  lievre
 #include <stdlib.h>    (Module): sump fixed, loop imx fixed, and simplifications.
 #include <unistd.h>    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 #define MAXLINE 256    (instead of missing=-1 in earlier versions) and his/her
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    contributions to the likelihood is 1 - Prob of dying from last
 #define FILENAMELENGTH 80    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /*#define DEBUG*/    the healthy state at last known wave). Version is 0.98
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.103  2005/09/30 15:54:49  lievre
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (Module): sump fixed, loop imx fixed, and simplifications.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.102  2004/09/15 17:31:30  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Add the possibility to read data file including tab characters.
   
 #define NINTERVMAX 8    Revision 1.101  2004/09/15 10:38:38  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Fix on curr_time
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.100  2004/07/12 18:29:06  brouard
 #define MAXN 20000    Add version for Mac OS X. Just define UNIX in Makefile
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.99  2004/06/05 08:57:40  brouard
 #define AGEBASE 40    *** empty log message ***
   
     Revision 1.98  2004/05/16 15:05:56  brouard
 int erreur; /* Error number */    New version 0.97 . First attempt to estimate force of mortality
 int nvar;    directly from the data i.e. without the need of knowing the health
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    state at each age, but using a Gompertz model: log u =a + b*age .
 int npar=NPARMAX;    This is the basic analysis of mortality and should be done before any
 int nlstate=2; /* Number of live states */    other analysis, in order to test if the mortality estimated from the
 int ndeath=1; /* Number of dead states */    cross-longitudinal survey is different from the mortality estimated
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    from other sources like vital statistic data.
 int popbased=0;  
     The same imach parameter file can be used but the option for mle should be -3.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Agnès, who wrote this part of the code, tried to keep most of the
 int jmin, jmax; /* min, max spacing between 2 waves */    former routines in order to include the new code within the former code.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    The output is very simple: only an estimate of the intercept and of
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    the slope with 95% confident intervals.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Current limitations:
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    A) Even if you enter covariates, i.e. with the
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 FILE *ficgp,*ficresprob,*ficpop;    B) There is no computation of Life Expectancy nor Life Table.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.97  2004/02/20 13:25:42  lievre
  FILE  *ficresvij;    Version 0.96d. Population forecasting command line is (temporarily)
   char fileresv[FILENAMELENGTH];    suppressed.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define NR_END 1    rewritten within the same printf. Workaround: many printfs.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 #define NRANSI    (Repository): Using imachwizard code to output a more meaningful covariance
 #define ITMAX 200    matrix (cov(a12,c31) instead of numbers.
   
 #define TOL 2.0e-4    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.93  2003/06/25 16:33:55  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define GOLD 1.618034    (Module): Version 0.96b
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 static double maxarg1,maxarg2;    exist so I changed back to asctime which exists.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.91  2003/06/25 15:30:29  brouard
      * imach.c (Repository): Duplicated warning errors corrected.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Repository): Elapsed time after each iteration is now output. It
 #define rint(a) floor(a+0.5)    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 static double sqrarg;    concerning matrix of covariance. It has extension -cov.htm.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 int imx;    mle=-1 a template is output in file "or"mypar.txt with the design
 int stepm;    of the covariance matrix to be input.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.89  2003/06/24 12:30:52  brouard
 int m,nb;    (Module): Some bugs corrected for windows. Also, when
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    mle=-1 a template is output in file "or"mypar.txt with the design
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    of the covariance matrix to be input.
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    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.
 double *weight;  
 int **s; /* Status */    Revision 1.87  2003/06/18 12:26:01  brouard
 double *agedc, **covar, idx;    Version 0.96
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.86  2003/06/17 20:04:08  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Change position of html and gnuplot routines and added
 double ftolhess; /* Tolerance for computing hessian */    routine fileappend.
   
 /**************** split *************************/    Revision 1.85  2003/06/17 13:12:43  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    * imach.c (Repository): Check when date of death was earlier that
 {    current date of interview. It may happen when the death was just
    char *s;                             /* pointer */    prior to the death. In this case, dh was negative and likelihood
    int  l1, l2;                         /* length counters */    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
    l1 = strlen( path );                 /* length of path */    interview.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Repository): Because some people have very long ID (first column)
 #ifdef windows    we changed int to long in num[] and we added a new lvector for
    s = strrchr( path, '\\' );           /* find last / */    memory allocation. But we also truncated to 8 characters (left
 #else    truncation)
    s = strrchr( path, '/' );            /* find last / */    (Repository): No more line truncation errors.
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.84  2003/06/13 21:44:43  brouard
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Repository): Replace "freqsummary" at a correct
       extern char       *getwd( );    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
       if ( getwd( dirc ) == NULL ) {    parcimony.
 #else    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       extern char       *getcwd( );  
     Revision 1.83  2003/06/10 13:39:11  lievre
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    *** empty log message ***
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.82  2003/06/05 15:57:20  brouard
       }    Add log in  imach.c and  fullversion number is now printed.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  */
       s++;                              /* after this, the filename */  /*
       l2 = strlen( s );                 /* length of filename */     Interpolated Markov Chain
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Short summary of the programme:
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    
       dirc[l1-l2] = 0;                  /* add zero */    This program computes Healthy Life Expectancies from
    }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    l1 = strlen( dirc );                 /* length of directory */    first survey ("cross") where individuals from different ages are
 #ifdef windows    interviewed on their health status or degree of disability (in the
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    case of a health survey which is our main interest) -2- at least a
 #else    second wave of interviews ("longitudinal") which measure each change
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (if any) in individual health status.  Health expectancies are
 #endif    computed from the time spent in each health state according to a
    s = strrchr( name, '.' );            /* find last / */    model. More health states you consider, more time is necessary to reach the
    s++;    Maximum Likelihood of the parameters involved in the model.  The
    strcpy(ext,s);                       /* save extension */    simplest model is the multinomial logistic model where pij is the
    l1= strlen( name);    probability to be observed in state j at the second wave
    l2= strlen( s)+1;    conditional to be observed in state i at the first wave. Therefore
    strncpy( finame, name, l1-l2);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    finame[l1-l2]= 0;    'age' is age and 'sex' is a covariate. If you want to have a more
    return( 0 );                         /* we're done */    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
     convergence.
 /******************************************/  
     The advantage of this computer programme, compared to a simple
 void replace(char *s, char*t)    multinomial logistic model, is clear when the delay between waves is not
 {    identical for each individual. Also, if a individual missed an
   int i;    intermediate interview, the information is lost, but taken into
   int lg=20;    account using an interpolation or extrapolation.  
   i=0;  
   lg=strlen(t);    hPijx is the probability to be observed in state i at age x+h
   for(i=0; i<= lg; i++) {    conditional to the observed state i at age x. The delay 'h' can be
     (s[i] = t[i]);    split into an exact number (nh*stepm) of unobserved intermediate
     if (t[i]== '\\') s[i]='/';    states. This elementary transition (by month, quarter,
   }    semester or year) is modelled as a multinomial logistic.  The hPx
 }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 int nbocc(char *s, char occ)    hPijx.
 {  
   int i,j=0;    Also this programme outputs the covariance matrix of the parameters but also
   int lg=20;    of the life expectancies. It also computes the period (stable) prevalence. 
   i=0;    
   lg=strlen(s);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for(i=0; i<= lg; i++) {             Institut national d'études démographiques, Paris.
   if  (s[i] == occ ) j++;    This software have been partly granted by Euro-REVES, a concerted action
   }    from the European Union.
   return j;    It is copyrighted identically to a GNU software product, ie programme and
 }    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 void cutv(char *u,char *v, char*t, char occ)  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int i,lg,j,p=0;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   i=0;    
   for(j=0; j<=strlen(t)-1; j++) {    **********************************************************************/
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  /*
   }    main
     read parameterfile
   lg=strlen(t);    read datafile
   for(j=0; j<p; j++) {    concatwav
     (u[j] = t[j]);    freqsummary
   }    if (mle >= 1)
      u[p]='\0';      mlikeli
     print results files
    for(j=0; j<= lg; j++) {    if mle==1 
     if (j>=(p+1))(v[j-p-1] = t[j]);       computes hessian
   }    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 /********************** nrerror ********************/    open html file
     period (stable) prevalence
 void nrerror(char error_text[])     for age prevalim()
 {    h Pij x
   fprintf(stderr,"ERREUR ...\n");    variance of p varprob
   fprintf(stderr,"%s\n",error_text);    forecasting if prevfcast==1 prevforecast call prevalence()
   exit(1);    health expectancies
 }    Variance-covariance of DFLE
 /*********************** vector *******************/    prevalence()
 double *vector(int nl, int nh)     movingaverage()
 {    varevsij() 
   double *v;    if popbased==1 varevsij(,popbased)
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    total life expectancies
   if (!v) nrerror("allocation failure in vector");    Variance of period (stable) prevalence
   return v-nl+NR_END;   end
 }  */
   
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  
 {   
   free((FREE_ARG)(v+nl-NR_END));  #include <math.h>
 }  #include <stdio.h>
   #include <stdlib.h>
 /************************ivector *******************************/  #include <string.h>
 int *ivector(long nl,long nh)  #include <unistd.h>
 {  
   int *v;  #include <limits.h>
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #include <sys/types.h>
   if (!v) nrerror("allocation failure in ivector");  #include <sys/stat.h>
   return v-nl+NR_END;  #include <errno.h>
 }  extern int errno;
   
 /******************free ivector **************************/  /* #include <sys/time.h> */
 void free_ivector(int *v, long nl, long nh)  #include <time.h>
 {  #include "timeval.h"
   free((FREE_ARG)(v+nl-NR_END));  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define MAXLINE 256
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  #define GNUPLOTPROGRAM "gnuplot"
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   int **m;  #define FILENAMELENGTH 132
    
   /* allocate pointers to rows */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   m -= nrl;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    
    #define NINTERVMAX 8
   /* allocate rows and set pointers to them */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NCOVMAX 8 /* Maximum number of covariates */
   m[nrl] += NR_END;  #define MAXN 20000
   m[nrl] -= ncl;  #define YEARM 12. /* Number of months per year */
    #define AGESUP 130
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define AGEBASE 40
    #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   /* return pointer to array of pointers to rows */  #ifdef UNIX
   return m;  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /****************** free_imatrix *************************/  #else
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define DIRSEPARATOR '\\'
       int **m;  #define CHARSEPARATOR "\\"
       long nch,ncl,nrh,nrl;  #define ODIRSEPARATOR '/'
      /* free an int matrix allocated by imatrix() */  #endif
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /* $Id$ */
   free((FREE_ARG) (m+nrl-NR_END));  /* $State$ */
 }  
   char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
 /******************* matrix *******************************/  char fullversion[]="$Revision$ $Date$"; 
 double **matrix(long nrl, long nrh, long ncl, long nch)  char strstart[80];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double **m;  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int npar=NPARMAX;
   if (!m) nrerror("allocation failure 1 in matrix()");  int nlstate=2; /* Number of live states */
   m += NR_END;  int ndeath=1; /* Number of dead states */
   m -= nrl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int *wav; /* Number of waves for this individuual 0 is possible */
   m[nrl] += NR_END;  int maxwav; /* Maxim number of waves */
   m[nrl] -= ncl;  int jmin, jmax; /* min, max spacing between 2 waves */
   int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int gipmx, gsw; /* Global variables on the number of contributions 
   return m;                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /*************************free matrix ************************/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double jmean; /* Mean space between 2 waves */
   free((FREE_ARG)(m+nrl-NR_END));  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 /******************* ma3x *******************************/  FILE *ficlog, *ficrespow;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  long ipmx; /* Number of contributions */
   double ***m;  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *ficresilk;
   m += NR_END;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m -= nrl;  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  FILE *ficreseij;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char filerese[FILENAMELENGTH];
   m[nrl] += NR_END;  FILE *ficresstdeij;
   m[nrl] -= ncl;  char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char fileresv[FILENAMELENGTH];
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  FILE  *ficresvpl;
   m[nrl][ncl] += NR_END;  char fileresvpl[FILENAMELENGTH];
   m[nrl][ncl] -= nll;  char title[MAXLINE];
   for (j=ncl+1; j<=nch; j++)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     m[nrl][j]=m[nrl][j-1]+nlay;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
    char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   for (i=nrl+1; i<=nrh; i++) {  char command[FILENAMELENGTH];
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int  outcmd=0;
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  
   return m;  char filelog[FILENAMELENGTH]; /* Log file */
 }  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 /*************************free ma3x ************************/  char popfile[FILENAMELENGTH];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   free((FREE_ARG)(m+nrl-NR_END));  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /***************** f1dim *************************/  long time_value;
 extern int ncom;  extern long time();
 extern double *pcom,*xicom;  char strcurr[80], strfor[80];
 extern double (*nrfunc)(double []);  
    char *endptr;
 double f1dim(double x)  long lval;
 {  
   int j;  #define NR_END 1
   double f;  #define FREE_ARG char*
   double *xt;  #define FTOL 1.0e-10
    
   xt=vector(1,ncom);  #define NRANSI 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define ITMAX 200 
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  #define TOL 2.0e-4 
   return f;  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /*****************brent *************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  #define GOLD 1.618034 
   int iter;  #define GLIMIT 100.0 
   double a,b,d,etemp;  #define TINY 1.0e-20 
   double fu,fv,fw,fx;  
   double ftemp;  static double maxarg1,maxarg2;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double e=0.0;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
   a=(ax < cx ? ax : cx);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   b=(ax > cx ? ax : cx);  #define rint(a) floor(a+0.5)
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  static double sqrarg;
   for (iter=1;iter<=ITMAX;iter++) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     xm=0.5*(a+b);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int agegomp= AGEGOMP;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  int imx; 
 #ifdef DEBUG  int stepm=1;
     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);  /* Stepm, step in month: minimum step interpolation*/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  int estepm;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       *xmin=x;  
       return fx;  int m,nb;
     }  long *num;
     ftemp=fu;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     if (fabs(e) > tol1) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       r=(x-w)*(fx-fv);  double **pmmij, ***probs;
       q=(x-v)*(fx-fw);  double *ageexmed,*agecens;
       p=(x-v)*q-(x-w)*r;  double dateintmean=0;
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  double *weight;
       q=fabs(q);  int **s; /* Status */
       etemp=e;  double *agedc, **covar, idx;
       e=d;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  double *lsurv, *lpop, *tpop;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
         d=p/q;  double ftolhess; /* Tolerance for computing hessian */
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  /**************** split *************************/
           d=SIGN(tol1,xm-x);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       }  {
     } else {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       d=CGOLD*(e=(x >= xm ? a-x : b-x));       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     }    */ 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    char  *ss;                            /* pointer */
     fu=(*f)(u);    int   l1, l2;                         /* length counters */
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;    l1 = strlen(path );                   /* length of path */
       SHFT(v,w,x,u)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         SHFT(fv,fw,fx,fu)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         } else {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
           if (u < x) a=u; else b=u;      strcpy( name, path );               /* we got the fullname name because no directory */
           if (fu <= fw || w == x) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
             v=w;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
             w=u;      /* get current working directory */
             fv=fw;      /*    extern  char* getcwd ( char *buf , int len);*/
             fw=fu;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
           } else if (fu <= fv || v == x || v == w) {        return( GLOCK_ERROR_GETCWD );
             v=u;      }
             fv=fu;      /* got dirc from getcwd*/
           }      printf(" DIRC = %s \n",dirc);
         }    } else {                              /* strip direcotry from path */
   }      ss++;                               /* after this, the filename */
   nrerror("Too many iterations in brent");      l2 = strlen( ss );                  /* length of filename */
   *xmin=x;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   return fx;      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /****************** mnbrak ***********************/      printf(" DIRC2 = %s \n",dirc);
     }
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    /* We add a separator at the end of dirc if not exists */
             double (*func)(double))    l1 = strlen( dirc );                  /* length of directory */
 {    if( dirc[l1-1] != DIRSEPARATOR ){
   double ulim,u,r,q, dum;      dirc[l1] =  DIRSEPARATOR;
   double fu;      dirc[l1+1] = 0; 
        printf(" DIRC3 = %s \n",dirc);
   *fa=(*func)(*ax);    }
   *fb=(*func)(*bx);    ss = strrchr( name, '.' );            /* find last / */
   if (*fb > *fa) {    if (ss >0){
     SHFT(dum,*ax,*bx,dum)      ss++;
       SHFT(dum,*fb,*fa,dum)      strcpy(ext,ss);                     /* save extension */
       }      l1= strlen( name);
   *cx=(*bx)+GOLD*(*bx-*ax);      l2= strlen(ss)+1;
   *fc=(*func)(*cx);      strncpy( finame, name, l1-l2);
   while (*fb > *fc) {      finame[l1-l2]= 0;
     r=(*bx-*ax)*(*fb-*fc);    }
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    return( 0 );                          /* we're done */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  }
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /******************************************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  void replace_back_to_slash(char *s, char*t)
       if (fu < *fc) {  {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    int i;
           SHFT(*fb,*fc,fu,(*func)(u))    int lg=0;
           }    i=0;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    lg=strlen(t);
       u=ulim;    for(i=0; i<= lg; i++) {
       fu=(*func)(u);      (s[i] = t[i]);
     } else {      if (t[i]== '\\') s[i]='/';
       u=(*cx)+GOLD*(*cx-*bx);    }
       fu=(*func)(u);  }
     }  
     SHFT(*ax,*bx,*cx,u)  int nbocc(char *s, char occ)
       SHFT(*fa,*fb,*fc,fu)  {
       }    int i,j=0;
 }    int lg=20;
     i=0;
 /*************** linmin ************************/    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 int ncom;    if  (s[i] == occ ) j++;
 double *pcom,*xicom;    }
 double (*nrfunc)(double []);    return j;
    }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  void cutv(char *u,char *v, char*t, char occ)
   double brent(double ax, double bx, double cx,  {
                double (*f)(double), double tol, double *xmin);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   double f1dim(double x);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,       gives u="abcedf" and v="ghi2j" */
               double *fc, double (*func)(double));    int i,lg,j,p=0;
   int j;    i=0;
   double xx,xmin,bx,ax;    for(j=0; j<=strlen(t)-1; j++) {
   double fx,fb,fa;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
      }
   ncom=n;  
   pcom=vector(1,n);    lg=strlen(t);
   xicom=vector(1,n);    for(j=0; j<p; j++) {
   nrfunc=func;      (u[j] = t[j]);
   for (j=1;j<=n;j++) {    }
     pcom[j]=p[j];       u[p]='\0';
     xicom[j]=xi[j];  
   }     for(j=0; j<= lg; j++) {
   ax=0.0;      if (j>=(p+1))(v[j-p-1] = t[j]);
   xx=1.0;    }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /********************** nrerror ********************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  void nrerror(char error_text[])
   for (j=1;j<=n;j++) {  {
     xi[j] *= xmin;    fprintf(stderr,"ERREUR ...\n");
     p[j] += xi[j];    fprintf(stderr,"%s\n",error_text);
   }    exit(EXIT_FAILURE);
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /*************** powell ************************/    double *v;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
             double (*func)(double []))    if (!v) nrerror("allocation failure in vector");
 {    return v-nl+NR_END;
   void linmin(double p[], double xi[], int n, double *fret,  }
               double (*func)(double []));  
   int i,ibig,j;  /************************ free vector ******************/
   double del,t,*pt,*ptt,*xit;  void free_vector(double*v, int nl, int nh)
   double fp,fptt;  {
   double *xits;    free((FREE_ARG)(v+nl-NR_END));
   pt=vector(1,n);  }
   ptt=vector(1,n);  
   xit=vector(1,n);  /************************ivector *******************************/
   xits=vector(1,n);  int *ivector(long nl,long nh)
   *fret=(*func)(p);  {
   for (j=1;j<=n;j++) pt[j]=p[j];    int *v;
   for (*iter=1;;++(*iter)) {    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     fp=(*fret);    if (!v) nrerror("allocation failure in ivector");
     ibig=0;    return v-nl+NR_END;
     del=0.0;  }
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /******************free ivector **************************/
       printf(" %d %.12f",i, p[i]);  void free_ivector(int *v, long nl, long nh)
     printf("\n");  {
     for (i=1;i<=n;i++) {    free((FREE_ARG)(v+nl-NR_END));
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  }
       fptt=(*fret);  
 #ifdef DEBUG  /************************lvector *******************************/
       printf("fret=%lf \n",*fret);  long *lvector(long nl,long nh)
 #endif  {
       printf("%d",i);fflush(stdout);    long *v;
       linmin(p,xit,n,fret,func);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       if (fabs(fptt-(*fret)) > del) {    if (!v) nrerror("allocation failure in ivector");
         del=fabs(fptt-(*fret));    return v-nl+NR_END;
         ibig=i;  }
       }  
 #ifdef DEBUG  /******************free lvector **************************/
       printf("%d %.12e",i,(*fret));  void free_lvector(long *v, long nl, long nh)
       for (j=1;j<=n;j++) {  {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    free((FREE_ARG)(v+nl-NR_END));
         printf(" x(%d)=%.12e",j,xit[j]);  }
       }  
       for(j=1;j<=n;j++)  /******************* imatrix *******************************/
         printf(" p=%.12e",p[j]);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       printf("\n");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 #endif  { 
     }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    int **m; 
 #ifdef DEBUG    
       int k[2],l;    /* allocate pointers to rows */ 
       k[0]=1;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       k[1]=-1;    if (!m) nrerror("allocation failure 1 in matrix()"); 
       printf("Max: %.12e",(*func)(p));    m += NR_END; 
       for (j=1;j<=n;j++)    m -= nrl; 
         printf(" %.12e",p[j]);    
       printf("\n");    
       for(l=0;l<=1;l++) {    /* allocate rows and set pointers to them */ 
         for (j=1;j<=n;j++) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    m[nrl] += NR_END; 
         }    m[nrl] -= ncl; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    
       }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 #endif    
     /* return pointer to array of pointers to rows */ 
     return m; 
       free_vector(xit,1,n);  } 
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  /****************** free_imatrix *************************/
       free_vector(pt,1,n);  void free_imatrix(m,nrl,nrh,ncl,nch)
       return;        int **m;
     }        long nch,ncl,nrh,nrl; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       /* free an int matrix allocated by imatrix() */ 
     for (j=1;j<=n;j++) {  { 
       ptt[j]=2.0*p[j]-pt[j];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       xit[j]=p[j]-pt[j];    free((FREE_ARG) (m+nrl-NR_END)); 
       pt[j]=p[j];  } 
     }  
     fptt=(*func)(ptt);  /******************* matrix *******************************/
     if (fptt < fp) {  double **matrix(long nrl, long nrh, long ncl, long nch)
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  {
       if (t < 0.0) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         linmin(p,xit,n,fret,func);    double **m;
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           xi[j][n]=xit[j];    if (!m) nrerror("allocation failure 1 in matrix()");
         }    m += NR_END;
 #ifdef DEBUG    m -= nrl;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           printf(" %.12e",xit[j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         printf("\n");    m[nrl] += NR_END;
 #endif    m[nrl] -= ncl;
       }  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   }    return m;
 }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
 /**** Prevalence limit ****************/  }
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /*************************free matrix ************************/
 {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  {
      matrix by transitions matrix until convergence is reached */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   int i, ii,j,k;  }
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  /******************* ma3x *******************************/
   double **out, cov[NCOVMAX], **pmij();  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double **newm;  {
   double agefin, delaymax=50 ; /* Max number of years to converge */    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     m -= nrl;
    cov[1]=1.;  
      m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m[nrl] += NR_END;
     newm=savm;    m[nrl] -= ncl;
     /* Covariates have to be included here again */  
      cov[2]=agefin;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    
       for (k=1; k<=cptcovn;k++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
       for (k=1; k<=cptcovage;k++)    for (j=ncl+1; j<=nch; j++) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      m[nrl][j]=m[nrl][j-1]+nlay;
       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]]];    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      for (j=ncl+1; j<=nch; j++) 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        m[i][j]=m[i][j-1]+nlay;
     }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     savm=oldm;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     oldm=newm;    */
     maxmax=0.;  }
     for(j=1;j<=nlstate;j++){  
       min=1.;  /*************************free ma3x ************************/
       max=0.;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       for(i=1; i<=nlstate; i++) {  {
         sumnew=0;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         prlim[i][j]= newm[i][j]/(1-sumnew);    free((FREE_ARG)(m+nrl-NR_END));
         max=FMAX(max,prlim[i][j]);  }
         min=FMIN(min,prlim[i][j]);  
       }  /*************** function subdirf ***********/
       maxmin=max-min;  char *subdirf(char fileres[])
       maxmax=FMAX(maxmax,maxmin);  {
     }    /* Caution optionfilefiname is hidden */
     if(maxmax < ftolpl){    strcpy(tmpout,optionfilefiname);
       return prlim;    strcat(tmpout,"/"); /* Add to the right */
     }    strcat(tmpout,fileres);
   }    return tmpout;
 }  }
   
 /*************** transition probabilities ***************/  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  {
 {    
   double s1, s2;    /* Caution optionfilefiname is hidden */
   /*double t34;*/    strcpy(tmpout,optionfilefiname);
   int i,j,j1, nc, ii, jj;    strcat(tmpout,"/");
     strcat(tmpout,preop);
     for(i=1; i<= nlstate; i++){    strcat(tmpout,fileres);
     for(j=1; j<i;j++){    return tmpout;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /*************** function subdirf3 ***********/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  char *subdirf3(char fileres[], char *preop, char *preop2)
       }  {
       ps[i][j]=s2;    
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     for(j=i+1; j<=nlstate+ndeath;j++){    strcat(tmpout,"/");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcat(tmpout,preop);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcat(tmpout,preop2);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    strcat(tmpout,fileres);
       }    return tmpout;
       ps[i][j]=s2;  }
     }  
   }  /***************** f1dim *************************/
     /*ps[3][2]=1;*/  extern int ncom; 
   extern double *pcom,*xicom;
   for(i=1; i<= nlstate; i++){  extern double (*nrfunc)(double []); 
      s1=0;   
     for(j=1; j<i; j++)  double f1dim(double x) 
       s1+=exp(ps[i][j]);  { 
     for(j=i+1; j<=nlstate+ndeath; j++)    int j; 
       s1+=exp(ps[i][j]);    double f;
     ps[i][i]=1./(s1+1.);    double *xt; 
     for(j=1; j<i; j++)   
       ps[i][j]= exp(ps[i][j])*ps[i][i];    xt=vector(1,ncom); 
     for(j=i+1; j<=nlstate+ndeath; j++)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    f=(*nrfunc)(xt); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    free_vector(xt,1,ncom); 
   } /* end i */    return f; 
   } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*****************brent *************************/
       ps[ii][jj]=0;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       ps[ii][ii]=1;  { 
     }    int iter; 
   }    double a,b,d,etemp;
     double fu,fv,fw,fx;
     double ftemp;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    double e=0.0; 
      printf("%lf ",ps[ii][jj]);   
    }    a=(ax < cx ? ax : cx); 
     printf("\n ");    b=(ax > cx ? ax : cx); 
     }    x=w=v=bx; 
     printf("\n ");printf("%lf ",cov[2]);*/    fw=fv=fx=(*f)(x); 
 /*    for (iter=1;iter<=ITMAX;iter++) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      xm=0.5*(a+b); 
   goto end;*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     return ps;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 /**************** Product of 2 matrices ******************/  #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);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #endif
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   /* in, b, out are matrice of pointers which should have been initialized        *xmin=x; 
      before: only the contents of out is modified. The function returns        return fx; 
      a pointer to pointers identical to out */      } 
   long i, j, k;      ftemp=fu;
   for(i=nrl; i<= nrh; i++)      if (fabs(e) > tol1) { 
     for(k=ncolol; k<=ncoloh; k++)        r=(x-w)*(fx-fv); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        q=(x-v)*(fx-fw); 
         out[i][k] +=in[i][j]*b[j][k];        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   return out;        if (q > 0.0) p = -p; 
 }        q=fabs(q); 
         etemp=e; 
         e=d; 
 /************* Higher Matrix Product ***************/        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)); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        else { 
 {          d=p/q; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          u=x+d; 
      duration (i.e. until          if (u-a < tol2 || b-u < tol2) 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.            d=SIGN(tol1,xm-x); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        } 
      (typically every 2 years instead of every month which is too big).      } else { 
      Model is determined by parameters x and covariates have to be        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      included manually here.      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
      */      fu=(*f)(u); 
       if (fu <= fx) { 
   int i, j, d, h, k;        if (u >= x) a=x; else b=x; 
   double **out, cov[NCOVMAX];        SHFT(v,w,x,u) 
   double **newm;          SHFT(fv,fw,fx,fu) 
           } else { 
   /* Hstepm could be zero and should return the unit matrix */            if (u < x) a=u; else b=u; 
   for (i=1;i<=nlstate+ndeath;i++)            if (fu <= fw || w == x) { 
     for (j=1;j<=nlstate+ndeath;j++){              v=w; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);              w=u; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);              fv=fw; 
     }              fw=fu; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */            } else if (fu <= fv || v == x || v == w) { 
   for(h=1; h <=nhstepm; h++){              v=u; 
     for(d=1; d <=hstepm; d++){              fv=fu; 
       newm=savm;            } 
       /* Covariates have to be included here again */          } 
       cov[1]=1.;    } 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    nrerror("Too many iterations in brent"); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    *xmin=x; 
       for (k=1; k<=cptcovage;k++)    return fx; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  } 
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /****************** mnbrak ***********************/
   
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/              double (*func)(double)) 
       /*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,    double ulim,u,r,q, dum;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double fu; 
       savm=oldm;   
       oldm=newm;    *fa=(*func)(*ax); 
     }    *fb=(*func)(*bx); 
     for(i=1; i<=nlstate+ndeath; i++)    if (*fb > *fa) { 
       for(j=1;j<=nlstate+ndeath;j++) {      SHFT(dum,*ax,*bx,dum) 
         po[i][j][h]=newm[i][j];        SHFT(dum,*fb,*fa,dum) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        } 
          */    *cx=(*bx)+GOLD*(*bx-*ax); 
       }    *fc=(*func)(*cx); 
   } /* end h */    while (*fb > *fc) { 
   return po;      r=(*bx-*ax)*(*fb-*fc); 
 }      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 /*************** log-likelihood *************/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 double func( double *x)      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   int i, ii, j, k, mi, d, kk;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        fu=(*func)(u); 
   double **out;        if (fu < *fc) { 
   double sw; /* Sum of weights */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double lli; /* Individual log likelihood */            SHFT(*fb,*fc,fu,(*func)(u)) 
   long ipmx;            } 
   /*extern weight */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   /* We are differentiating ll according to initial status */        u=ulim; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        fu=(*func)(u); 
   /*for(i=1;i<imx;i++)      } else { 
     printf(" %d\n",s[4][i]);        u=(*cx)+GOLD*(*cx-*bx); 
   */        fu=(*func)(u); 
   cov[1]=1.;      } 
       SHFT(*ax,*bx,*cx,u) 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        SHFT(*fa,*fb,*fc,fu) 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        } 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  } 
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  /*************** linmin ************************/
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){  int ncom; 
         newm=savm;  double *pcom,*xicom;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  double (*nrfunc)(double []); 
         for (kk=1; kk<=cptcovage;kk++) {   
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         }  { 
            double brent(double ax, double bx, double cx, 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,                 double (*f)(double), double tol, double *xmin); 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    double f1dim(double x); 
         savm=oldm;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         oldm=newm;                double *fc, double (*func)(double)); 
            int j; 
            double xx,xmin,bx,ax; 
       } /* end mult */    double fx,fb,fa;
         
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    ncom=n; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    pcom=vector(1,n); 
       ipmx +=1;    xicom=vector(1,n); 
       sw += weight[i];    nrfunc=func; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    for (j=1;j<=n;j++) { 
     } /* end of wave */      pcom[j]=p[j]; 
   } /* end of individual */      xicom[j]=xi[j]; 
     } 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    ax=0.0; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    xx=1.0; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   return -l;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 }  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 /*********** Maximum Likelihood Estimation ***************/  #endif
     for (j=1;j<=n;j++) { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      xi[j] *= xmin; 
 {      p[j] += xi[j]; 
   int i,j, iter;    } 
   double **xi,*delti;    free_vector(xicom,1,n); 
   double fret;    free_vector(pcom,1,n); 
   xi=matrix(1,npar,1,npar);  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  char *asc_diff_time(long time_sec, char ascdiff[])
       xi[i][j]=(i==j ? 1.0 : 0.0);  {
   printf("Powell\n");    long sec_left, days, hours, minutes;
   powell(p,xi,npar,ftol,&iter,&fret,func);    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    hours = (sec_left) / (60*60) ;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
 }    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 /**** Computes Hessian and covariance matrix ***/    return ascdiff;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  /*************** powell ************************/
   double **hess;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   int i, j,jk;              double (*func)(double [])) 
   int *indx;  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   double hessii(double p[], double delta, int theta, double delti[]);                double (*func)(double [])); 
   double hessij(double p[], double delti[], int i, int j);    int i,ibig,j; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double del,t,*pt,*ptt,*xit;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double fp,fptt;
     double *xits;
   hess=matrix(1,npar,1,npar);    int niterf, itmp;
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    pt=vector(1,n); 
   for (i=1;i<=npar;i++){    ptt=vector(1,n); 
     printf("%d",i);fflush(stdout);    xit=vector(1,n); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    xits=vector(1,n); 
     /*printf(" %f ",p[i]);*/    *fret=(*func)(p); 
     /*printf(" %lf ",hess[i][i]);*/    for (j=1;j<=n;j++) pt[j]=p[j]; 
   }    for (*iter=1;;++(*iter)) { 
        fp=(*fret); 
   for (i=1;i<=npar;i++) {      ibig=0; 
     for (j=1;j<=npar;j++)  {      del=0.0; 
       if (j>i) {      last_time=curr_time;
         printf(".%d%d",i,j);fflush(stdout);      (void) gettimeofday(&curr_time,&tzp);
         hess[i][j]=hessij(p,delti,i,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);
         hess[j][i]=hess[i][j];          /*    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(" %lf ",hess[i][j]);*/      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       }      */
     }     for (i=1;i<=n;i++) {
   }        printf(" %d %.12f",i, p[i]);
   printf("\n");        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      }
        printf("\n");
   a=matrix(1,npar,1,npar);      fprintf(ficlog,"\n");
   y=matrix(1,npar,1,npar);      fprintf(ficrespow,"\n");fflush(ficrespow);
   x=vector(1,npar);      if(*iter <=3){
   indx=ivector(1,npar);        tm = *localtime(&curr_time.tv_sec);
   for (i=1;i<=npar;i++)        strcpy(strcurr,asctime(&tm));
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*       asctime_r(&tm,strcurr); */
   ludcmp(a,npar,indx,&pd);        forecast_time=curr_time; 
         itmp = strlen(strcurr);
   for (j=1;j<=npar;j++) {        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     for (i=1;i<=npar;i++) x[i]=0;          strcurr[itmp-1]='\0';
     x[j]=1;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     lubksb(a,npar,indx,x);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (i=1;i<=npar;i++){        for(niterf=10;niterf<=30;niterf+=10){
       matcov[i][j]=x[i];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     }          tmf = *localtime(&forecast_time.tv_sec);
   }  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
   printf("\n#Hessian matrix#\n");          itmp = strlen(strfor);
   for (i=1;i<=npar;i++) {          if(strfor[itmp-1]=='\n')
     for (j=1;j<=npar;j++) {          strfor[itmp-1]='\0';
       printf("%.3e ",hess[i][j]);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     printf("\n");        }
   }      }
       for (i=1;i<=n;i++) { 
   /* Recompute Inverse */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   for (i=1;i<=npar;i++)        fptt=(*fret); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  #ifdef DEBUG
   ludcmp(a,npar,indx,&pd);        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   /*  printf("\n#Hessian matrix recomputed#\n");  #endif
         printf("%d",i);fflush(stdout);
   for (j=1;j<=npar;j++) {        fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=1;i<=npar;i++) x[i]=0;        linmin(p,xit,n,fret,func); 
     x[j]=1;        if (fabs(fptt-(*fret)) > del) { 
     lubksb(a,npar,indx,x);          del=fabs(fptt-(*fret)); 
     for (i=1;i<=npar;i++){          ibig=i; 
       y[i][j]=x[i];        } 
       printf("%.3e ",y[i][j]);  #ifdef DEBUG
     }        printf("%d %.12e",i,(*fret));
     printf("\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
   }        for (j=1;j<=n;j++) {
   */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   free_matrix(a,1,npar,1,npar);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   free_matrix(y,1,npar,1,npar);        }
   free_vector(x,1,npar);        for(j=1;j<=n;j++) {
   free_ivector(indx,1,npar);          printf(" p=%.12e",p[j]);
   free_matrix(hess,1,npar,1,npar);          fprintf(ficlog," p=%.12e",p[j]);
         }
         printf("\n");
 }        fprintf(ficlog,"\n");
   #endif
 /*************** hessian matrix ****************/      } 
 double hessii( double x[], double delta, int theta, double delti[])      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 {  #ifdef DEBUG
   int i;        int k[2],l;
   int l=1, lmax=20;        k[0]=1;
   double k1,k2;        k[1]=-1;
   double p2[NPARMAX+1];        printf("Max: %.12e",(*func)(p));
   double res;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for (j=1;j<=n;j++) {
   double fx;          printf(" %.12e",p[j]);
   int k=0,kmax=10;          fprintf(ficlog," %.12e",p[j]);
   double l1;        }
         printf("\n");
   fx=func(x);        fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++) p2[i]=x[i];        for(l=0;l<=1;l++) {
   for(l=0 ; l <=lmax; l++){          for (j=1;j<=n;j++) {
     l1=pow(10,l);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     delts=delt;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for(k=1 ; k <kmax; k=k+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]);
       delt = delta*(l1*k);          }
       p2[theta]=x[theta] +delt;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       k1=func(p2)-fx;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       p2[theta]=x[theta]-delt;        }
       k2=func(p2)-fx;  #endif
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
              free_vector(xit,1,n); 
 #ifdef DEBUG        free_vector(xits,1,n); 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        free_vector(ptt,1,n); 
 #endif        free_vector(pt,1,n); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        return; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      } 
         k=kmax;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       }      for (j=1;j<=n;j++) { 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        ptt[j]=2.0*p[j]-pt[j]; 
         k=kmax; l=lmax*10.;        xit[j]=p[j]-pt[j]; 
       }        pt[j]=p[j]; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      } 
         delts=delt;      fptt=(*func)(ptt); 
       }      if (fptt < fp) { 
     }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   }        if (t < 0.0) { 
   delti[theta]=delts;          linmin(p,xit,n,fret,func); 
   return res;          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; 
 }            xi[j][n]=xit[j]; 
           }
 double hessij( double x[], double delti[], int thetai,int thetaj)  #ifdef DEBUG
 {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int i;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int l=1, l1, lmax=20;          for(j=1;j<=n;j++){
   double k1,k2,k3,k4,res,fx;            printf(" %.12e",xit[j]);
   double p2[NPARMAX+1];            fprintf(ficlog," %.12e",xit[j]);
   int k;          }
           printf("\n");
   fx=func(x);          fprintf(ficlog,"\n");
   for (k=1; k<=2; k++) {  #endif
     for (i=1;i<=npar;i++) p2[i]=x[i];        }
     p2[thetai]=x[thetai]+delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    } 
     k1=func(p2)-fx;  } 
    
     p2[thetai]=x[thetai]+delti[thetai]/k;  /**** Prevalence limit (stable or period prevalence)  ****************/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       matrix by transitions matrix until convergence is reached */
     k3=func(p2)-fx;  
      int i, ii,j,k;
     p2[thetai]=x[thetai]-delti[thetai]/k;    double min, max, maxmin, maxmax,sumnew=0.;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double **matprod2();
     k4=func(p2)-fx;    double **out, cov[NCOVMAX], **pmij();
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double **newm;
 #ifdef DEBUG    double agefin, delaymax=50 ; /* Max number of years to converge */
     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);  
 #endif    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   return res;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }      }
   
 /************** Inverse of matrix **************/     cov[1]=1.;
 void ludcmp(double **a, int n, int *indx, double *d)   
 {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i,imax,j,k;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double big,dum,sum,temp;      newm=savm;
   double *vv;      /* Covariates have to be included here again */
         cov[2]=agefin;
   vv=vector(1,n);    
   *d=1.0;        for (k=1; k<=cptcovn;k++) {
   for (i=1;i<=n;i++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     big=0.0;          /*      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]]);*/
     for (j=1;j<=n;j++)        }
       if ((temp=fabs(a[i][j])) > big) big=temp;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        for (k=1; k<=cptcovprod;k++)
     vv[i]=1.0/big;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }  
   for (j=1;j<=n;j++) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for (i=1;i<j;i++) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       sum=a[i][j];        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       a[i][j]=sum;  
     }      savm=oldm;
     big=0.0;      oldm=newm;
     for (i=j;i<=n;i++) {      maxmax=0.;
       sum=a[i][j];      for(j=1;j<=nlstate;j++){
       for (k=1;k<j;k++)        min=1.;
         sum -= a[i][k]*a[k][j];        max=0.;
       a[i][j]=sum;        for(i=1; i<=nlstate; i++) {
       if ( (dum=vv[i]*fabs(sum)) >= big) {          sumnew=0;
         big=dum;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         imax=i;          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          max=FMAX(max,prlim[i][j]);
     }          min=FMIN(min,prlim[i][j]);
     if (j != imax) {        }
       for (k=1;k<=n;k++) {        maxmin=max-min;
         dum=a[imax][k];        maxmax=FMAX(maxmax,maxmin);
         a[imax][k]=a[j][k];      }
         a[j][k]=dum;      if(maxmax < ftolpl){
       }        return prlim;
       *d = -(*d);      }
       vv[imax]=vv[j];    }
     }  }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  /*************** transition probabilities ***************/ 
     if (j != n) {  
       dum=1.0/(a[j][j]);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  {
     }    double s1, s2;
   }    /*double t34;*/
   free_vector(vv,1,n);  /* Doesn't work */    int i,j,j1, nc, ii, jj;
 ;  
 }      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
 void lubksb(double **a, int n, int *indx, double b[])          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {            /*s2 += param[i][j][nc]*cov[nc];*/
   int i,ii=0,ip,j;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double sum;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
            }
   for (i=1;i<=n;i++) {          ps[i][j]=s2;
     ip=indx[i];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     sum=b[ip];        }
     b[ip]=b[i];        for(j=i+1; j<=nlstate+ndeath;j++){
     if (ii)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     else if (sum) ii=i;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     b[i]=sum;          }
   }          ps[i][j]=s2;
   for (i=n;i>=1;i--) {        }
     sum=b[i];      }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      /*ps[3][2]=1;*/
     b[i]=sum/a[i][i];      
   }      for(i=1; i<= nlstate; i++){
 }        s1=0;
         for(j=1; j<i; j++)
 /************ Frequencies ********************/          s1+=exp(ps[i][j]);
 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)        for(j=i+1; j<=nlstate+ndeath; j++)
 {  /* Some frequencies */          s1+=exp(ps[i][j]);
          ps[i][i]=1./(s1+1.);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for(j=1; j<i; j++)
   double ***freq; /* Frequencies */          ps[i][j]= exp(ps[i][j])*ps[i][i];
   double *pp;        for(j=i+1; j<=nlstate+ndeath; j++)
   double pos, k2, dateintsum=0,k2cpt=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   FILE *ficresp;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   char fileresp[FILENAMELENGTH];      } /* end i */
        
   pp=vector(1,nlstate);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(jj=1; jj<= nlstate+ndeath; jj++){
   strcpy(fileresp,"p");          ps[ii][jj]=0;
   strcat(fileresp,fileres);          ps[ii][ii]=1;
   if((ficresp=fopen(fileresp,"w"))==NULL) {        }
     printf("Problem with prevalence resultfile: %s\n", fileresp);      }
     exit(0);      
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   j1=0;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
   j=cptcoveff;  /*       } */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*       printf("\n "); */
   /*        } */
   for(k1=1; k1<=j;k1++){  /*        printf("\n ");printf("%lf ",cov[2]); */
    for(i1=1; i1<=ncodemax[k1];i1++){         /*
        j1++;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        goto end;*/
          scanf("%d", i);*/      return ps;
         for (i=-1; i<=nlstate+ndeath; i++)    }
          for (jk=-1; jk<=nlstate+ndeath; jk++)    
            for(m=agemin; m <= agemax+3; m++)  /**************** Product of 2 matrices ******************/
              freq[i][jk][m]=0;  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         dateintsum=0;  {
         k2cpt=0;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        for (i=1; i<=imx; i++) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
          bool=1;    /* in, b, out are matrice of pointers which should have been initialized 
          if  (cptcovn>0) {       before: only the contents of out is modified. The function returns
            for (z1=1; z1<=cptcoveff; z1++)       a pointer to pointers identical to out */
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    long i, j, k;
                bool=0;    for(i=nrl; i<= nrh; i++)
          }      for(k=ncolol; k<=ncoloh; k++)
          if (bool==1) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
            for(m=firstpass; m<=lastpass; m++){          out[i][k] +=in[i][j]*b[j][k];
              k2=anint[m][i]+(mint[m][i]/12.);  
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    return out;
                if(agev[m][i]==0) agev[m][i]=agemax+1;  }
                if(agev[m][i]==1) agev[m][i]=agemax+2;  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /************* Higher Matrix Product ***************/
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  
                  dateintsum=dateintsum+k2;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
                  k2cpt++;  {
                }    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
              }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
            }       nhstepm*hstepm matrices. 
          }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        }       (typically every 2 years instead of every month which is too big 
               for the memory).
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       Model is determined by parameters x and covariates have to be 
        included manually here. 
         if  (cptcovn>0) {  
          fprintf(ficresp, "\n#********** Variable ");       */
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
        fprintf(ficresp, "**********\n#");    int i, j, d, h, k;
         }    double **out, cov[NCOVMAX];
        for(i=1; i<=nlstate;i++)    double **newm;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");    /* Hstepm could be zero and should return the unit matrix */
            for (i=1;i<=nlstate+ndeath;i++)
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for (j=1;j<=nlstate+ndeath;j++){
     if(i==(int)agemax+3)        oldm[i][j]=(i==j ? 1.0 : 0.0);
       printf("Total");        po[i][j][0]=(i==j ? 1.0 : 0.0);
     else      }
       printf("Age %d", i);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(jk=1; jk <=nlstate ; jk++){    for(h=1; h <=nhstepm; h++){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for(d=1; d <=hstepm; d++){
         pp[jk] += freq[jk][m][i];        newm=savm;
     }        /* Covariates have to be included here again */
     for(jk=1; jk <=nlstate ; jk++){        cov[1]=1.;
       for(m=-1, pos=0; m <=0 ; m++)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         pos += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       if(pp[jk]>=1.e-10)        for (k=1; k<=cptcovage;k++)
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       else        for (k=1; k<=cptcovprod;k++)
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }  
   
      for(jk=1; jk <=nlstate ; jk++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         pp[jk] += freq[jk][m][i];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
      }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
     for(jk=1,pos=0; jk <=nlstate ; jk++)        oldm=newm;
       pos += pp[jk];      }
     for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<=nlstate+ndeath; i++)
       if(pos>=1.e-5)        for(j=1;j<=nlstate+ndeath;j++) {
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          po[i][j][h]=newm[i][j];
       else          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           */
       if( i <= (int) agemax){        }
         if(pos>=1.e-5){    } /* end h */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    return po;
           probs[i][jk][j1]= pp[jk]/pos;  }
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
         }  
       else  /*************** log-likelihood *************/
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  double func( double *x)
       }  {
     }    int i, ii, j, k, mi, d, kk;
     for(jk=-1; jk <=nlstate+ndeath; jk++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       for(m=-1; m <=nlstate+ndeath; m++)    double **out;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    double sw; /* Sum of weights */
     if(i <= (int) agemax)    double lli; /* Individual log likelihood */
       fprintf(ficresp,"\n");    int s1, s2;
     printf("\n");    double bbh, survp;
     }    long ipmx;
     }    /*extern weight */
  }    /* We are differentiating ll according to initial status */
   dateintmean=dateintsum/k2cpt;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   fclose(ficresp);      printf(" %d\n",s[4][i]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    */
   free_vector(pp,1,nlstate);    cov[1]=1.;
   
   /* End of Freq */    for(k=1; k<=nlstate; k++) ll[k]=0.;
 }  
     if(mle==1){
 /************ Prevalence ********************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 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)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {  /* Some frequencies */        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            for (j=1;j<=nlstate+ndeath;j++){
   double ***freq; /* Frequencies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *pp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2;            }
           for(d=0; d<dh[mi][i]; d++){
   pp=vector(1,nlstate);            newm=savm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   j1=0;            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   j=cptcoveff;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            savm=oldm;
              oldm=newm;
  for(k1=1; k1<=j;k1++){          } /* end mult */
     for(i1=1; i1<=ncodemax[k1];i1++){        
       j1++;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            /* But now since version 0.9 we anticipate for bias at large stepm.
       for (i=-1; i<=nlstate+ndeath; i++)             * If stepm is larger than one month (smallest stepm) and if the exact delay 
         for (jk=-1; jk<=nlstate+ndeath; jk++)             * (in months) between two waves is not a multiple of stepm, we rounded to 
           for(m=agemin; m <= agemax+3; m++)           * the nearest (and in case of equal distance, to the lowest) interval but now
             freq[i][jk][m]=0;           * 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
       for (i=1; i<=imx; i++) {           * probability in order to take into account the bias as a fraction of the way
         bool=1;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         if  (cptcovn>0) {           * -stepm/2 to stepm/2 .
           for (z1=1; z1<=cptcoveff; z1++)           * For stepm=1 the results are the same as for previous versions of Imach.
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * For stepm > 1 the results are less biased than in previous versions. 
               bool=0;           */
         }          s1=s[mw[mi][i]][i];
         if (bool==1) {          s2=s[mw[mi+1][i]][i];
           for(m=firstpass; m<=lastpass; m++){          bbh=(double)bh[mi][i]/(double)stepm; 
             k2=anint[m][i]+(mint[m][i]/12.);          /* bias bh is positive if real duration
             if ((k2>=dateprev1) && (k2<=dateprev2)) {           * is higher than the multiple of stepm and negative otherwise.
               if(agev[m][i]==0) agev[m][i]=agemax+1;           */
               if(agev[m][i]==1) agev[m][i]=agemax+2;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          if( s2 > nlstate){ 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            /* i.e. if s2 is a death state and if the date of death is known 
             }               then the contribution to the likelihood is the probability to 
           }               die between last step unit time and current  step unit time, 
         }               which is also equal to probability to die before dh 
       }               minus probability to die before dh-stepm . 
         for(i=(int)agemin; i <= (int)agemax+3; i++){               In version up to 0.92 likelihood was computed
           for(jk=1; jk <=nlstate ; jk++){          as if date of death was unknown. Death was treated as any other
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          health state: the date of the interview describes the actual state
               pp[jk] += freq[jk][m][i];          and not the date of a change in health state. The former idea was
           }          to consider that at each interview the state was recorded
           for(jk=1; jk <=nlstate ; jk++){          (healthy, disable or death) and IMaCh was corrected; but when we
             for(m=-1, pos=0; m <=0 ; m++)          introduced the exact date of death then we should have modified
             pos += freq[jk][m][i];          the contribution of an exact death to the likelihood. This new
         }          contribution is smaller and very dependent of the step unit
                  stepm. It is no more the probability to die between last interview
          for(jk=1; jk <=nlstate ; jk++){          and month of death but the probability to survive from last
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          interview up to one month before death multiplied by the
              pp[jk] += freq[jk][m][i];          probability to die within a month. Thanks to Chris
          }          Jackson for correcting this bug.  Former versions increased
                    mortality artificially. The bad side is that we add another loop
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          which slows down the processing. The difference can be up to 10%
           lower mortality.
          for(jk=1; jk <=nlstate ; jk++){                      */
            if( i <= (int) agemax){            lli=log(out[s1][s2] - savm[s1][s2]);
              if(pos>=1.e-5){  
                probs[i][jk][j1]= pp[jk]/pos;  
              }          } else if  (s2==-2) {
            }            for (j=1,survp=0. ; j<=nlstate; j++) 
          }              survp += out[s1][j];
                      lli= survp;
         }          }
     }          
   }          else if  (s2==-4) {
              for (j=3,survp=0. ; j<=nlstate; j++) 
                survp += out[s1][j];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            lli= survp;
   free_vector(pp,1,nlstate);          }
            
 }  /* End of Freq */          else if  (s2==-5) {
             for (j=1,survp=0. ; j<=2; j++) 
 /************* Waves Concatenation ***************/              survp += out[s1][j];
             lli= survp;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          }
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).          else{
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][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 */
      and mw[mi+1][i]. dh depends on stepm.          } 
      */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
   int i, mi, m;          /*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); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          ipmx +=1;
      double sum=0., jmean=0.;*/          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int j, k=0,jk, ju, jl;        } /* end of wave */
   double sum=0.;      } /* end of individual */
   jmin=1e+5;    }  else if(mle==2){
   jmax=-1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   jmean=0.;        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++){
     mi=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
     m=firstpass;            for (j=1;j<=nlstate+ndeath;j++){
     while(s[m][i] <= nlstate){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(s[m][i]>=1)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         mw[++mi][i]=m;            }
       if(m >=lastpass)          for(d=0; d<=dh[mi][i]; d++){
         break;            newm=savm;
       else            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         m++;            for (kk=1; kk<=cptcovage;kk++) {
     }/* end while */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (s[m][i] > nlstate){            }
       mi++;     /* Death is another wave */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       /* if(mi==0)  never been interviewed correctly before death */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          /* Only death is a correct wave */            savm=oldm;
       mw[mi][i]=m;            oldm=newm;
     }          } /* end mult */
         
     wav[i]=mi;          s1=s[mw[mi][i]][i];
     if(mi==0)          s2=s[mw[mi+1][i]][i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          bbh=(double)bh[mi][i]/(double)stepm; 
   }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
   for(i=1; i<=imx; i++){          sw += weight[i];
     for(mi=1; mi<wav[i];mi++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if (stepm <=0)        } /* end of wave */
         dh[mi][i]=1;      } /* end of individual */
       else{    }  else if(mle==3){  /* exponential inter-extrapolation */
         if (s[mw[mi+1][i]][i] > nlstate) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if (agedc[i] < 2*AGESUP) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for(mi=1; mi<= wav[i]-1; mi++){
           if(j==0) j=1;  /* Survives at least one month after exam */          for (ii=1;ii<=nlstate+ndeath;ii++)
           k=k+1;            for (j=1;j<=nlstate+ndeath;j++){
           if (j >= jmax) jmax=j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (j <= jmin) jmin=j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           sum=sum+j;            }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         else{            for (kk=1; kk<=cptcovage;kk++) {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           k=k+1;            }
           if (j >= jmax) jmax=j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           else if (j <= jmin)jmin=j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            savm=oldm;
           sum=sum+j;            oldm=newm;
         }          } /* end mult */
         jk= j/stepm;        
         jl= j -jk*stepm;          s1=s[mw[mi][i]][i];
         ju= j -(jk+1)*stepm;          s2=s[mw[mi+1][i]][i];
         if(jl <= -ju)          bbh=(double)bh[mi][i]/(double)stepm; 
           dh[mi][i]=jk;          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 */
         else          ipmx +=1;
           dh[mi][i]=jk+1;          sw += weight[i];
         if(dh[mi][i]==0)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           dh[mi][i]=1; /* At least one step */        } /* end of wave */
       }      } /* end of individual */
     }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   jmean=sum/k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for(mi=1; mi<= wav[i]-1; mi++){
  }          for (ii=1;ii<=nlstate+ndeath;ii++)
 /*********** Tricode ****************************/            for (j=1;j<=nlstate+ndeath;j++){
 void tricode(int *Tvar, int **nbcode, int imx)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int Ndum[20],ij=1, k, j, i;            }
   int cptcode=0;          for(d=0; d<dh[mi][i]; d++){
   cptcoveff=0;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (k=0; k<19; k++) Ndum[k]=0;            for (kk=1; kk<=cptcovage;kk++) {
   for (k=1; k<=7; k++) ncodemax[k]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          
     for (i=1; i<=imx; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       ij=(int)(covar[Tvar[j]][i]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       Ndum[ij]++;            savm=oldm;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            oldm=newm;
       if (ij > cptcode) cptcode=ij;          } /* end mult */
     }        
           s1=s[mw[mi][i]][i];
     for (i=0; i<=cptcode; i++) {          s2=s[mw[mi+1][i]][i];
       if(Ndum[i]!=0) ncodemax[j]++;          if( s2 > nlstate){ 
     }            lli=log(out[s1][s2] - savm[s1][s2]);
     ij=1;          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
     for (i=1; i<=ncodemax[j]; i++) {          ipmx +=1;
       for (k=0; k<=19; k++) {          sw += weight[i];
         if (Ndum[k] != 0) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           nbcode[Tvar[j]][ij]=k;  /*      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]); */
           ij++;        } /* end of wave */
         }      } /* end of individual */
         if (ij > ncodemax[j]) break;    }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++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
  for (k=0; k<19; k++) Ndum[k]=0;            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (i=1; i<=ncovmodel-2; i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=Tvar[i];            }
       Ndum[ij]++;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  ij=1;            for (kk=1; kk<=cptcovage;kk++) {
  for (i=1; i<=10; i++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    if((Ndum[i]!=0) && (i<=ncov)){            }
      Tvaraff[ij]=i;          
      ij++;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  }            savm=oldm;
              oldm=newm;
     cptcoveff=ij-1;          } /* end mult */
 }        
           s1=s[mw[mi][i]][i];
 /*********** Health Expectancies ****************/          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          ipmx +=1;
 {          sw += weight[i];
   /* Health expectancies */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i, j, nhstepm, hstepm, h;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   double age, agelim,hf;        } /* end of wave */
   double ***p3mat;      } /* end of individual */
      } /* End of if */
   fprintf(ficreseij,"# Health expectancies\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   fprintf(ficreseij,"# Age");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for(i=1; i<=nlstate;i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(j=1; j<=nlstate;j++)    return -l;
       fprintf(ficreseij," %1d-%1d",i,j);  }
   fprintf(ficreseij,"\n");  
   /*************** log-likelihood *************/
   hstepm=1*YEARM; /*  Every j years of age (in month) */  double funcone( double *x)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  {
     /* Same as likeli but slower because of a lot of printf and if */
   agelim=AGESUP;    int i, ii, j, k, mi, d, kk;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     /* nhstepm age range expressed in number of stepm */    double **out;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    double lli; /* Individual log likelihood */
     /* Typically if 20 years = 20*12/6=40 stepm */    double llt;
     /*if (stepm >= YEARM) hstepm=1;*/    int s1, s2;
 hstepm=1;    double bbh, survp;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    /*extern weight */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We are differentiating ll according to initial status */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    /*for(i=1;i<imx;i++) 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        printf(" %d\n",s[4][i]);
 hf=stepm/YEARM;    */
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/    cov[1]=1.;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;    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++){
     /* hf=1;        for (ii=1;ii<=nlstate+ndeath;ii++)
        if (stepm >= YEARM) hf=stepm/YEARM;*/          for (j=1;j<=nlstate+ndeath;j++){
 hf=stepm/YEARM;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficreseij,"%3.0f",age );          }
     for(i=1; i<=nlstate;i++)        for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<=nlstate;j++){          newm=savm;
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }          for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficreseij,"\n");            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
 /************ Variance ******************/          oldm=newm;
 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 mult */
 {        
   /* Variance of health expectancies */        s1=s[mw[mi][i]][i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        s2=s[mw[mi+1][i]][i];
   double **newm;        bbh=(double)bh[mi][i]/(double)stepm; 
   double **dnewm,**doldm;        /* bias is positive if real duration
   int i, j, nhstepm, hstepm, h;         * is higher than the multiple of stepm and negative otherwise.
   int k, cptcode;         */
   double *xp;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   double **gp, **gm;          lli=log(out[s1][s2] - savm[s1][s2]);
   double ***gradg, ***trgradg;        } else if (mle==1){
   double ***p3mat;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double age,agelim;        } else if(mle==2){
   int theta;          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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
    fprintf(ficresvij,"# Covariances of life expectancies\n");          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   fprintf(ficresvij,"# Age");        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   for(i=1; i<=nlstate;i++)          lli=log(out[s1][s2]); /* Original formula */
     for(j=1; j<=nlstate;j++)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          lli=log(out[s1][s2]); /* Original formula */
   fprintf(ficresvij,"\n");        } /* End of if */
         ipmx +=1;
   xp=vector(1,npar);        sw += weight[i];
   dnewm=matrix(1,nlstate,1,npar);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   doldm=matrix(1,nlstate,1,nlstate);  /*       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){
   hstepm=1*YEARM; /* Every year of age */          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */   %10.6f %10.6f %10.6f ", \
   agelim = AGESUP;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     if (stepm >= YEARM) hstepm=1;            llt +=ll[k]*gipmx/gsw;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          fprintf(ficresilk," %10.6f\n", -llt);
     gp=matrix(0,nhstepm,1,nlstate);        }
     gm=matrix(0,nhstepm,1,nlstate);      } /* end of wave */
     } /* end of individual */
     for(theta=1; theta <=npar; theta++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       }    if(globpr==0){ /* First time we count the contributions and weights */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        gipmx=ipmx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      gsw=sw;
     }
       if (popbased==1) {    return -l;
         for(i=1; i<=nlstate;i++)  }
           prlim[i][i]=probs[(int)age][i][ij];  
       }  
    /*************** function likelione ***********/
       for(j=1; j<= nlstate; j++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         for(h=0; h<=nhstepm; h++){  {
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    /* This routine should help understanding what is done with 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];       the selection of individuals/waves and
         }       to check the exact contribution to the likelihood.
       }       Plotting could be done.
         */
       for(i=1; i<=npar; i++) /* Computes gradient */    int k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      if(*globpri !=0){ /* Just counts and sums, no printings */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      strcpy(fileresilk,"ilk"); 
        strcat(fileresilk,fileres);
       if (popbased==1) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         for(i=1; i<=nlstate;i++)        printf("Problem with resultfile: %s\n", fileresilk);
           prlim[i][i]=probs[(int)age][i][ij];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }      }
       fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       for(j=1; j<= nlstate; j++){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         for(h=0; h<=nhstepm; h++){      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(k=1; k<=nlstate; k++) 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       }    }
   
       for(j=1; j<= nlstate; j++)    *fretone=(*funcone)(p);
         for(h=0; h<=nhstepm; h++){    if(*globpri !=0){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      fclose(ficresilk);
         }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     } /* End theta */      fflush(fichtm); 
     } 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    return;
   }
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  /*********** Maximum Likelihood Estimation ***************/
           trgradg[h][j][theta]=gradg[h][theta][j];  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     for(i=1;i<=nlstate;i++)  {
       for(j=1;j<=nlstate;j++)    int i,j, iter;
         vareij[i][j][(int)age] =0.;    double **xi;
     for(h=0;h<=nhstepm;h++){    double fret;
       for(k=0;k<=nhstepm;k++){    double fretone; /* Only one call to likelihood */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /*  char filerespow[FILENAMELENGTH];*/
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    xi=matrix(1,npar,1,npar);
         for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++)
           for(j=1;j<=nlstate;j++)      for (j=1;j<=npar;j++)
             vareij[i][j][(int)age] += doldm[i][j];        xi[i][j]=(i==j ? 1.0 : 0.0);
       }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     }    strcpy(filerespow,"pow"); 
     h=1;    strcat(filerespow,fileres);
     if (stepm >= YEARM) h=stepm/YEARM;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     fprintf(ficresvij,"%.0f ",age );      printf("Problem with resultfile: %s\n", filerespow);
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       for(j=1; j<=nlstate;j++){    }
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       }    for (i=1;i<=nlstate;i++)
     fprintf(ficresvij,"\n");      for(j=1;j<=nlstate+ndeath;j++)
     free_matrix(gp,0,nhstepm,1,nlstate);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     free_matrix(gm,0,nhstepm,1,nlstate);    fprintf(ficrespow,"\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    powell(p,xi,npar,ftol,&iter,&fret,func);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   free_vector(xp,1,npar);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   free_matrix(doldm,1,nlstate,1,npar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_matrix(dnewm,1,nlstate,1,nlstate);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
 }  }
   
 /************ Variance of prevlim ******************/  /**** Computes Hessian and covariance matrix ***/
 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)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 {  {
   /* Variance of prevalence limit */    double  **a,**y,*x,pd;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double **hess;
   double **newm;    int i, j,jk;
   double **dnewm,**doldm;    int *indx;
   int i, j, nhstepm, hstepm;  
   int k, cptcode;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double *xp;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   double *gp, *gm;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double **gradg, **trgradg;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double age,agelim;    double gompertz(double p[]);
   int theta;    hess=matrix(1,npar,1,npar);
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficresvpl,"# Age");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++){
       fprintf(ficresvpl," %1d-%1d",i,i);      printf("%d",i);fflush(stdout);
   fprintf(ficresvpl,"\n");      fprintf(ficlog,"%d",i);fflush(ficlog);
      
   xp=vector(1,npar);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   dnewm=matrix(1,nlstate,1,npar);      
   doldm=matrix(1,nlstate,1,nlstate);      /*  printf(" %f ",p[i]);
            printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   hstepm=1*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    
   agelim = AGESUP;    for (i=1;i<=npar;i++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=npar;j++)  {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if (j>i) { 
     if (stepm >= YEARM) hstepm=1;          printf(".%d%d",i,j);fflush(stdout);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     gradg=matrix(1,npar,1,nlstate);          hess[i][j]=hessij(p,delti,i,j,func,npar);
     gp=vector(1,nlstate);          
     gm=vector(1,nlstate);          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
     for(theta=1; theta <=npar; theta++){        }
       for(i=1; i<=npar; i++){ /* Computes gradient */      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    printf("\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    fprintf(ficlog,"\n");
       for(i=1;i<=nlstate;i++)  
         gp[i] = prlim[i][i];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    a=matrix(1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    y=matrix(1,npar,1,npar);
       for(i=1;i<=nlstate;i++)    x=vector(1,npar);
         gm[i] = prlim[i][i];    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
       for(i=1;i<=nlstate;i++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    ludcmp(a,npar,indx,&pd);
     } /* End theta */  
     for (j=1;j<=npar;j++) {
     trgradg =matrix(1,nlstate,1,npar);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for(j=1; j<=nlstate;j++)      lubksb(a,npar,indx,x);
       for(theta=1; theta <=npar; theta++)      for (i=1;i<=npar;i++){ 
         trgradg[j][theta]=gradg[theta][j];        matcov[i][j]=x[i];
       }
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    printf("\n#Hessian matrix#\n");
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    fprintf(ficlog,"\n#Hessian matrix#\n");
     for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++) { 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
     fprintf(ficresvpl,"%.0f ",age );        fprintf(ficlog,"%.3e ",hess[i][j]);
     for(i=1; i<=nlstate;i++)      }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      printf("\n");
     fprintf(ficresvpl,"\n");      fprintf(ficlog,"\n");
     free_vector(gp,1,nlstate);    }
     free_vector(gm,1,nlstate);  
     free_matrix(gradg,1,npar,1,nlstate);    /* Recompute Inverse */
     free_matrix(trgradg,1,nlstate,1,npar);    for (i=1;i<=npar;i++)
   } /* End age */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    /*  printf("\n#Hessian matrix recomputed#\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
 /************ Variance of one-step probabilities  ******************/      lubksb(a,npar,indx,x);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      for (i=1;i<=npar;i++){ 
 {        y[i][j]=x[i];
   int i, j;        printf("%.3e ",y[i][j]);
   int k=0, cptcode;        fprintf(ficlog,"%.3e ",y[i][j]);
   double **dnewm,**doldm;      }
   double *xp;      printf("\n");
   double *gp, *gm;      fprintf(ficlog,"\n");
   double **gradg, **trgradg;    }
   double age,agelim, cov[NCOVMAX];    */
   int theta;  
   char fileresprob[FILENAMELENGTH];    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   strcpy(fileresprob,"prob");    free_vector(x,1,npar);
   strcat(fileresprob,fileres);    free_ivector(indx,1,npar);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    free_matrix(hess,1,npar,1,npar);
     printf("Problem with resultfile: %s\n", fileresprob);  
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  }
    
   /*************** hessian matrix ****************/
   xp=vector(1,npar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  {
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    int i;
      int l=1, lmax=20;
   cov[1]=1;    double k1,k2;
   for (age=bage; age<=fage; age ++){    double p2[NPARMAX+1];
     cov[2]=age;    double res;
     gradg=matrix(1,npar,1,9);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     trgradg=matrix(1,9,1,npar);    double fx;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int k=0,kmax=10;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double l1;
      
     for(theta=1; theta <=npar; theta++){    fx=func(x);
       for(i=1; i<=npar; i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for(l=0 ; l <=lmax; l++){
            l1=pow(10,l);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      delts=delt;
          for(k=1 ; k <kmax; k=k+1){
       k=0;        delt = delta*(l1*k);
       for(i=1; i<= (nlstate+ndeath); i++){        p2[theta]=x[theta] +delt;
         for(j=1; j<=(nlstate+ndeath);j++){        k1=func(p2)-fx;
            k=k+1;        p2[theta]=x[theta]-delt;
           gp[k]=pmmij[i][j];        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 */
         
       for(i=1; i<=npar; i++)  #ifdef DEBUG
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
            fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       k=0;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for(i=1; i<=(nlstate+ndeath); i++){          k=kmax;
         for(j=1; j<=(nlstate+ndeath);j++){        }
           k=k+1;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           gm[k]=pmmij[i][j];          k=kmax; l=lmax*10.;
         }        }
       }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                delts=delt;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        }
     }    }
     delti[theta]=delts;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    return res; 
       for(theta=1; theta <=npar; theta++)    
       trgradg[j][theta]=gradg[theta][j];  }
    
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  {
     int i;
      pmij(pmmij,cov,ncovmodel,x,nlstate);    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
      k=0;    double p2[NPARMAX+1];
      for(i=1; i<=(nlstate+ndeath); i++){    int k;
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;    fx=func(x);
          gm[k]=pmmij[i][j];    for (k=1; k<=2; k++) {
         }      for (i=1;i<=npar;i++) p2[i]=x[i];
      }      p2[thetai]=x[thetai]+delti[thetai]/k;
            p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      /*printf("\n%d ",(int)age);      k1=func(p2)-fx;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    
              p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      k2=func(p2)-fx;
      }*/    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   fprintf(ficresprob,"\n%d ",(int)age);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      p2[thetai]=x[thetai]-delti[thetai]/k;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  #ifdef DEBUG
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      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);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      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);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  #endif
 }    }
  free_vector(xp,1,npar);    return res;
 fclose(ficresprob);  }
   
 }  /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
 /******************* Printing html file ***********/  { 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){    int i,imax,j,k; 
   int jj1, k1, i1, cpt;    double big,dum,sum,temp; 
   FILE *fichtm;    double *vv; 
   /*char optionfilehtm[FILENAMELENGTH];*/   
     vv=vector(1,n); 
   strcpy(optionfilehtm,optionfile);    *d=1.0; 
   strcat(optionfilehtm,".htm");    for (i=1;i<=n;i++) { 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      big=0.0; 
     printf("Problem with %s \n",optionfilehtm), exit(0);      for (j=1;j<=n;j++) 
   }        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">      vv[i]=1.0/big; 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    } 
     for (j=1;j<=n;j++) { 
 Total number of observations=%d <br>      for (i=1;i<j;i++) { 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        sum=a[i][j]; 
 <hr  size=\"2\" color=\"#EC5E5E\">        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 <li>Outputs files<br><br>\n        a[i][j]=sum; 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      } 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      big=0.0; 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      for (i=j;i<=n;i++) { 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        sum=a[i][j]; 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        for (k=1;k<j;k++) 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          sum -= a[i][k]*a[k][j]; 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        a[i][j]=sum; 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>          big=dum; 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>          imax=i; 
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>        } 
         <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);      } 
        if (j != imax) { 
 fprintf(fichtm," <li>Graphs</li><p>");        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
  m=cptcoveff;          a[imax][k]=a[j][k]; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          a[j][k]=dum; 
         } 
  jj1=0;        *d = -(*d); 
  for(k1=1; k1<=m;k1++){        vv[imax]=vv[j]; 
    for(i1=1; i1<=ncodemax[k1];i1++){      } 
        jj1++;      indx[j]=imax; 
        if (cptcovn > 0) {      if (a[j][j] == 0.0) a[j][j]=TINY; 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      if (j != n) { 
          for (cpt=1; cpt<=cptcoveff;cpt++)        dum=1.0/(a[j][j]); 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      } 
        }    } 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    free_vector(vv,1,n);  /* Doesn't work */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      ;
        for(cpt=1; cpt<nlstate;cpt++){  } 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  void lubksb(double **a, int n, int *indx, double b[]) 
        }  { 
     for(cpt=1; cpt<=nlstate;cpt++) {    int i,ii=0,ip,j; 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double sum; 
 interval) in state (%d): v%s%d%d.gif <br>   
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for (i=1;i<=n;i++) { 
      }      ip=indx[i]; 
      for(cpt=1; cpt<=nlstate;cpt++) {      sum=b[ip]; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      b[ip]=b[i]; 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      if (ii) 
      }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      else if (sum) ii=i; 
 health expectancies in states (1) and (2): e%s%d.gif<br>      b[i]=sum; 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    } 
 fprintf(fichtm,"\n</body>");    for (i=n;i>=1;i--) { 
    }      sum=b[i]; 
    }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 fclose(fichtm);      b[i]=sum/a[i][i]; 
 }    } 
   } 
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){  void pstamp(FILE *fichier)
   {
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".plt");  /************ Frequencies ********************/
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     printf("Problem with file %s",optionfilegnuplot);  {  /* Some frequencies */
   }    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 #ifdef windows    int first;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double ***freq; /* Frequencies */
 #endif    double *pp, **prop;
 m=pow(2,cptcoveff);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      char fileresp[FILENAMELENGTH];
  /* 1eme*/    
   for (cpt=1; cpt<= nlstate ; cpt ++) {    pp=vector(1,nlstate);
    for (k1=1; k1<= m ; k1 ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
 #ifdef windows    strcat(fileresp,fileres);
     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((ficresp=fopen(fileresp,"w"))==NULL) {
 #endif      printf("Problem with prevalence resultfile: %s\n", fileresp);
 #ifdef unix      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      exit(0);
 #endif    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 for (i=1; i<= nlstate ; i ++) {    j1=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    j=cptcoveff;
 }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {    first=1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(k1=1; k1<=j;k1++){
 }      for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        j1++;
      for (i=1; i<= nlstate ; i ++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          scanf("%d", i);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (i=-5; i<=nlstate+ndeath; i++)  
 }            for (jk=-5; jk<=nlstate+ndeath; jk++)  
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            for(m=iagemin; m <= iagemax+3; m++)
 #ifdef unix              freq[i][jk][m]=0;
 fprintf(ficgp,"\nset ter gif small size 400,300");  
 #endif      for (i=1; i<=nlstate; i++)  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(m=iagemin; m <= iagemax+3; m++)
    }          prop[i][m]=0;
   }        
   /*2 eme*/        dateintsum=0;
         k2cpt=0;
   for (k1=1; k1<= m ; k1 ++) {        for (i=1; i<=imx; i++) {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          bool=1;
              if  (cptcovn>0) {
     for (i=1; i<= nlstate+1 ; i ++) {            for (z1=1; z1<=cptcoveff; z1++) 
       k=2*i;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                bool=0;
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (bool==1){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=firstpass; m<=lastpass; m++){
 }                k2=anint[m][i]+(mint[m][i]/12.);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       for (j=1; j<= nlstate+1 ; j ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                if (m<lastpass) {
         else fprintf(ficgp," \%%*lf (\%%*lf)");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 }                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       fprintf(ficgp,"\" t\"\" w l 0,");                }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                
       for (j=1; j<= nlstate+1 ; j ++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                  dateintsum=dateintsum+k2;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  k2cpt++;
 }                  }
       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);        }
   }         
          /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   /*3eme*/        pstamp(ficresp);
         if  (cptcovn>0) {
   for (k1=1; k1<= m ; k1 ++) {          fprintf(ficresp, "\n#********** Variable "); 
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=2+nlstate*(cpt-1);          fprintf(ficresp, "**********\n#");
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        }
       for (i=1; i< nlstate ; i ++) {        for(i=1; i<=nlstate;i++) 
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       }        fprintf(ficresp, "\n");
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        
     }        for(i=iagemin; i <= iagemax+3; i++){
     }          if(i==iagemax+3){
              fprintf(ficlog,"Total");
   /* CV preval stat */          }else{
     for (k1=1; k1<= m ; k1 ++) {            if(first==1){
     for (cpt=1; cpt<nlstate ; cpt ++) {              first=0;
       k=3;              printf("See log file for details...\n");
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);            }
             fprintf(ficlog,"Age %d", i);
       for (i=1; i< nlstate ; i ++)          }
         fprintf(ficgp,"+$%d",k+i+1);          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                    pp[jk] += freq[jk][m][i]; 
       l=3+(nlstate+ndeath)*cpt;          }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i< nlstate ; i ++) {            for(m=-1, pos=0; m <=0 ; m++)
         l=3+(nlstate+ndeath)*cpt;              pos += freq[jk][m][i];
         fprintf(ficgp,"+$%d",l+i+1);            if(pp[jk]>=1.e-10){
       }              if(first==1){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
     }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }else{
                if(first==1)
   /* proba elementaires */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    for(i=1,jk=1; i <=nlstate; i++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(k=1; k <=(nlstate+ndeath); k++){            }
       if (k != i) {          }
         for(j=1; j <=ncovmodel; j++){  
                  for(jk=1; jk <=nlstate ; jk++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           jk++;              pp[jk] += freq[jk][m][i];
           fprintf(ficgp,"\n");          }       
         }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       }            pos += pp[jk];
     }            posprop += prop[jk][i];
     }          }
           for(jk=1; jk <=nlstate ; jk++){
     for(jk=1; jk <=m; jk++) {            if(pos>=1.e-5){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);              if(first==1)
    i=1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    for(k2=1; k2<=nlstate; k2++) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      k3=i;            }else{
      for(k=1; k<=(nlstate+ndeath); k++) {              if(first==1)
        if (k != k2){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 ij=1;            }
         for(j=3; j <=ncovmodel; j++) {            if( i <= iagemax){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if(pos>=1.e-5){
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
             ij++;                /*probs[i][jk][j1]= pp[jk]/pos;*/
           }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           else              }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              else
         }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           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);          for(jk=-1; jk <=nlstate+ndeath; jk++)
 ij=1;            for(m=-1; m <=nlstate+ndeath; m++)
           for(j=3; j <=ncovmodel; j++){              if(freq[jk][m][i] !=0 ) {
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if(first==1)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
             ij++;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           }              }
           else          if(i <= iagemax)
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            fprintf(ficresp,"\n");
           }          if(first==1)
           fprintf(ficgp,")");            printf("Others in log...\n");
         }          fprintf(ficlog,"\n");
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      }
         i=i+ncovmodel;    }
        }    dateintmean=dateintsum/k2cpt; 
      }   
    }    fclose(ficresp);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    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);
   fclose(ficgp);    /* End of Freq */
 }  /* end gnuplot */  }
   
   /************ Prevalence ********************/
 /*************** Moving average **************/  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)
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   int i, cpt, cptcod;       in each health status at the date of interview (if between dateprev1 and dateprev2).
     for (agedeb=agemin; agedeb<=fage; agedeb++)       We still use firstpass and lastpass as another selection.
       for (i=1; i<=nlstate;i++)    */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   
           mobaverage[(int)agedeb][i][cptcod]=0.;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
        double ***freq; /* Frequencies */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    double *pp, **prop;
       for (i=1; i<=nlstate;i++){    double pos,posprop; 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double  y2; /* in fractional years */
           for (cpt=0;cpt<=4;cpt++){    int iagemin, iagemax;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }    iagemin= (int) agemin;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    iagemax= (int) agemax;
         }    /*pp=vector(1,nlstate);*/
       }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        j1=0;
 }    
     j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
 /************** 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){    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        j1++;
   int *popage;        
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        for (i=1; i<=nlstate; i++)  
   double *popeffectif,*popcount;          for(m=iagemin; m <= iagemax+3; m++)
   double ***p3mat;            prop[i][m]=0.0;
   char fileresf[FILENAMELENGTH];       
         for (i=1; i<=imx; i++) { /* Each individual */
  agelim=AGESUP;          bool=1;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=0;
            } 
   strcpy(fileresf,"f");          if (bool==1) { 
   strcat(fileresf,fileres);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   if((ficresf=fopen(fileresf,"w"))==NULL) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     printf("Problem with forecast resultfile: %s\n", fileresf);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   printf("Computing forecasting: result on file '%s' \n", fileresf);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 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); 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*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]]);*/
   if (mobilav==1) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                  prop[s[m][i]][iagemax+3] += weight[i]; 
     movingaverage(agedeb, fage, agemin, mobaverage);                } 
   }              }
             } /* end selection of waves */
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;        }
          for(i=iagemin; i <= iagemax+3; i++){  
   agelim=AGESUP;          
            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   hstepm=1;            posprop += prop[jk][i]; 
   hstepm=hstepm/stepm;          } 
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;          for(jk=1; jk <=nlstate ; jk++){     
   yp2=modf((yp1*12),&yp);            if( i <=  iagemax){ 
   mprojmean=yp;              if(posprop>=1.e-5){ 
   yp1=modf((yp2*30.5),&yp);                probs[i][jk][j1]= prop[jk][i]/posprop;
   jprojmean=yp;              } 
   if(jprojmean==0) jprojmean=1;            } 
   if(mprojmean==0) jprojmean=1;          }/* end jk */ 
          }/* end i */ 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      } /* end i1 */
      } /* end k1 */
   for(cptcov=1;cptcov<=i2;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       k=k+1;    /*free_vector(pp,1,nlstate);*/
       fprintf(ficresf,"\n#******");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       for(j=1;j<=cptcoveff;j++) {  }  /* End of prevalence */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }  /************* Waves Concatenation ***************/
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");  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)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  {
          /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
             Death is a valid wave (if date is known).
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         fprintf(ficresf,"\n");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         and mw[mi+1][i]. dh depends on stepm.
        */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int i, mi, m;
           nhstepm = nhstepm/hstepm;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                 double sum=0., jmean=0.;*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int first;
           oldm=oldms;savm=savms;    int j, k=0,jk, ju, jl;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double sum=0.;
            first=0;
           for (h=0; h<=nhstepm; h++){    jmin=1e+5;
             if (h==(int) (calagedate+YEARM*cpt)) {    jmax=-1;
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    jmean=0.;
             }    for(i=1; i<=imx; i++){
             for(j=1; j<=nlstate+ndeath;j++) {      mi=0;
               kk1=0.;kk2=0;      m=firstpass;
               for(i=1; i<=nlstate;i++) {                    while(s[m][i] <= nlstate){
                 if (mobilav==1)        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          mw[++mi][i]=m;
                 else {        if(m >=lastpass)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          break;
                 }        else
                          m++;
               }      }/* end while */
               if (h==(int)(calagedate+12*cpt)){      if (s[m][i] > nlstate){
                 fprintf(ficresf," %.3f", kk1);        mi++;     /* Death is another wave */
                                /* if(mi==0)  never been interviewed correctly before death */
               }           /* Only death is a correct wave */
             }        mw[mi][i]=m;
           }      }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      wav[i]=mi;
       }      if(mi==0){
     }        nbwarn++;
   }        if(first==0){
                  printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          first=1;
         }
   fclose(ficresf);        if(first==1){
 }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
 /************** Forecasting ******************/        }
 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){      } /* end mi==0 */
      } /* End individuals */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;    for(i=1; i<=imx; i++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      for(mi=1; mi<wav[i];mi++){
   double *popeffectif,*popcount;        if (stepm <=0)
   double ***p3mat,***tabpop,***tabpopprev;          dh[mi][i]=1;
   char filerespop[FILENAMELENGTH];        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if (agedc[i] < 2*AGESUP) {
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   agelim=AGESUP;              if(j==0) j=1;  /* Survives at least one month after exam */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              else if(j<0){
                  nberr++;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  j=1; /* Temporary Dangerous patch */
                  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);
   strcpy(filerespop,"pop");                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]);
   strcat(filerespop,fileres);                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);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              }
     printf("Problem with forecast resultfile: %s\n", filerespop);              k=k+1;
   }              if (j >= jmax){
   printf("Computing forecasting: result on file '%s' \n", filerespop);                jmax=j;
                 ijmax=i;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              }
               if (j <= jmin){
   if (mobilav==1) {                jmin=j;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                ijmin=i;
     movingaverage(agedeb, fage, agemin, mobaverage);              }
   }              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   if (stepm<=12) stepsize=1;            }
            }
   agelim=AGESUP;          else{
              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   hstepm=1;  /*        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]); */
   hstepm=hstepm/stepm;  
              k=k+1;
   if (popforecast==1) {            if (j >= jmax) {
     if((ficpop=fopen(popfile,"r"))==NULL) {              jmax=j;
       printf("Problem with population file : %s\n",popfile);exit(0);              ijmax=i;
     }            }
     popage=ivector(0,AGESUP);            else if (j <= jmin){
     popeffectif=vector(0,AGESUP);              jmin=j;
     popcount=vector(0,AGESUP);              ijmin=i;
                }
     i=1;              /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                if(j<0){
     imx=i;              nberr++;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
   for(cptcov=1;cptcov<=i2;cptcov++){            sum=sum+j;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
       k=k+1;          jk= j/stepm;
       fprintf(ficrespop,"\n#******");          jl= j -jk*stepm;
       for(j=1;j<=cptcoveff;j++) {          ju= j -(jk+1)*stepm;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       }            if(jl==0){
       fprintf(ficrespop,"******\n");              dh[mi][i]=jk;
       fprintf(ficrespop,"# Age");              bh[mi][i]=0;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            }else{ /* We want a negative bias in order to only have interpolation ie
       if (popforecast==1)  fprintf(ficrespop," [Population]");                    * at the price of an extra matrix product in likelihood */
                    dh[mi][i]=jk+1;
       for (cpt=0; cpt<=0;cpt++) {              bh[mi][i]=ju;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              }
                  }else{
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            if(jl <= -ju){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              dh[mi][i]=jk;
           nhstepm = nhstepm/hstepm;              bh[mi][i]=jl;       /* bias is positive if real duration
                                             * is higher than the multiple of stepm and negative otherwise.
           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);              else{
                      dh[mi][i]=jk+1;
           for (h=0; h<=nhstepm; h++){              bh[mi][i]=ju;
             if (h==(int) (calagedate+YEARM*cpt)) {            }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            if(dh[mi][i]==0){
             }              dh[mi][i]=1; /* At least one step */
             for(j=1; j<=nlstate+ndeath;j++) {              bh[mi][i]=ju; /* At least one step */
               kk1=0.;kk2=0;              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
               for(i=1; i<=nlstate;i++) {                          }
                 if (mobilav==1)          } /* end if mle */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        }
                 else {      } /* end wave */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    }
                 }    jmean=sum/k;
               }    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);
               if (h==(int)(calagedate+12*cpt)){    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);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;   }
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  /*********** Tricode ****************************/
               }  void tricode(int *Tvar, int **nbcode, int imx)
             }  {
             for(i=1; i<=nlstate;i++){    
               kk1=0.;    int Ndum[20],ij=1, k, j, i, maxncov=19;
                 for(j=1; j<=nlstate;j++){    int cptcode=0;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    cptcoveff=0; 
                 }   
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    for (k=0; k<maxncov; k++) Ndum[k]=0;
             }    for (k=1; k<=7; k++) ncodemax[k]=0;
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           }                                 modality*/ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         }        Ndum[ij]++; /*store the modality */
       }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
          if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   /******/                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
       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--){      for (i=0; i<=cptcode; i++) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        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 */
           nhstepm = nhstepm/hstepm;      }
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      ij=1; 
           oldm=oldms;savm=savms;      for (i=1; i<=ncodemax[j]; i++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for (k=0; k<= maxncov; k++) {
           for (h=0; h<=nhstepm; h++){          if (Ndum[k] != 0) {
             if (h==(int) (calagedate+YEARM*cpt)) {            nbcode[Tvar[j]][ij]=k; 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            /* 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(j=1; j<=nlstate+ndeath;j++) {            ij++;
               kk1=0.;kk2=0;          }
               for(i=1; i<=nlstate;i++) {                        if (ij > ncodemax[j]) break; 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            }  
               }      } 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    }  
             }  
           }   for (k=0; k< maxncov; k++) Ndum[k]=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }   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];
   }     Ndum[ij]++;
     }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
    ij=1;
   if (popforecast==1) {   for (i=1; i<= maxncov; i++) {
     free_ivector(popage,0,AGESUP);     if((Ndum[i]!=0) && (i<=ncovcol)){
     free_vector(popeffectif,0,AGESUP);       Tvaraff[ij]=i; /*For printing */
     free_vector(popcount,0,AGESUP);       ij++;
   }     }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   fclose(ficrespop);   cptcoveff=ij-1; /*Number of simple covariates*/
 }  }
   
 /***********************************************/  /*********** Health Expectancies ****************/
 /**************** Main Program *****************/  
 /***********************************************/  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   
 int main(int argc, char *argv[])  {
 {    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    double age, agelim, hf;
   double agedeb, agefin,hf;    double ***p3mat;
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double eip;
   
   double fret;    pstamp(ficreseij);
   double **xi,tmp,delta;    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
   double dum; /* Dummy variable */    for(i=1; i<=nlstate;i++){
   double ***p3mat;      for(j=1; j<=nlstate;j++){
   int *indx;        fprintf(ficreseij," e%1d%1d ",i,j);
   char line[MAXLINE], linepar[MAXLINE];      }
   char title[MAXLINE];      fprintf(ficreseij," e%1d. ",i);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    fprintf(ficreseij,"\n");
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    
     if(estepm < stepm){
   char filerest[FILENAMELENGTH];      printf ("Problem %d lower than %d\n",estepm, stepm);
   char fileregp[FILENAMELENGTH];    }
   char popfile[FILENAMELENGTH];    else  hstepm=estepm;   
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    /* We compute the life expectancy from trapezoids spaced every estepm months
   int firstobs=1, lastobs=10;     * This is mainly to measure the difference between two models: for example
   int sdeb, sfin; /* Status at beginning and end */     * if stepm=24 months pijx are given only every 2 years and by summing them
   int c,  h , cpt,l;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   int ju,jl, mi;     * progression in between and thus overestimating or underestimating according
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;     * to the curvature of the survival function. If, for the same date, we 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   int mobilav=0,popforecast=0;     * to compare the new estimate of Life expectancy with the same linear 
   int hstepm, nhstepm;     * hypothesis. A more precise result, taking into account a more precise
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;     * curvature will be obtained if estepm is as small as stepm. */
   
   double bage, fage, age, agelim, agebase;    /* For example we decided to compute the life expectancy with the smallest unit */
   double ftolpl=FTOL;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double **prlim;       nhstepm is the number of hstepm from age to agelim 
   double *severity;       nstepm is the number of stepm from age to agelin. 
   double ***param; /* Matrix of parameters */       Look at hpijx to understand the reason of that which relies in memory size
   double  *p;       and note for a fixed period like estepm months */
   double **matcov; /* Matrix of covariance */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double ***delti3; /* Scale */       survival function given by stepm (the optimization length). Unfortunately it
   double *delti; /* Scale */       means that if the survival funtion is printed only each two years of age and if
   double ***eij, ***vareij;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double **varpl; /* Variances of prevalence limits by age */       results. So we changed our mind and took the option of the best precision.
   double *epj, vepp;    */
   double kk1, kk2;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
      agelim=AGESUP;
     /* nhstepm age range expressed in number of stepm */
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char z[1]="c", occ;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #include <sys/time.h>  
 #include <time.h>    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   /* long total_usecs;  
   struct timeval start_time, end_time;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
   printf("\n%s",version);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   if(argc <=1){         decrease memory allocation */
     printf("\nEnter the parameter file name: ");       printf("%d|",(int)age);fflush(stdout);
     scanf("%s",pathtot);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   }      /* Computing expectancies */
   else{      for(i=1; i<=nlstate;i++)
     strcpy(pathtot,argv[1]);        for(j=1; j<=nlstate;j++)
   }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   /*cygwin_split_path(pathtot,path,optionfile);            
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  /* 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]);*/
   /* cutv(path,optionfile,pathtot,'\\');*/  
           }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      fprintf(ficreseij,"%3.0f",age );
   chdir(path);      for(i=1; i<=nlstate;i++){
   replace(pathc,path);        eip=0;
         for(j=1; j<=nlstate;j++){
 /*-------- arguments in the command line --------*/          eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   strcpy(fileres,"r");        }
   strcat(fileres, optionfilefiname);        fprintf(ficreseij,"%9.4f", eip );
   strcat(fileres,".txt");    /* Other files have txt extension */      }
       fprintf(ficreseij,"\n");
   /*---------arguments file --------*/  
     }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with optionfile %s\n",optionfile);    printf("\n");
     goto end;    fprintf(ficlog,"\n");
   }  
   }
   strcpy(filereso,"o");  
   strcat(filereso,fileres);  void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  {
   }    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
   /* Reads comments: lines beginning with '#' */    */
   while((c=getc(ficpar))=='#' && c!= EOF){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     ungetc(c,ficpar);    double age, agelim, hf;
     fgets(line, MAXLINE, ficpar);    double ***p3matp, ***p3matm, ***varhe;
     puts(line);    double **dnewm,**doldm;
     fputs(line,ficparo);    double *xp, *xm;
   }    double **gp, **gm;
   ungetc(c,ficpar);    double ***gradg, ***trgradg;
     int theta;
   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);  
   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);    double eip, vip;
   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);  
 while((c=getc(ficpar))=='#' && c!= EOF){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     ungetc(c,ficpar);    xp=vector(1,npar);
     fgets(line, MAXLINE, ficpar);    xm=vector(1,npar);
     puts(line);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     fputs(line,ficparo);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   }    
   ungetc(c,ficpar);    pstamp(ficresstdeij);
      fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
        fprintf(ficresstdeij,"# Age");
   covar=matrix(0,NCOVMAX,1,n);    for(i=1; i<=nlstate;i++){
   cptcovn=0;      for(j=1; j<=nlstate;j++)
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
   ncovmodel=2+cptcovn;    }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficresstdeij,"\n");
    
   /* Read guess parameters */    pstamp(ficrescveij);
   /* Reads comments: lines beginning with '#' */    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficrescveij,"# Age");
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=nlstate;j++){
     puts(line);        cptj= (j-1)*nlstate+i;
     fputs(line,ficparo);        for(i2=1; i2<=nlstate;i2++)
   }          for(j2=1; j2<=nlstate;j2++){
   ungetc(c,ficpar);            cptj2= (j2-1)*nlstate+i2;
              if(cptj2 <= cptj)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     for(i=1; i <=nlstate; i++)          }
     for(j=1; j <=nlstate+ndeath-1; j++){      }
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficrescveij,"\n");
       fprintf(ficparo,"%1d%1d",i1,j1);    
       printf("%1d%1d",i,j);    if(estepm < stepm){
       for(k=1; k<=ncovmodel;k++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         fscanf(ficpar," %lf",&param[i][j][k]);    }
         printf(" %lf",param[i][j][k]);    else  hstepm=estepm;   
         fprintf(ficparo," %lf",param[i][j][k]);    /* We compute the life expectancy from trapezoids spaced every estepm months
       }     * This is mainly to measure the difference between two models: for example
       fscanf(ficpar,"\n");     * if stepm=24 months pijx are given only every 2 years and by summing them
       printf("\n");     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficparo,"\n");     * progression in between and thus overestimating or underestimating according
     }     * to the curvature of the survival function. If, for the same date, we 
       * estimate the model with stepm=1 month, we can keep estepm to 24 months
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   p=param[1][1];     * curvature will be obtained if estepm is as small as stepm. */
    
   /* Reads comments: lines beginning with '#' */    /* For example we decided to compute the life expectancy with the smallest unit */
   while((c=getc(ficpar))=='#' && c!= EOF){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     ungetc(c,ficpar);       nhstepm is the number of hstepm from age to agelim 
     fgets(line, MAXLINE, ficpar);       nstepm is the number of stepm from age to agelin. 
     puts(line);       Look at hpijx to understand the reason of that which relies in memory size
     fputs(line,ficparo);       and note for a fixed period like estepm months */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   ungetc(c,ficpar);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       results. So we changed our mind and took the option of the best precision.
   for(i=1; i <=nlstate; i++){    */
     for(j=1; j <=nlstate+ndeath-1; j++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    /* If stepm=6 months */
       fprintf(ficparo,"%1d%1d",i1,j1);    /* nhstepm age range expressed in number of stepm */
       for(k=1; k<=ncovmodel;k++){    agelim=AGESUP;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         printf(" %le",delti3[i][j][k]);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficparo," %le",delti3[i][j][k]);    /* if (stepm >= YEARM) hstepm=1;*/
       }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fscanf(ficpar,"\n");    
       printf("\n");    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo,"\n");    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   delti=delti3[1][1];    gp=matrix(0,nhstepm,1,nlstate*nlstate);
      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    for (age=bage; age<=fage; age ++){ 
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     puts(line);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     fputs(line,ficparo);   
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   ungetc(c,ficpar);  
        /* Computing  Variances of health expectancies */
   matcov=matrix(1,npar,1,npar);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   for(i=1; i <=npar; i++){         decrease memory allocation */
     fscanf(ficpar,"%s",&str);      for(theta=1; theta <=npar; theta++){
     printf("%s",str);        for(i=1; i<=npar; i++){ 
     fprintf(ficparo,"%s",str);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(j=1; j <=i; j++){          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       fscanf(ficpar," %le",&matcov[i][j]);        }
       printf(" %.5le",matcov[i][j]);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficparo," %.5le",matcov[i][j]);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     }    
     fscanf(ficpar,"\n");        for(j=1; j<= nlstate; j++){
     printf("\n");          for(i=1; i<=nlstate; i++){
     fprintf(ficparo,"\n");            for(h=0; h<=nhstepm-1; h++){
   }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   for(i=1; i <=npar; i++)              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     for(j=i+1;j<=npar;j++)            }
       matcov[i][j]=matcov[j][i];          }
            }
   printf("\n");       
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
     /*-------- Rewriting paramater file ----------*/            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
      strcpy(rfileres,"r");    /* "Rparameterfile */          }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      }/* End theta */
      strcat(rfileres,".");    /* */      
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      
     if((ficres =fopen(rfileres,"w"))==NULL) {      for(h=0; h<=nhstepm-1; h++)
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        for(j=1; j<=nlstate*nlstate;j++)
     }          for(theta=1; theta <=npar; theta++)
     fprintf(ficres,"#%s\n",version);            trgradg[h][j][theta]=gradg[h][theta][j];
          
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {       for(ij=1;ij<=nlstate*nlstate;ij++)
       printf("Problem with datafile: %s\n", datafile);goto end;        for(ji=1;ji<=nlstate*nlstate;ji++)
     }          varhe[ij][ji][(int)age] =0.;
   
     n= lastobs;       printf("%d|",(int)age);fflush(stdout);
     severity = vector(1,maxwav);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     outcome=imatrix(1,maxwav+1,1,n);       for(h=0;h<=nhstepm-1;h++){
     num=ivector(1,n);        for(k=0;k<=nhstepm-1;k++){
     moisnais=vector(1,n);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     annais=vector(1,n);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     moisdc=vector(1,n);          for(ij=1;ij<=nlstate*nlstate;ij++)
     andc=vector(1,n);            for(ji=1;ji<=nlstate*nlstate;ji++)
     agedc=vector(1,n);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     cod=ivector(1,n);        }
     weight=vector(1,n);      }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      /* Computing expectancies */
     mint=matrix(1,maxwav,1,n);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     anint=matrix(1,maxwav,1,n);      for(i=1; i<=nlstate;i++)
     s=imatrix(1,maxwav+1,1,n);        for(j=1; j<=nlstate;j++)
     adl=imatrix(1,maxwav+1,1,n);              for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     tab=ivector(1,NCOVMAX);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     ncodemax=ivector(1,8);            
             /* 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]);*/
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {          }
       if ((i >= firstobs) && (i <=lastobs)) {  
              fprintf(ficresstdeij,"%3.0f",age );
         for (j=maxwav;j>=1;j--){      for(i=1; i<=nlstate;i++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        eip=0.;
           strcpy(line,stra);        vip=0.;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<=nlstate;j++){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          eip += eij[i][j][(int)age];
         }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                    vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficresstdeij,"\n");
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficrescveij,"%3.0f",age );
         for (j=ncov;j>=1;j--){      for(i=1; i<=nlstate;i++)
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<=nlstate;j++){
         }          cptj= (j-1)*nlstate+i;
         num[i]=atol(stra);          for(i2=1; i2<=nlstate;i2++)
                    for(j2=1; j2<=nlstate;j2++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              cptj2= (j2-1)*nlstate+i2;
           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;}*/              if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         i=i+1;            }
       }        }
     }      fprintf(ficrescveij,"\n");
     /* printf("ii=%d", ij);     
        scanf("%d",i);*/    }
   imx=i-1; /* Number of individuals */    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   /* for (i=1; i<=imx; i++){    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    printf("\n");
     fprintf(ficlog,"\n");
     for (i=1; i<=imx; i++)  
     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]));*/    free_vector(xm,1,npar);
     free_vector(xp,1,npar);
   /* Calculation of the number of parameter from char model*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   Tvar=ivector(1,15);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   Tprod=ivector(1,15);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   Tvaraff=ivector(1,15);  }
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);        /************ 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[])
   if (strlen(model) >1){  {
     j=0, j1=0, k1=1, k2=1;    /* Variance of health expectancies */
     j=nbocc(model,'+');    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     j1=nbocc(model,'*');    /* double **newm;*/
     cptcovn=j+1;    double **dnewm,**doldm;
     cptcovprod=j1;    double **dnewmp,**doldmp;
        int i, j, nhstepm, hstepm, h, nstepm ;
        int k, cptcode;
     strcpy(modelsav,model);    double *xp;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double **gp, **gm;  /* for var eij */
       printf("Error. Non available option model=%s ",model);    double ***gradg, ***trgradg; /*for var eij */
       goto end;    double **gradgp, **trgradgp; /* for var p point j */
     }    double *gpp, *gmp; /* for var p point j */
        double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     for(i=(j+1); i>=1;i--){    double ***p3mat;
       cutv(stra,strb,modelsav,'+');    double age,agelim, hf;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    double ***mobaverage;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    int theta;
       /*scanf("%d",i);*/    char digit[4];
       if (strchr(strb,'*')) {    char digitp[25];
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {    char fileresprobmorprev[FILENAMELENGTH];
           cptcovprod--;  
           cutv(strb,stre,strd,'V');    if(popbased==1){
           Tvar[i]=atoi(stre);      if(mobilav!=0)
           cptcovage++;        strcpy(digitp,"-populbased-mobilav-");
             Tage[cptcovage]=i;      else strcpy(digitp,"-populbased-nomobil-");
             /*printf("stre=%s ", stre);*/    }
         }    else 
         else if (strcmp(strd,"age")==0) {      strcpy(digitp,"-stablbased-");
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    if (mobilav!=0) {
           Tvar[i]=atoi(stre);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cptcovage++;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           Tage[cptcovage]=i;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         else {      }
           cutv(strb,stre,strc,'V');    }
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');    strcpy(fileresprobmorprev,"prmorprev"); 
           Tprod[k1]=i;    sprintf(digit,"%-d",ij);
           Tvard[k1][1]=atoi(strc);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           Tvard[k1][2]=atoi(stre);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           Tvar[cptcovn+k2]=Tvard[k1][1];    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    strcat(fileresprobmorprev,fileres);
           for (k=1; k<=lastobs;k++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           k1++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           k2=k2+2;    }
         }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }   
       else {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    pstamp(ficresprobmorprev);
        /*  scanf("%d",i);*/    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);
       cutv(strd,strc,strb,'V');    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       Tvar[i]=atoi(strc);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       }      fprintf(ficresprobmorprev," p.%-d SE",j);
       strcpy(modelsav,stra);        for(i=1; i<=nlstate;i++)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         scanf("%d",i);*/    }  
     }    fprintf(ficresprobmorprev,"\n");
 }    fprintf(ficgp,"\n# Routine varevsij");
      /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    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");
   printf("cptcovprod=%d ", cptcovprod);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   scanf("%d ",i);*/  /*   } */
     fclose(fic);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     /*  if(mle==1){*/    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if (weightopt != 1) { /* Maximisation without weights*/    if(popbased==1)
       for(i=1;i<=n;i++) weight[i]=1.0;      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
     }    else
     /*-calculation of age at interview from date of interview and age at death -*/      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     agev=matrix(1,maxwav,1,imx);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
    for (i=1; i<=imx; i++)      for(j=1; j<=nlstate;j++)
      for(m=2; (m<= maxwav); m++)        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fprintf(ficresvij,"\n");
          anint[m][i]=9999;  
          s[m][i]=-1;    xp=vector(1,npar);
        }    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     for (i=1; i<=imx; i++)  {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           if (s[m][i] == nlstate+1) {    gpp=vector(nlstate+1,nlstate+ndeath);
             if(agedc[i]>0)    gmp=vector(nlstate+1,nlstate+ndeath);
               if(moisdc[i]!=99 && andc[i]!=9999)    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
               agev[m][i]=agedc[i];    
             else {    if(estepm < stepm){
               if (andc[i]!=9999){      printf ("Problem %d lower than %d\n",estepm, stepm);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    }
               agev[m][i]=-1;    else  hstepm=estepm;   
               }    /* 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 
           else if(s[m][i] !=9){ /* Should no more exist */       nstepm is the number of stepm from age to agelin. 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);       Look at hpijx to understand the reason of that which relies in memory size
             if(mint[m][i]==99 || anint[m][i]==9999)       and note for a fixed period like k years */
               agev[m][i]=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             else if(agev[m][i] <agemin){       survival function given by stepm (the optimization length). Unfortunately it
               agemin=agev[m][i];       means that if the survival funtion is printed every two years of age and if
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             }       results. So we changed our mind and took the option of the best precision.
             else if(agev[m][i] >agemax){    */
               agemax=agev[m][i];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    agelim = AGESUP;
             }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             /*agev[m][i]=anint[m][i]-annais[i];*/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             /*   agev[m][i] = age[i]+2*m;*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           else { /* =9 */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
             agev[m][i]=1;      gp=matrix(0,nhstepm,1,nlstate);
             s[m][i]=-1;      gm=matrix(0,nhstepm,1,nlstate);
           }  
         }  
         else /*= 0 Unknown */      for(theta=1; theta <=npar; theta++){
           agev[m][i]=1;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            }
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for (i=1; i<=imx; i++)  {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {        if (popbased==1) {
           printf("Error: Wrong value in nlstate or ndeath\n");            if(mobilav ==0){
           goto end;            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=probs[(int)age][i][ij];
       }          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          }
         }
     free_vector(severity,1,maxwav);    
     free_imatrix(outcome,1,maxwav+1,1,n);        for(j=1; j<= nlstate; j++){
     free_vector(moisnais,1,n);          for(h=0; h<=nhstepm; h++){
     free_vector(annais,1,n);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     /* free_matrix(mint,1,maxwav,1,n);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
        free_matrix(anint,1,maxwav,1,n);*/          }
     free_vector(moisdc,1,n);        }
     free_vector(andc,1,n);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
               as a weighted average of prlim.
     wav=ivector(1,imx);        */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
                gpp[j] += prlim[i][i]*p3mat[i][j][1];
     /* Concatenates waves */        }    
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       Tcode=ivector(1,100);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       ncodemax[1]=1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   
              if (popbased==1) {
    codtab=imatrix(1,100,1,10);          if(mobilav ==0){
    h=0;            for(i=1; i<=nlstate;i++)
    m=pow(2,cptcoveff);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
    for(k=1;k<=cptcoveff; k++){            for(i=1; i<=nlstate;i++)
      for(i=1; i <=(m/pow(2,k));i++){              prlim[i][i]=mobaverage[(int)age][i][ij];
        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;        for(j=1; j<= nlstate; j++){
          }          for(h=0; h<=nhstepm; h++){
        }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
    }          }
         }
         /* This for computing probability of death (h=1 means
    /*for(i=1; i <=m ;i++){           computed over hstepm matrices product = hstepm*stepm months) 
      for(k=1; k <=cptcovn; k++){           as a weighted average of prlim.
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        */
      }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      printf("\n");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
    }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
    scanf("%d",i);*/        }    
            /* end probability of death */
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
              }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
            } /* End theta */
     /* 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] */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
       for(h=0; h<=nhstepm; h++) /* veij */
     if(mle==1){        for(j=1; j<=nlstate;j++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          for(theta=1; theta <=npar; theta++)
     }            trgradg[h][j][theta]=gradg[h][theta][j];
      
     /*--------- results files --------------*/      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     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);        for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
     
    jk=1;  
    fprintf(ficres,"# Parameters\n");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    printf("# Parameters\n");      for(i=1;i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){        for(j=1;j<=nlstate;j++)
      for(k=1; k <=(nlstate+ndeath); k++){          vareij[i][j][(int)age] =0.;
        if (k != i)  
          {      for(h=0;h<=nhstepm;h++){
            printf("%d%d ",i,k);        for(k=0;k<=nhstepm;k++){
            fprintf(ficres,"%1d%1d ",i,k);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            for(j=1; j <=ncovmodel; j++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
              printf("%f ",p[jk]);          for(i=1;i<=nlstate;i++)
              fprintf(ficres,"%f ",p[jk]);            for(j=1;j<=nlstate;j++)
              jk++;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
            }        }
            printf("\n");      }
            fprintf(ficres,"\n");    
          }      /* pptj */
      }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
    }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
  if(mle==1){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     /* Computing hessian and covariance matrix */        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     ftolhess=ftol; /* Usually correct */          varppt[j][i]=doldmp[j][i];
     hesscov(matcov, p, npar, delti, ftolhess, func);      /* end ppptj */
  }      /*  x centered again */
     fprintf(ficres,"# Scales\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     printf("# Scales\n");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
      for(i=1,jk=1; i <=nlstate; i++){   
       for(j=1; j <=nlstate+ndeath; j++){      if (popbased==1) {
         if (j!=i) {        if(mobilav ==0){
           fprintf(ficres,"%1d%1d",i,j);          for(i=1; i<=nlstate;i++)
           printf("%1d%1d",i,j);            prlim[i][i]=probs[(int)age][i][ij];
           for(k=1; k<=ncovmodel;k++){        }else{ /* mobilav */ 
             printf(" %.5e",delti[jk]);          for(i=1; i<=nlstate;i++)
             fprintf(ficres," %.5e",delti[jk]);            prlim[i][i]=mobaverage[(int)age][i][ij];
             jk++;        }
           }      }
           printf("\n");               
           fprintf(ficres,"\n");      /* This for computing probability of death (h=1 means
         }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       }         as a weighted average of prlim.
      }      */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
     k=1;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     fprintf(ficres,"# Covariance\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     printf("# Covariance\n");      }    
     for(i=1;i<=npar;i++){      /* end probability of death */
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       fprintf(ficres,"%3d",i);        for(i=1; i<=nlstate;i++){
       printf("%3d",i);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       for(j=1; j<=i;j++){        }
         fprintf(ficres," %.5e",matcov[i][j]);      } 
         printf(" %.5e",matcov[i][j]);      fprintf(ficresprobmorprev,"\n");
       }  
       fprintf(ficres,"\n");      fprintf(ficresvij,"%.0f ",age );
       printf("\n");      for(i=1; i<=nlstate;i++)
       k++;        for(j=1; j<=nlstate;j++){
     }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
            }
     while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresvij,"\n");
       ungetc(c,ficpar);      free_matrix(gp,0,nhstepm,1,nlstate);
       fgets(line, MAXLINE, ficpar);      free_matrix(gm,0,nhstepm,1,nlstate);
       puts(line);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fputs(line,ficparo);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);    } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);    free_vector(gmp,nlstate+1,nlstate+ndeath);
        free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     if (fage <= 2) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       bage = agemin;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       fage = agemaxpar;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     ungetc(c,ficpar);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fgets(line, MAXLINE, ficpar);    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);
     puts(line);    /*  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);
     fputs(line,ficparo);  */
   }  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   ungetc(c,ficpar);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    free_vector(xp,1,npar);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    free_matrix(doldm,1,nlstate,1,nlstate);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    free_matrix(dnewm,1,nlstate,1,npar);
          free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     ungetc(c,ficpar);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     puts(line);    fclose(ficresprobmorprev);
     fputs(line,ficparo);    fflush(ficgp);
   }    fflush(fichtm); 
   ungetc(c,ficpar);  }  /* end varevsij */
    
   /************ Variance of prevlim ******************/
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  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[])
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  {
     /* Variance of prevalence limit */
   fscanf(ficpar,"pop_based=%d\n",&popbased);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   fprintf(ficparo,"pop_based=%d\n",popbased);      double **newm;
   fprintf(ficres,"pop_based=%d\n",popbased);      double **dnewm,**doldm;
      int i, j, nhstepm, hstepm;
   while((c=getc(ficpar))=='#' && c!= EOF){    int k, cptcode;
     ungetc(c,ficpar);    double *xp;
     fgets(line, MAXLINE, ficpar);    double *gp, *gm;
     puts(line);    double **gradg, **trgradg;
     fputs(line,ficparo);    double age,agelim;
   }    int theta;
   ungetc(c,ficpar);    
     pstamp(ficresvpl);
   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(ficresvpl,"# Standard deviation of period (stable) prevalences \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(ficresvpl,"# Age");
 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);    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    xp=vector(1,npar);
     fgets(line, MAXLINE, ficpar);    dnewm=matrix(1,nlstate,1,npar);
     puts(line);    doldm=matrix(1,nlstate,1,nlstate);
     fputs(line,ficparo);    
   }    hstepm=1*YEARM; /* Every year of age */
   ungetc(c,ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
 /*------------ gnuplot -------------*/      gm=vector(1,nlstate);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);  
        for(theta=1; theta <=npar; theta++){
 /*------------ free_vector  -------------*/        for(i=1; i<=npar; i++){ /* Computes gradient */
  chdir(path);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
  free_ivector(wav,1,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(i=1;i<=nlstate;i++)
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            gp[i] = prlim[i][i];
  free_ivector(num,1,n);      
  free_vector(agedc,1,n);        for(i=1; i<=npar; i++) /* Computes gradient */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
  fclose(ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  fclose(ficres);        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
 /*--------- index.htm --------*/  
         for(i=1;i<=nlstate;i++)
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
    
   /*--------------- Prevalence limit --------------*/      trgradg =matrix(1,nlstate,1,npar);
    
   strcpy(filerespl,"pl");      for(j=1; j<=nlstate;j++)
   strcat(filerespl,fileres);        for(theta=1; theta <=npar; theta++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          trgradg[j][theta]=gradg[theta][j];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }      for(i=1;i<=nlstate;i++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        varpl[i][(int)age] =0.;
   fprintf(ficrespl,"#Prevalence limit\n");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   fprintf(ficrespl,"#Age ");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(i=1;i<=nlstate;i++)
   fprintf(ficrespl,"\n");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   prlim=matrix(1,nlstate,1,nlstate);      fprintf(ficresvpl,"%.0f ",age );
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficresvpl,"\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      free_vector(gp,1,nlstate);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      free_vector(gm,1,nlstate);
   k=0;      free_matrix(gradg,1,npar,1,nlstate);
   agebase=agemin;      free_matrix(trgradg,1,nlstate,1,npar);
   agelim=agemaxpar;    } /* End age */
   ftolpl=1.e-10;  
   i1=cptcoveff;    free_vector(xp,1,npar);
   if (cptcovn < 1){i1=1;}    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   for(cptcov=1;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]);*/  /************ Variance of one-step probabilities  ******************/
         fprintf(ficrespl,"\n#******");  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[])
         for(j=1;j<=cptcoveff;j++)  {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int i, j=0,  i1, k1, l1, t, tj;
         fprintf(ficrespl,"******\n");    int k2, l2, j1,  z1;
            int k=0,l, cptcode;
         for (age=agebase; age<=agelim; age++){    int first=1, first1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           fprintf(ficrespl,"%.0f",age );    double **dnewm,**doldm;
           for(i=1; i<=nlstate;i++)    double *xp;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double *gp, *gm;
           fprintf(ficrespl,"\n");    double **gradg, **trgradg;
         }    double **mu;
       }    double age,agelim, cov[NCOVMAX];
     }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   fclose(ficrespl);    int theta;
     char fileresprob[FILENAMELENGTH];
   /*------------- h Pij x at various ages ------------*/    char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double ***varpij;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }    strcpy(fileresprob,"prob"); 
   printf("Computing pij: result on file '%s' \n", filerespij);    strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;      printf("Problem with resultfile: %s\n", fileresprob);
   /*if (stepm<=24) stepsize=2;*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   agelim=AGESUP;    strcpy(fileresprobcov,"probcov"); 
   hstepm=stepsize*YEARM; /* Every year of age */    strcat(fileresprobcov,fileres);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
   k=0;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcpy(fileresprobcor,"probcor"); 
       k=k+1;    strcat(fileresprobcor,fileres);
         fprintf(ficrespij,"\n#****** ");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         for(j=1;j<=cptcoveff;j++)      printf("Problem with resultfile: %s\n", fileresprobcor);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         fprintf(ficrespij,"******\n");    }
            printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           oldm=oldms;savm=savms;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      pstamp(ficresprob);
           fprintf(ficrespij,"# Age");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           for(i=1; i<=nlstate;i++)    fprintf(ficresprob,"# Age");
             for(j=1; j<=nlstate+ndeath;j++)    pstamp(ficresprobcov);
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           fprintf(ficrespij,"\n");    fprintf(ficresprobcov,"# Age");
           for (h=0; h<=nhstepm; h++){    pstamp(ficresprobcor);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
             for(i=1; i<=nlstate;i++)    fprintf(ficresprobcor,"# Age");
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    for(i=1; i<=nlstate;i++)
           }      for(j=1; j<=(nlstate+ndeath);j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           fprintf(ficrespij,"\n");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     }      }  
   }   /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    fprintf(ficresprobcor,"\n");
    */
   fclose(ficrespij);   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   /*---------- Forecasting ------------------*/    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   if((stepm == 1) && (model==".")){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    first=1;
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    fprintf(ficgp,"\n# Routine varprob");
     free_matrix(mint,1,maxwav,1,n);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    fprintf(fichtm,"\n");
     free_vector(weight,1,n);}  
   else{    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     erreur=108;    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     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);    file %s<br>\n",optionfilehtmcov);
   }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
    and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   /*---------- Health expectancies and variances ------------*/    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   strcpy(filerest,"t");  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   strcat(filerest,fileres);  standard deviations wide on each axis. <br>\
   if((ficrest=fopen(filerest,"w"))==NULL) {   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   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");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
     cov[1]=1;
     tj=cptcoveff;
   strcpy(filerese,"e");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   strcat(filerese,fileres);    j1=0;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    for(t=1; t<=tj;t++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(i1=1; i1<=ncodemax[t];i1++){ 
   }        j1++;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
  strcpy(fileresv,"v");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(fileresv,fileres);          fprintf(ficresprob, "**********\n#\n");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          fprintf(ficresprobcov, "\n#********** Variable "); 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprobcov, "**********\n#\n");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          
           fprintf(ficgp, "\n#********** Variable "); 
   k=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficgp, "**********\n#\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          
       k=k+1;          
       fprintf(ficrest,"\n#****** ");          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       for(j=1;j<=cptcoveff;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       fprintf(ficrest,"******\n");          
           fprintf(ficresprobcor, "\n#********** Variable ");    
       fprintf(ficreseij,"\n#****** ");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcor, "**********\n#");    
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        }
       fprintf(ficreseij,"******\n");        
         for (age=bage; age<=fage; age ++){ 
       fprintf(ficresvij,"\n#****** ");          cov[2]=age;
       for(j=1;j<=cptcoveff;j++)          for (k=1; k<=cptcovn;k++) {
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       fprintf(ficresvij,"******\n");          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for (k=1; k<=cptcovprod;k++)
       oldm=oldms;savm=savms;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       oldm=oldms;savm=savms;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          gp=vector(1,(nlstate)*(nlstate+ndeath));
              gm=vector(1,(nlstate)*(nlstate+ndeath));
       
            for(theta=1; theta <=npar; theta++){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            for(i=1; i<=npar; i++)
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       fprintf(ficrest,"\n");            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
       hf=1;            
       if (stepm >= YEARM) hf=stepm/YEARM;            k=0;
       epj=vector(1,nlstate+1);            for(i=1; i<= (nlstate); i++){
       for(age=bage; age <=fage ;age++){              for(j=1; j<=(nlstate+ndeath);j++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                k=k+1;
         if (popbased==1) {                gp[k]=pmmij[i][j];
           for(i=1; i<=nlstate;i++)              }
             prlim[i][i]=probs[(int)age][i][k];            }
         }            
                    for(i=1; i<=npar; i++)
         fprintf(ficrest," %.0f",age);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];            k=0;
           }            for(i=1; i<=(nlstate); i++){
           epj[nlstate+1] +=epj[j];              for(j=1; j<=(nlstate+ndeath);j++){
         }                k=k+1;
         for(i=1, vepp=0.;i <=nlstate;i++)                gm[k]=pmmij[i][j];
           for(j=1;j <=nlstate;j++)              }
             vepp += vareij[i][j][(int)age];            }
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));       
         for(j=1;j <=nlstate;j++){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         }          }
         fprintf(ficrest,"\n");  
       }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     }            for(theta=1; theta <=npar; theta++)
   }              trgradg[j][theta]=gradg[theta][j];
           
   fclose(ficreseij);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   fclose(ficresvij);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   fclose(ficrest);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   fclose(ficpar);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   free_vector(epj,1,nlstate+1);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   /*------- Variance limit prevalence------*/    
           pmij(pmmij,cov,ncovmodel,x,nlstate);
   strcpy(fileresvpl,"vpl");          
   strcat(fileresvpl,fileres);          k=0;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          for(i=1; i<=(nlstate); i++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            for(j=1; j<=(nlstate+ndeath);j++){
     exit(0);              k=k+1;
   }              mu[k][(int) age]=pmmij[i][j];
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            }
           }
   k=0;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   for(cptcov=1;cptcov<=i1;cptcov++){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              varpij[i][j][(int)age] = doldm[i][j];
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");          /*printf("\n%d ",(int)age);
       for(j=1;j<=cptcoveff;j++)            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fprintf(ficresvpl,"******\n");            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                  }*/
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;          fprintf(ficresprob,"\n%d ",(int)age);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          fprintf(ficresprobcov,"\n%d ",(int)age);
     }          fprintf(ficresprobcor,"\n%d ",(int)age);
  }  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   fclose(ficresvpl);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /*---------- End : free ----------------*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          i=0;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          for (k=1; k<=(nlstate);k++){
              for (l=1; l<=(nlstate+ndeath);l++){ 
                i=i++;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);              for (j=1; j<=i;j++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                  fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   free_matrix(matcov,1,npar,1,npar);              }
   free_vector(delti,1,npar);            }
   free_matrix(agev,1,maxwav,1,imx);          }/* end of loop for state */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        } /* end of loop for age */
   
   if(erreur >0)        /* Confidence intervalle of pij  */
     printf("End of Imach with error %d\n",erreur);        /*
   else   printf("End of Imach\n");          fprintf(ficgp,"\nset noparametric;unset label");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   /* 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);*/          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);
   /*printf("Total time was %d uSec.\n", total_usecs);*/          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   /*------ End -----------*/          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
  end:  
 #ifdef windows        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   /* chdir(pathcd);*/        first1=1;
 #endif        for (k2=1; k2<=(nlstate);k2++){
  /*system("wgnuplot graph.plt");*/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
  /*system("../gp37mgw/wgnuplot graph.plt");*/            if(l2==k2) continue;
  /*system("cd ../gp37mgw");*/            j=(k2-1)*(nlstate+ndeath)+l2;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            for (k1=1; k1<=(nlstate);k1++){
  strcpy(plotcmd,GNUPLOTPROGRAM);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
  strcat(plotcmd," ");                if(l1==k1) continue;
  strcat(plotcmd,optionfilegnuplot);                i=(k1-1)*(nlstate+ndeath)+l1;
  system(plotcmd);                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
 #ifdef windows                  if ((int)age %5==0){
   while (z[0] != 'q') {                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     chdir(path);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     scanf("%s",z);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     if (z[0] == 'c') system("./imach");                    mu2=mu[j][(int) age]/stepm*YEARM;
     else if (z[0] == 'e') {                    c12=cv12/sqrt(v1*v2);
       chdir(path);                    /* Computing eigen value of matrix of covariance */
       system(optionfilehtm);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     else if (z[0] == 'q') exit(0);                    /* Eigen vectors */
   }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 #endif                    /*v21=sqrt(1.-v11*v11); *//* error */
 }                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (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); */
         k=2+(nlstate+1)*(cpt-1);
         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+i,cpt,i+1);
           /*      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);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* 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];
     char dummy[]="                         ";
     /*  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]; 
     char **bp, *tok, *val; /* pathtot */
     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  *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: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     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, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,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,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,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,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         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,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,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, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\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,linei, i,line,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 */
     fclose(fic);
     /* 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);*/
   
       /*  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\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\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,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             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]=0.0268; p[NDIM]=0.083;
       /*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  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (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*/
       pstamp(ficrespij);
       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 Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: 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(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       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#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\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, strstart);  
           cvevsij(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);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state ( 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(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (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(prlim,1,nlstate,1,nlstate);
       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);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     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);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.30  
changed lines
  Added in v.1.117


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