Diff for /imach/src/imach.c between versions 1.36 and 1.120

version 1.36, 2002/03/29 15:27:27 version 1.120, 2006/03/16 15:10:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.120  2006/03/16 15:10:38  lievre
      (Module): refinements in the computation of lli if
   This program computes Healthy Life Expectancies from    status=-2 in order to have more reliable computation if stepm is
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    not 1 month. Version 0.98f
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.119  2006/03/15 17:42:26  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): Bug if status = -2, the loglikelihood was
   second wave of interviews ("longitudinal") which measure each change    computed as likelihood omitting the logarithm. Version O.98e
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.118  2006/03/14 18:20:07  brouard
   model. More health states you consider, more time is necessary to reach the    (Module): varevsij Comments added explaining the second
   Maximum Likelihood of the parameters involved in the model.  The    table of variances if popbased=1 .
   simplest model is the multinomial logistic model where pij is the    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   probabibility to be observed in state j at the second wave    (Module): Function pstamp added
   conditional to be observed in state i at the first wave. Therefore    (Module): Version 0.98d
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.117  2006/03/14 17:16:22  brouard
   complex model than "constant and age", you should modify the program    (Module): varevsij Comments added explaining the second
   where the markup *Covariates have to be included here again* invites    table of variances if popbased=1 .
   you to do it.  More covariates you add, slower the    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   convergence.    (Module): Function pstamp added
     (Module): Version 0.98d
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.116  2006/03/06 10:29:27  brouard
   identical for each individual. Also, if a individual missed an    (Module): Variance-covariance wrong links and
   intermediate interview, the information is lost, but taken into    varian-covariance of ej. is needed (Saito).
   account using an interpolation or extrapolation.    
     Revision 1.115  2006/02/27 12:17:45  brouard
   hPijx is the probability to be observed in state i at age x+h    (Module): One freematrix added in mlikeli! 0.98c
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.114  2006/02/26 12:57:58  brouard
   states. This elementary transition (by month or quarter trimester,    (Module): Some improvements in processing parameter
   semester or year) is model as a multinomial logistic.  The hPx    filename with strsep.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.113  2006/02/24 14:20:24  brouard
   hPijx.    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
   Also this programme outputs the covariance matrix of the parameters but also    allocation too.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.112  2006/01/30 09:55:26  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): Back to gnuplot.exe instead of wgnuplot.exe
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.111  2006/01/25 20:38:18  brouard
   from the European Union.    (Module): Lots of cleaning and bugs added (Gompertz)
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Comments can be added in data file. Missing date values
   software can be distributed freely for non commercial use. Latest version    can be a simple dot '.'.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.110  2006/01/25 00:51:50  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
 #include <math.h>  
 #include <stdio.h>    Revision 1.109  2006/01/24 19:37:15  brouard
 #include <stdlib.h>    (Module): Comments (lines starting with a #) are allowed in data.
 #include <unistd.h>  
     Revision 1.108  2006/01/19 18:05:42  lievre
 #define MAXLINE 256    Gnuplot problem appeared...
 #define GNUPLOTPROGRAM "wgnuplot"    To be fixed
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.107  2006/01/19 16:20:37  brouard
 /*#define DEBUG*/    Test existence of gnuplot in imach path
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.106  2006/01/19 13:24:36  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Some cleaning and links added in html output
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.105  2006/01/05 20:23:19  lievre
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    *** empty log message ***
   
 #define NINTERVMAX 8    Revision 1.104  2005/09/30 16:11:43  lievre
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): sump fixed, loop imx fixed, and simplifications.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): If the status is missing at the last wave but we know
 #define NCOVMAX 8 /* Maximum number of covariates */    that the person is alive, then we can code his/her status as -2
 #define MAXN 20000    (instead of missing=-1 in earlier versions) and his/her
 #define YEARM 12. /* Number of months per year */    contributions to the likelihood is 1 - Prob of dying from last
 #define AGESUP 130    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define AGEBASE 40    the healthy state at last known wave). Version is 0.98
   
     Revision 1.103  2005/09/30 15:54:49  lievre
 int erreur; /* Error number */    (Module): sump fixed, loop imx fixed, and simplifications.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.102  2004/09/15 17:31:30  brouard
 int npar=NPARMAX;    Add the possibility to read data file including tab characters.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.101  2004/09/15 10:38:38  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Fix on curr_time
 int popbased=0;  
     Revision 1.100  2004/07/12 18:29:06  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Add version for Mac OS X. Just define UNIX in Makefile
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.99  2004/06/05 08:57:40  brouard
 int mle, weightopt;    *** empty log message ***
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.98  2004/05/16 15:05:56  brouard
 double jmean; /* Mean space between 2 waves */    New version 0.97 . First attempt to estimate force of mortality
 double **oldm, **newm, **savm; /* Working pointers to matrices */    directly from the data i.e. without the need of knowing the health
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    state at each age, but using a Gompertz model: log u =a + b*age .
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    This is the basic analysis of mortality and should be done before any
 FILE *ficgp,*ficresprob,*ficpop;    other analysis, in order to test if the mortality estimated from the
 FILE *ficreseij;    cross-longitudinal survey is different from the mortality estimated
   char filerese[FILENAMELENGTH];    from other sources like vital statistic data.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    The same imach parameter file can be used but the option for mle should be -3.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
 #define NR_END 1  
 #define FREE_ARG char*    The output is very simple: only an estimate of the intercept and of
 #define FTOL 1.0e-10    the slope with 95% confident intervals.
   
 #define NRANSI    Current limitations:
 #define ITMAX 200    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define TOL 2.0e-4    B) There is no computation of Life Expectancy nor Life Table.
   
 #define CGOLD 0.3819660    Revision 1.97  2004/02/20 13:25:42  lievre
 #define ZEPS 1.0e-10    Version 0.96d. Population forecasting command line is (temporarily)
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    suppressed.
   
 #define GOLD 1.618034    Revision 1.96  2003/07/15 15:38:55  brouard
 #define GLIMIT 100.0    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define TINY 1.0e-20    rewritten within the same printf. Workaround: many printfs.
   
 static double maxarg1,maxarg2;    Revision 1.95  2003/07/08 07:54:34  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Repository):
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Repository): Using imachwizard code to output a more meaningful covariance
      matrix (cov(a12,c31) instead of numbers.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.93  2003/06/25 16:33:55  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 int imx;    (Module): Version 0.96b
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 int estepm;    exist so I changed back to asctime which exists.
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.91  2003/06/25 15:30:29  brouard
 int m,nb;    * imach.c (Repository): Duplicated warning errors corrected.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Repository): Elapsed time after each iteration is now output. It
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    helps to forecast when convergence will be reached. Elapsed time
 double **pmmij, ***probs, ***mobaverage;    is stamped in powell.  We created a new html file for the graphs
 double dateintmean=0;    concerning matrix of covariance. It has extension -cov.htm.
   
 double *weight;    Revision 1.90  2003/06/24 12:34:15  brouard
 int **s; /* Status */    (Module): Some bugs corrected for windows. Also, when
 double *agedc, **covar, idx;    mle=-1 a template is output in file "or"mypar.txt with the design
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    of the covariance matrix to be input.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.89  2003/06/24 12:30:52  brouard
 double ftolhess; /* Tolerance for computing hessian */    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /**************** split *************************/    of the covariance matrix to be input.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.88  2003/06/23 17:54:56  brouard
    char *s;                             /* pointer */    * 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.
    int  l1, l2;                         /* length counters */  
     Revision 1.87  2003/06/18 12:26:01  brouard
    l1 = strlen( path );                 /* length of path */    Version 0.96
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.86  2003/06/17 20:04:08  brouard
    s = strrchr( path, '\\' );           /* find last / */    (Module): Change position of html and gnuplot routines and added
 #else    routine fileappend.
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.85  2003/06/17 13:12:43  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Repository): Check when date of death was earlier that
 #if     defined(__bsd__)                /* get current working directory */    current date of interview. It may happen when the death was just
       extern char       *getwd( );    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
       if ( getwd( dirc ) == NULL ) {    assuming that the date of death was just one stepm after the
 #else    interview.
       extern char       *getcwd( );    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    memory allocation. But we also truncated to 8 characters (left
 #endif    truncation)
          return( GLOCK_ERROR_GETCWD );    (Repository): No more line truncation errors.
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.84  2003/06/13 21:44:43  brouard
    } else {                             /* strip direcotry from path */    * imach.c (Repository): Replace "freqsummary" at a correct
       s++;                              /* after this, the filename */    place. It differs from routine "prevalence" which may be called
       l2 = strlen( s );                 /* length of filename */    many times. Probs is memory consuming and must be used with
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    parcimony.
       strcpy( name, s );                /* save file name */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.83  2003/06/10 13:39:11  lievre
    }    *** empty log message ***
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.82  2003/06/05 15:57:20  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Add log in  imach.c and  fullversion number is now printed.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  */
 #endif  /*
    s = strrchr( name, '.' );            /* find last / */     Interpolated Markov Chain
    s++;  
    strcpy(ext,s);                       /* save extension */    Short summary of the programme:
    l1= strlen( name);    
    l2= strlen( s)+1;    This program computes Healthy Life Expectancies from
    strncpy( finame, name, l1-l2);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    finame[l1-l2]= 0;    first survey ("cross") where individuals from different ages are
    return( 0 );                         /* we're done */    interviewed on their health status or degree of disability (in the
 }    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 /******************************************/    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 void replace(char *s, char*t)    Maximum Likelihood of the parameters involved in the model.  The
 {    simplest model is the multinomial logistic model where pij is the
   int i;    probability to be observed in state j at the second wave
   int lg=20;    conditional to be observed in state i at the first wave. Therefore
   i=0;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   lg=strlen(t);    'age' is age and 'sex' is a covariate. If you want to have a more
   for(i=0; i<= lg; i++) {    complex model than "constant and age", you should modify the program
     (s[i] = t[i]);    where the markup *Covariates have to be included here again* invites
     if (t[i]== '\\') s[i]='/';    you to do it.  More covariates you add, slower the
   }    convergence.
 }  
     The advantage of this computer programme, compared to a simple
 int nbocc(char *s, char occ)    multinomial logistic model, is clear when the delay between waves is not
 {    identical for each individual. Also, if a individual missed an
   int i,j=0;    intermediate interview, the information is lost, but taken into
   int lg=20;    account using an interpolation or extrapolation.  
   i=0;  
   lg=strlen(s);    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
   if  (s[i] == occ ) j++;    split into an exact number (nh*stepm) of unobserved intermediate
   }    states. This elementary transition (by month, quarter,
   return j;    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
 void cutv(char *u,char *v, char*t, char occ)    hPijx.
 {  
   int i,lg,j,p=0;    Also this programme outputs the covariance matrix of the parameters but also
   i=0;    of the life expectancies. It also computes the period (stable) prevalence. 
   for(j=0; j<=strlen(t)-1; j++) {    
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   }             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
   lg=strlen(t);    from the European Union.
   for(j=0; j<p; j++) {    It is copyrighted identically to a GNU software product, ie programme and
     (u[j] = t[j]);    software can be distributed freely for non commercial use. Latest version
   }    can be accessed at http://euroreves.ined.fr/imach .
      u[p]='\0';  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    for(j=0; j<= lg; j++) {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     if (j>=(p+1))(v[j-p-1] = t[j]);    
   }    **********************************************************************/
 }  /*
     main
 /********************** nrerror ********************/    read parameterfile
     read datafile
 void nrerror(char error_text[])    concatwav
 {    freqsummary
   fprintf(stderr,"ERREUR ...\n");    if (mle >= 1)
   fprintf(stderr,"%s\n",error_text);      mlikeli
   exit(1);    print results files
 }    if mle==1 
 /*********************** vector *******************/       computes hessian
 double *vector(int nl, int nh)    read end of parameter file: agemin, agemax, bage, fage, estepm
 {        begin-prev-date,...
   double *v;    open gnuplot file
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    open html file
   if (!v) nrerror("allocation failure in vector");    period (stable) prevalence
   return v-nl+NR_END;     for age prevalim()
 }    h Pij x
     variance of p varprob
 /************************ free vector ******************/    forecasting if prevfcast==1 prevforecast call prevalence()
 void free_vector(double*v, int nl, int nh)    health expectancies
 {    Variance-covariance of DFLE
   free((FREE_ARG)(v+nl-NR_END));    prevalence()
 }     movingaverage()
     varevsij() 
 /************************ivector *******************************/    if popbased==1 varevsij(,popbased)
 int *ivector(long nl,long nh)    total life expectancies
 {    Variance of period (stable) prevalence
   int *v;   end
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  */
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  
 }  
    
 /******************free ivector **************************/  #include <math.h>
 void free_ivector(int *v, long nl, long nh)  #include <stdio.h>
 {  #include <stdlib.h>
   free((FREE_ARG)(v+nl-NR_END));  #include <string.h>
 }  #include <unistd.h>
   
 /******************* imatrix *******************************/  #include <limits.h>
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #include <sys/types.h>
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #include <sys/stat.h>
 {  #include <errno.h>
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  extern int errno;
   int **m;  
    /* #include <sys/time.h> */
   /* allocate pointers to rows */  #include <time.h>
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #include "timeval.h"
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /* #include <libintl.h> */
   m -= nrl;  /* #define _(String) gettext (String) */
    
    #define MAXLINE 256
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define GNUPLOTPROGRAM "gnuplot"
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m[nrl] += NR_END;  #define FILENAMELENGTH 132
   m[nrl] -= ncl;  
    #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
   /* return pointer to array of pointers to rows */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   return m;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /****************** free_imatrix *************************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       int **m;  #define NCOVMAX 8 /* Maximum number of covariates */
       long nch,ncl,nrh,nrl;  #define MAXN 20000
      /* free an int matrix allocated by imatrix() */  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define AGEBASE 40
   free((FREE_ARG) (m+nrl-NR_END));  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 }  #ifdef UNIX
   #define DIRSEPARATOR '/'
 /******************* matrix *******************************/  #define CHARSEPARATOR "/"
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define ODIRSEPARATOR '\\'
 {  #else
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define DIRSEPARATOR '\\'
   double **m;  #define CHARSEPARATOR "\\"
   #define ODIRSEPARATOR '/'
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #endif
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /* $Id$ */
   m -= nrl;  /* $State$ */
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char fullversion[]="$Revision$ $Date$"; 
   m[nrl] += NR_END;  char strstart[80];
   m[nrl] -= ncl;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int nvar;
   return m;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /*************************free matrix ************************/  int ndeath=1; /* Number of dead states */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 {  int popbased=0;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  int *wav; /* Number of waves for this individuual 0 is possible */
 }  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 /******************* ma3x *******************************/  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int mle, weightopt;
   double ***m;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   if (!m) nrerror("allocation failure 1 in matrix()");             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   m += NR_END;  double jmean; /* Mean space between 2 waves */
   m -= nrl;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *ficlog, *ficrespow;
   m[nrl] += NR_END;  int globpr; /* Global variable for printing or not */
   m[nrl] -= ncl;  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  FILE *ficresilk;
   m[nrl][ncl] += NR_END;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m[nrl][ncl] -= nll;  FILE *ficresprobmorprev;
   for (j=ncl+1; j<=nch; j++)  FILE *fichtm, *fichtmcov; /* Html File */
     m[nrl][j]=m[nrl][j-1]+nlay;  FILE *ficreseij;
    char filerese[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) {  FILE *ficresstdeij;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char fileresstde[FILENAMELENGTH];
     for (j=ncl+1; j<=nch; j++)  FILE *ficrescveij;
       m[i][j]=m[i][j-1]+nlay;  char filerescve[FILENAMELENGTH];
   }  FILE  *ficresvij;
   return m;  char fileresv[FILENAMELENGTH];
 }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 /*************************free ma3x ************************/  char title[MAXLINE];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char command[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /***************** f1dim *************************/  
 extern int ncom;  char filelog[FILENAMELENGTH]; /* Log file */
 extern double *pcom,*xicom;  char filerest[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  char fileregp[FILENAMELENGTH];
    char popfile[FILENAMELENGTH];
 double f1dim(double x)  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   int j;  
   double f;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   double *xt;  struct timezone tzp;
    extern int gettimeofday();
   xt=vector(1,ncom);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  long time_value;
   f=(*nrfunc)(xt);  extern long time();
   free_vector(xt,1,ncom);  char strcurr[80], strfor[80];
   return f;  
 }  char *endptr;
   long lval;
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define NR_END 1
 {  #define FREE_ARG char*
   int iter;  #define FTOL 1.0e-10
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  #define NRANSI 
   double ftemp;  #define ITMAX 200 
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  #define TOL 2.0e-4 
    
   a=(ax < cx ? ax : cx);  #define CGOLD 0.3819660 
   b=(ax > cx ? ax : cx);  #define ZEPS 1.0e-10 
   x=w=v=bx;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  #define GOLD 1.618034 
     xm=0.5*(a+b);  #define GLIMIT 100.0 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define TINY 1.0e-20 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  static double maxarg1,maxarg2;
 #ifdef DEBUG  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     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);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    
 #endif  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #define rint(a) floor(a+0.5)
       *xmin=x;  
       return fx;  static double sqrarg;
     }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     ftemp=fu;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     if (fabs(e) > tol1) {  int agegomp= AGEGOMP;
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  int imx; 
       p=(x-v)*q-(x-w)*r;  int stepm=1;
       q=2.0*(q-r);  /* Stepm, step in month: minimum step interpolation*/
       if (q > 0.0) p = -p;  
       q=fabs(q);  int estepm;
       etemp=e;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int m,nb;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  long *num;
       else {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         d=p/q;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         u=x+d;  double **pmmij, ***probs;
         if (u-a < tol2 || b-u < tol2)  double *ageexmed,*agecens;
           d=SIGN(tol1,xm-x);  double dateintmean=0;
       }  
     } else {  double *weight;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  int **s; /* Status */
     }  double *agedc, **covar, idx;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     fu=(*f)(u);  double *lsurv, *lpop, *tpop;
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       SHFT(v,w,x,u)  double ftolhess; /* Tolerance for computing hessian */
         SHFT(fv,fw,fx,fu)  
         } else {  /**************** split *************************/
           if (u < x) a=u; else b=u;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
           if (fu <= fw || w == x) {  {
             v=w;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
             w=u;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
             fv=fw;    */ 
             fw=fu;    char  *ss;                            /* pointer */
           } else if (fu <= fv || v == x || v == w) {    int   l1, l2;                         /* length counters */
             v=u;  
             fv=fu;    l1 = strlen(path );                   /* length of path */
           }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   nrerror("Too many iterations in brent");      strcpy( name, path );               /* we got the fullname name because no directory */
   *xmin=x;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   return fx;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 /****************** mnbrak ***********************/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      }
             double (*func)(double))      /* got dirc from getcwd*/
 {      printf(" DIRC = %s \n",dirc);
   double ulim,u,r,q, dum;    } else {                              /* strip direcotry from path */
   double fu;      ss++;                               /* after this, the filename */
        l2 = strlen( ss );                  /* length of filename */
   *fa=(*func)(*ax);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   *fb=(*func)(*bx);      strcpy( name, ss );         /* save file name */
   if (*fb > *fa) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     SHFT(dum,*ax,*bx,dum)      dirc[l1-l2] = 0;                    /* add zero */
       SHFT(dum,*fb,*fa,dum)      printf(" DIRC2 = %s \n",dirc);
       }    }
   *cx=(*bx)+GOLD*(*bx-*ax);    /* We add a separator at the end of dirc if not exists */
   *fc=(*func)(*cx);    l1 = strlen( dirc );                  /* length of directory */
   while (*fb > *fc) {    if( dirc[l1-1] != DIRSEPARATOR ){
     r=(*bx-*ax)*(*fb-*fc);      dirc[l1] =  DIRSEPARATOR;
     q=(*bx-*cx)*(*fb-*fa);      dirc[l1+1] = 0; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      printf(" DIRC3 = %s \n",dirc);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    }
     ulim=(*bx)+GLIMIT*(*cx-*bx);    ss = strrchr( name, '.' );            /* find last / */
     if ((*bx-u)*(u-*cx) > 0.0) {    if (ss >0){
       fu=(*func)(u);      ss++;
     } else if ((*cx-u)*(u-ulim) > 0.0) {      strcpy(ext,ss);                     /* save extension */
       fu=(*func)(u);      l1= strlen( name);
       if (fu < *fc) {      l2= strlen(ss)+1;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      strncpy( finame, name, l1-l2);
           SHFT(*fb,*fc,fu,(*func)(u))      finame[l1-l2]= 0;
           }    }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;    return( 0 );                          /* we're done */
       fu=(*func)(u);  }
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  /******************************************/
     }  
     SHFT(*ax,*bx,*cx,u)  void replace_back_to_slash(char *s, char*t)
       SHFT(*fa,*fb,*fc,fu)  {
       }    int i;
 }    int lg=0;
     i=0;
 /*************** linmin ************************/    lg=strlen(t);
     for(i=0; i<= lg; i++) {
 int ncom;      (s[i] = t[i]);
 double *pcom,*xicom;      if (t[i]== '\\') s[i]='/';
 double (*nrfunc)(double []);    }
    }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  int nbocc(char *s, char occ)
   double brent(double ax, double bx, double cx,  {
                double (*f)(double), double tol, double *xmin);    int i,j=0;
   double f1dim(double x);    int lg=20;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    i=0;
               double *fc, double (*func)(double));    lg=strlen(s);
   int j;    for(i=0; i<= lg; i++) {
   double xx,xmin,bx,ax;    if  (s[i] == occ ) j++;
   double fx,fb,fa;    }
      return j;
   ncom=n;  }
   pcom=vector(1,n);  
   xicom=vector(1,n);  void cutv(char *u,char *v, char*t, char occ)
   nrfunc=func;  {
   for (j=1;j<=n;j++) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     pcom[j]=p[j];       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     xicom[j]=xi[j];       gives u="abcedf" and v="ghi2j" */
   }    int i,lg,j,p=0;
   ax=0.0;    i=0;
   xx=1.0;    for(j=0; j<=strlen(t)-1; j++) {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    }
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    lg=strlen(t);
 #endif    for(j=0; j<p; j++) {
   for (j=1;j<=n;j++) {      (u[j] = t[j]);
     xi[j] *= xmin;    }
     p[j] += xi[j];       u[p]='\0';
   }  
   free_vector(xicom,1,n);     for(j=0; j<= lg; j++) {
   free_vector(pcom,1,n);      if (j>=(p+1))(v[j-p-1] = t[j]);
 }    }
   }
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /********************** nrerror ********************/
             double (*func)(double []))  
 {  void nrerror(char error_text[])
   void linmin(double p[], double xi[], int n, double *fret,  {
               double (*func)(double []));    fprintf(stderr,"ERREUR ...\n");
   int i,ibig,j;    fprintf(stderr,"%s\n",error_text);
   double del,t,*pt,*ptt,*xit;    exit(EXIT_FAILURE);
   double fp,fptt;  }
   double *xits;  /*********************** vector *******************/
   pt=vector(1,n);  double *vector(int nl, int nh)
   ptt=vector(1,n);  {
   xit=vector(1,n);    double *v;
   xits=vector(1,n);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   *fret=(*func)(p);    if (!v) nrerror("allocation failure in vector");
   for (j=1;j<=n;j++) pt[j]=p[j];    return v-nl+NR_END;
   for (*iter=1;;++(*iter)) {  }
     fp=(*fret);  
     ibig=0;  /************************ free vector ******************/
     del=0.0;  void free_vector(double*v, int nl, int nh)
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  {
     for (i=1;i<=n;i++)    free((FREE_ARG)(v+nl-NR_END));
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  /************************ivector *******************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int *ivector(long nl,long nh)
       fptt=(*fret);  {
 #ifdef DEBUG    int *v;
       printf("fret=%lf \n",*fret);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 #endif    if (!v) nrerror("allocation failure in ivector");
       printf("%d",i);fflush(stdout);    return v-nl+NR_END;
       linmin(p,xit,n,fret,func);  }
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  /******************free ivector **************************/
         ibig=i;  void free_ivector(int *v, long nl, long nh)
       }  {
 #ifdef DEBUG    free((FREE_ARG)(v+nl-NR_END));
       printf("%d %.12e",i,(*fret));  }
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /************************lvector *******************************/
         printf(" x(%d)=%.12e",j,xit[j]);  long *lvector(long nl,long nh)
       }  {
       for(j=1;j<=n;j++)    long *v;
         printf(" p=%.12e",p[j]);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       printf("\n");    if (!v) nrerror("allocation failure in ivector");
 #endif    return v-nl+NR_END;
     }  }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /******************free lvector **************************/
       int k[2],l;  void free_lvector(long *v, long nl, long nh)
       k[0]=1;  {
       k[1]=-1;    free((FREE_ARG)(v+nl-NR_END));
       printf("Max: %.12e",(*func)(p));  }
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /******************* imatrix *******************************/
       printf("\n");  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       for(l=0;l<=1;l++) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         for (j=1;j<=n;j++) {  { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    int **m; 
         }    
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    /* allocate pointers to rows */ 
       }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 #endif    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
     m -= nrl; 
       free_vector(xit,1,n);    
       free_vector(xits,1,n);    
       free_vector(ptt,1,n);    /* allocate rows and set pointers to them */ 
       free_vector(pt,1,n);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       return;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m[nrl] -= ncl; 
     for (j=1;j<=n;j++) {    
       ptt[j]=2.0*p[j]-pt[j];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       xit[j]=p[j]-pt[j];    
       pt[j]=p[j];    /* return pointer to array of pointers to rows */ 
     }    return m; 
     fptt=(*func)(ptt);  } 
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /****************** free_imatrix *************************/
       if (t < 0.0) {  void free_imatrix(m,nrl,nrh,ncl,nch)
         linmin(p,xit,n,fret,func);        int **m;
         for (j=1;j<=n;j++) {        long nch,ncl,nrh,nrl; 
           xi[j][ibig]=xi[j][n];       /* free an int matrix allocated by imatrix() */ 
           xi[j][n]=xit[j];  { 
         }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 #ifdef DEBUG    free((FREE_ARG) (m+nrl-NR_END)); 
         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++)  
           printf(" %.12e",xit[j]);  /******************* matrix *******************************/
         printf("\n");  double **matrix(long nrl, long nrh, long ncl, long nch)
 #endif  {
       }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
   }  
 }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /**** Prevalence limit ****************/    m += NR_END;
     m -= nrl;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      matrix by transitions matrix until convergence is reached */    m[nrl] += NR_END;
     m[nrl] -= ncl;
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double **matprod2();    return m;
   double **out, cov[NCOVMAX], **pmij();    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   double **newm;     */
   double agefin, delaymax=50 ; /* Max number of years to converge */  }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /*************************free matrix ************************/
     for (j=1;j<=nlstate+ndeath;j++){  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
    cov[1]=1.;  }
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /******************* ma3x *******************************/
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     newm=savm;  {
     /* Covariates have to be included here again */    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
      cov[2]=agefin;    double ***m;
    
       for (k=1; k<=cptcovn;k++) {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (!m) nrerror("allocation failure 1 in matrix()");
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    m += NR_END;
       }    m -= nrl;
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    m[nrl] -= ncl;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     savm=oldm;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     oldm=newm;    m[nrl][ncl] += NR_END;
     maxmax=0.;    m[nrl][ncl] -= nll;
     for(j=1;j<=nlstate;j++){    for (j=ncl+1; j<=nch; j++) 
       min=1.;      m[nrl][j]=m[nrl][j-1]+nlay;
       max=0.;    
       for(i=1; i<=nlstate; i++) {    for (i=nrl+1; i<=nrh; i++) {
         sumnew=0;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      for (j=ncl+1; j<=nch; j++) 
         prlim[i][j]= newm[i][j]/(1-sumnew);        m[i][j]=m[i][j-1]+nlay;
         max=FMAX(max,prlim[i][j]);    }
         min=FMIN(min,prlim[i][j]);    return m; 
       }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       maxmin=max-min;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       maxmax=FMAX(maxmax,maxmin);    */
     }  }
     if(maxmax < ftolpl){  
       return prlim;  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
 }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /*************** transition probabilities ***************/    free((FREE_ARG)(m+nrl-NR_END));
   }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /*************** function subdirf ***********/
   double s1, s2;  char *subdirf(char fileres[])
   /*double t34;*/  {
   int i,j,j1, nc, ii, jj;    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     for(i=1; i<= nlstate; i++){    strcat(tmpout,"/"); /* Add to the right */
     for(j=1; j<i;j++){    strcat(tmpout,fileres);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return tmpout;
         /*s2 += param[i][j][nc]*cov[nc];*/  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /*************** function subdirf2 ***********/
       }  char *subdirf2(char fileres[], char *preop)
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    
     }    /* Caution optionfilefiname is hidden */
     for(j=i+1; j<=nlstate+ndeath;j++){    strcpy(tmpout,optionfilefiname);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcat(tmpout,"/");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcat(tmpout,preop);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    strcat(tmpout,fileres);
       }    return tmpout;
       ps[i][j]=s2;  }
     }  
   }  /*************** function subdirf3 ***********/
     /*ps[3][2]=1;*/  char *subdirf3(char fileres[], char *preop, char *preop2)
   {
   for(i=1; i<= nlstate; i++){    
      s1=0;    /* Caution optionfilefiname is hidden */
     for(j=1; j<i; j++)    strcpy(tmpout,optionfilefiname);
       s1+=exp(ps[i][j]);    strcat(tmpout,"/");
     for(j=i+1; j<=nlstate+ndeath; j++)    strcat(tmpout,preop);
       s1+=exp(ps[i][j]);    strcat(tmpout,preop2);
     ps[i][i]=1./(s1+1.);    strcat(tmpout,fileres);
     for(j=1; j<i; j++)    return tmpout;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /***************** f1dim *************************/
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  extern int ncom; 
   } /* end i */  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){   
     for(jj=1; jj<= nlstate+ndeath; jj++){  double f1dim(double x) 
       ps[ii][jj]=0;  { 
       ps[ii][ii]=1;    int j; 
     }    double f;
   }    double *xt; 
    
     xt=vector(1,ncom); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    f=(*nrfunc)(xt); 
      printf("%lf ",ps[ii][jj]);    free_vector(xt,1,ncom); 
    }    return f; 
     printf("\n ");  } 
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /*****************brent *************************/
 /*  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  { 
   goto end;*/    int iter; 
     return ps;    double a,b,d,etemp;
 }    double fu,fv,fw,fx;
     double ftemp;
 /**************** Product of 2 matrices ******************/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)   
 {    a=(ax < cx ? ax : cx); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    b=(ax > cx ? ax : cx); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    x=w=v=bx; 
   /* in, b, out are matrice of pointers which should have been initialized    fw=fv=fx=(*f)(x); 
      before: only the contents of out is modified. The function returns    for (iter=1;iter<=ITMAX;iter++) { 
      a pointer to pointers identical to out */      xm=0.5*(a+b); 
   long i, j, k;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for(i=nrl; i<= nrh; i++)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for(k=ncolol; k<=ncoloh; k++)      printf(".");fflush(stdout);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      fprintf(ficlog,".");fflush(ficlog);
         out[i][k] +=in[i][j]*b[j][k];  #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);
   return out;      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)))) { */
   #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 /************* Higher Matrix Product ***************/        *xmin=x; 
         return fx; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      } 
 {      ftemp=fu;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      if (fabs(e) > tol1) { 
      duration (i.e. until        r=(x-w)*(fx-fv); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        q=(x-v)*(fx-fw); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        p=(x-v)*q-(x-w)*r; 
      (typically every 2 years instead of every month which is too big).        q=2.0*(q-r); 
      Model is determined by parameters x and covariates have to be        if (q > 0.0) p = -p; 
      included manually here.        q=fabs(q); 
         etemp=e; 
      */        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   int i, j, d, h, k;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double **out, cov[NCOVMAX];        else { 
   double **newm;          d=p/q; 
           u=x+d; 
   /* Hstepm could be zero and should return the unit matrix */          if (u-a < tol2 || b-u < tol2) 
   for (i=1;i<=nlstate+ndeath;i++)            d=SIGN(tol1,xm-x); 
     for (j=1;j<=nlstate+ndeath;j++){        } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      } else { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   for(h=1; h <=nhstepm; h++){      fu=(*f)(u); 
     for(d=1; d <=hstepm; d++){      if (fu <= fx) { 
       newm=savm;        if (u >= x) a=x; else b=x; 
       /* Covariates have to be included here again */        SHFT(v,w,x,u) 
       cov[1]=1.;          SHFT(fv,fw,fx,fu) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          } else { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            if (u < x) a=u; else b=u; 
       for (k=1; k<=cptcovage;k++)            if (fu <= fw || w == x) { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              v=w; 
       for (k=1; k<=cptcovprod;k++)              w=u; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              fv=fw; 
               fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/              v=u; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/              fv=fu; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,            } 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          } 
       savm=oldm;    } 
       oldm=newm;    nrerror("Too many iterations in brent"); 
     }    *xmin=x; 
     for(i=1; i<=nlstate+ndeath; i++)    return fx; 
       for(j=1;j<=nlstate+ndeath;j++) {  } 
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /****************** mnbrak ***********************/
          */  
       }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   } /* end h */              double (*func)(double)) 
   return po;  { 
 }    double ulim,u,r,q, dum;
     double fu; 
    
 /*************** log-likelihood *************/    *fa=(*func)(*ax); 
 double func( double *x)    *fb=(*func)(*bx); 
 {    if (*fb > *fa) { 
   int i, ii, j, k, mi, d, kk;      SHFT(dum,*ax,*bx,dum) 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        SHFT(dum,*fb,*fa,dum) 
   double **out;        } 
   double sw; /* Sum of weights */    *cx=(*bx)+GOLD*(*bx-*ax); 
   double lli; /* Individual log likelihood */    *fc=(*func)(*cx); 
   long ipmx;    while (*fb > *fc) { 
   /*extern weight */      r=(*bx-*ax)*(*fb-*fc); 
   /* We are differentiating ll according to initial status */      q=(*bx-*cx)*(*fb-*fa); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   /*for(i=1;i<imx;i++)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     printf(" %d\n",s[4][i]);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   */      if ((*bx-u)*(u-*cx) > 0.0) { 
   cov[1]=1.;        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        fu=(*func)(u); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        if (fu < *fc) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for(mi=1; mi<= wav[i]-1; mi++){            SHFT(*fb,*fc,fu,(*func)(u)) 
       for (ii=1;ii<=nlstate+ndeath;ii++)            } 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for(d=0; d<dh[mi][i]; d++){        u=ulim; 
         newm=savm;        fu=(*func)(u); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      } else { 
         for (kk=1; kk<=cptcovage;kk++) {        u=(*cx)+GOLD*(*cx-*bx); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        fu=(*func)(u); 
         }      } 
              SHFT(*ax,*bx,*cx,u) 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        SHFT(*fa,*fb,*fc,fu) 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        } 
         savm=oldm;  } 
         oldm=newm;  
          /*************** linmin ************************/
          
       } /* end mult */  int ncom; 
        double *pcom,*xicom;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  double (*nrfunc)(double []); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/   
       ipmx +=1;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       sw += weight[i];  { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double brent(double ax, double bx, double cx, 
     } /* end of wave */                 double (*f)(double), double tol, double *xmin); 
   } /* end of individual */    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];                double *fc, double (*func)(double)); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    int j; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    double xx,xmin,bx,ax; 
   return -l;    double fx,fb,fa;
 }   
     ncom=n; 
     pcom=vector(1,n); 
 /*********** Maximum Likelihood Estimation ***************/    xicom=vector(1,n); 
     nrfunc=func; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    for (j=1;j<=n;j++) { 
 {      pcom[j]=p[j]; 
   int i,j, iter;      xicom[j]=xi[j]; 
   double **xi,*delti;    } 
   double fret;    ax=0.0; 
   xi=matrix(1,npar,1,npar);    xx=1.0; 
   for (i=1;i<=npar;i++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for (j=1;j<=npar;j++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       xi[i][j]=(i==j ? 1.0 : 0.0);  #ifdef DEBUG
   printf("Powell\n");    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   powell(p,xi,npar,ftol,&iter,&fret,func);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    for (j=1;j<=n;j++) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      xi[j] *= xmin; 
       p[j] += xi[j]; 
 }    } 
     free_vector(xicom,1,n); 
 /**** Computes Hessian and covariance matrix ***/    free_vector(pcom,1,n); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  } 
 {  
   double  **a,**y,*x,pd;  char *asc_diff_time(long time_sec, char ascdiff[])
   double **hess;  {
   int i, j,jk;    long sec_left, days, hours, minutes;
   int *indx;    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
   double hessii(double p[], double delta, int theta, double delti[]);    hours = (sec_left) / (60*60) ;
   double hessij(double p[], double delti[], int i, int j);    sec_left = (sec_left) %(60*60);
   void lubksb(double **a, int npar, int *indx, double b[]) ;    minutes = (sec_left) /60;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   hess=matrix(1,npar,1,npar);    return ascdiff;
   }
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  /*************** powell ************************/
     printf("%d",i);fflush(stdout);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     hess[i][i]=hessii(p,ftolhess,i,delti);              double (*func)(double [])) 
     /*printf(" %f ",p[i]);*/  { 
     /*printf(" %lf ",hess[i][i]);*/    void linmin(double p[], double xi[], int n, double *fret, 
   }                double (*func)(double [])); 
      int i,ibig,j; 
   for (i=1;i<=npar;i++) {    double del,t,*pt,*ptt,*xit;
     for (j=1;j<=npar;j++)  {    double fp,fptt;
       if (j>i) {    double *xits;
         printf(".%d%d",i,j);fflush(stdout);    int niterf, itmp;
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];        pt=vector(1,n); 
         /*printf(" %lf ",hess[i][j]);*/    ptt=vector(1,n); 
       }    xit=vector(1,n); 
     }    xits=vector(1,n); 
   }    *fret=(*func)(p); 
   printf("\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      fp=(*fret); 
        ibig=0; 
   a=matrix(1,npar,1,npar);      del=0.0; 
   y=matrix(1,npar,1,npar);      last_time=curr_time;
   x=vector(1,npar);      (void) gettimeofday(&curr_time,&tzp);
   indx=ivector(1,npar);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   for (i=1;i<=npar;i++)      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   ludcmp(a,npar,indx,&pd);      */
      for (i=1;i<=n;i++) {
   for (j=1;j<=npar;j++) {        printf(" %d %.12f",i, p[i]);
     for (i=1;i<=npar;i++) x[i]=0;        fprintf(ficlog," %d %.12lf",i, p[i]);
     x[j]=1;        fprintf(ficrespow," %.12lf", p[i]);
     lubksb(a,npar,indx,x);      }
     for (i=1;i<=npar;i++){      printf("\n");
       matcov[i][j]=x[i];      fprintf(ficlog,"\n");
     }      fprintf(ficrespow,"\n");fflush(ficrespow);
   }      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
   printf("\n#Hessian matrix#\n");        strcpy(strcurr,asctime(&tm));
   for (i=1;i<=npar;i++) {  /*       asctime_r(&tm,strcurr); */
     for (j=1;j<=npar;j++) {        forecast_time=curr_time; 
       printf("%.3e ",hess[i][j]);        itmp = strlen(strcurr);
     }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     printf("\n");          strcurr[itmp-1]='\0';
   }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   /* Recompute Inverse */        for(niterf=10;niterf<=30;niterf+=10){
   for (i=1;i<=npar;i++)          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          tmf = *localtime(&forecast_time.tv_sec);
   ludcmp(a,npar,indx,&pd);  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
   /*  printf("\n#Hessian matrix recomputed#\n");          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   for (j=1;j<=npar;j++) {          strfor[itmp-1]='\0';
     for (i=1;i<=npar;i++) x[i]=0;          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);
     x[j]=1;          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);
     lubksb(a,npar,indx,x);        }
     for (i=1;i<=npar;i++){      }
       y[i][j]=x[i];      for (i=1;i<=n;i++) { 
       printf("%.3e ",y[i][j]);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     }        fptt=(*fret); 
     printf("\n");  #ifdef DEBUG
   }        printf("fret=%lf \n",*fret);
   */        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
   free_matrix(a,1,npar,1,npar);        printf("%d",i);fflush(stdout);
   free_matrix(y,1,npar,1,npar);        fprintf(ficlog,"%d",i);fflush(ficlog);
   free_vector(x,1,npar);        linmin(p,xit,n,fret,func); 
   free_ivector(indx,1,npar);        if (fabs(fptt-(*fret)) > del) { 
   free_matrix(hess,1,npar,1,npar);          del=fabs(fptt-(*fret)); 
           ibig=i; 
         } 
 }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 /*************** hessian matrix ****************/        fprintf(ficlog,"%d %.12e",i,(*fret));
 double hessii( double x[], double delta, int theta, double delti[])        for (j=1;j<=n;j++) {
 {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int i;          printf(" x(%d)=%.12e",j,xit[j]);
   int l=1, lmax=20;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double k1,k2;        }
   double p2[NPARMAX+1];        for(j=1;j<=n;j++) {
   double res;          printf(" p=%.12e",p[j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          fprintf(ficlog," p=%.12e",p[j]);
   double fx;        }
   int k=0,kmax=10;        printf("\n");
   double l1;        fprintf(ficlog,"\n");
   #endif
   fx=func(x);      } 
   for (i=1;i<=npar;i++) p2[i]=x[i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   for(l=0 ; l <=lmax; l++){  #ifdef DEBUG
     l1=pow(10,l);        int k[2],l;
     delts=delt;        k[0]=1;
     for(k=1 ; k <kmax; k=k+1){        k[1]=-1;
       delt = delta*(l1*k);        printf("Max: %.12e",(*func)(p));
       p2[theta]=x[theta] +delt;        fprintf(ficlog,"Max: %.12e",(*func)(p));
       k1=func(p2)-fx;        for (j=1;j<=n;j++) {
       p2[theta]=x[theta]-delt;          printf(" %.12e",p[j]);
       k2=func(p2)-fx;          fprintf(ficlog," %.12e",p[j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */        }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        printf("\n");
              fprintf(ficlog,"\n");
 #ifdef DEBUG        for(l=0;l<=1;l++) {
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          for (j=1;j<=n;j++) {
 #endif            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         k=kmax;          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         k=kmax; l=lmax*10.;        }
       }  #endif
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  
       }        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
   }        free_vector(ptt,1,n); 
   delti[theta]=delts;        free_vector(pt,1,n); 
   return res;        return; 
        } 
 }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 double hessij( double x[], double delti[], int thetai,int thetaj)        ptt[j]=2.0*p[j]-pt[j]; 
 {        xit[j]=p[j]-pt[j]; 
   int i;        pt[j]=p[j]; 
   int l=1, l1, lmax=20;      } 
   double k1,k2,k3,k4,res,fx;      fptt=(*func)(ptt); 
   double p2[NPARMAX+1];      if (fptt < fp) { 
   int k;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   fx=func(x);          linmin(p,xit,n,fret,func); 
   for (k=1; k<=2; k++) {          for (j=1;j<=n;j++) { 
     for (i=1;i<=npar;i++) p2[i]=x[i];            xi[j][ibig]=xi[j][n]; 
     p2[thetai]=x[thetai]+delti[thetai]/k;            xi[j][n]=xit[j]; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          }
     k1=func(p2)-fx;  #ifdef DEBUG
            printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     p2[thetai]=x[thetai]+delti[thetai]/k;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for(j=1;j<=n;j++){
     k2=func(p2)-fx;            printf(" %.12e",xit[j]);
              fprintf(ficlog," %.12e",xit[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;          }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          printf("\n");
     k3=func(p2)-fx;          fprintf(ficlog,"\n");
    #endif
     p2[thetai]=x[thetai]-delti[thetai]/k;        }
     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 */  } 
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  /**** Prevalence limit (stable or period prevalence)  ****************/
 #endif  
   }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   return res;  {
 }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    int i, ii,j,k;
 {    double min, max, maxmin, maxmax,sumnew=0.;
   int i,imax,j,k;    double **matprod2();
   double big,dum,sum,temp;    double **out, cov[NCOVMAX], **pmij();
   double *vv;    double **newm;
      double agefin, delaymax=50 ; /* Max number of years to converge */
   vv=vector(1,n);  
   *d=1.0;    for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=n;i++) {      for (j=1;j<=nlstate+ndeath;j++){
     big=0.0;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=n;j++)      }
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");     cov[1]=1.;
     vv[i]=1.0/big;   
   }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (j=1;j<=n;j++) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for (i=1;i<j;i++) {      newm=savm;
       sum=a[i][j];      /* Covariates have to be included here again */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];       cov[2]=agefin;
       a[i][j]=sum;    
     }        for (k=1; k<=cptcovn;k++) {
     big=0.0;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (i=j;i<=n;i++) {          /*      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]]);*/
       sum=a[i][j];        }
       for (k=1;k<j;k++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovprod;k++)
       a[i][j]=sum;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         imax=i;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     if (j != imax) {  
       for (k=1;k<=n;k++) {      savm=oldm;
         dum=a[imax][k];      oldm=newm;
         a[imax][k]=a[j][k];      maxmax=0.;
         a[j][k]=dum;      for(j=1;j<=nlstate;j++){
       }        min=1.;
       *d = -(*d);        max=0.;
       vv[imax]=vv[j];        for(i=1; i<=nlstate; i++) {
     }          sumnew=0;
     indx[j]=imax;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     if (a[j][j] == 0.0) a[j][j]=TINY;          prlim[i][j]= newm[i][j]/(1-sumnew);
     if (j != n) {          max=FMAX(max,prlim[i][j]);
       dum=1.0/(a[j][j]);          min=FMIN(min,prlim[i][j]);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        }
     }        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
   free_vector(vv,1,n);  /* Doesn't work */      }
 ;      if(maxmax < ftolpl){
 }        return prlim;
       }
 void lubksb(double **a, int n, int *indx, double b[])    }
 {  }
   int i,ii=0,ip,j;  
   double sum;  /*************** transition probabilities ***************/ 
    
   for (i=1;i<=n;i++) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     ip=indx[i];  {
     sum=b[ip];    double s1, s2;
     b[ip]=b[i];    /*double t34;*/
     if (ii)    int i,j,j1, nc, ii, jj;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;      for(i=1; i<= nlstate; i++){
     b[i]=sum;        for(j=1; j<i;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=n;i>=1;i--) {            /*s2 += param[i][j][nc]*cov[nc];*/
     sum=b[i];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     b[i]=sum/a[i][i];          }
   }          ps[i][j]=s2;
 }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         }
 /************ Frequencies ********************/        for(j=i+1; j<=nlstate+ndeath;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 (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {  /* Some frequencies */            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
    /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          }
   double ***freq; /* Frequencies */          ps[i][j]=s2;
   double *pp;        }
   double pos, k2, dateintsum=0,k2cpt=0;      }
   FILE *ficresp;      /*ps[3][2]=1;*/
   char fileresp[FILENAMELENGTH];      
        for(i=1; i<= nlstate; i++){
   pp=vector(1,nlstate);        s1=0;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<i; j++)
   strcpy(fileresp,"p");          s1+=exp(ps[i][j]);
   strcat(fileresp,fileres);        for(j=i+1; j<=nlstate+ndeath; j++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {          s1+=exp(ps[i][j]);
     printf("Problem with prevalence resultfile: %s\n", fileresp);        ps[i][i]=1./(s1+1.);
     exit(0);        for(j=1; j<i; j++)
   }          ps[i][j]= exp(ps[i][j])*ps[i][i];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for(j=i+1; j<=nlstate+ndeath; j++)
   j1=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
          /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   j=cptcoveff;      } /* end i */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      
        for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   for(k1=1; k1<=j;k1++){        for(jj=1; jj<= nlstate+ndeath; jj++){
     for(i1=1; i1<=ncodemax[k1];i1++){          ps[ii][jj]=0;
       j1++;          ps[ii][ii]=1;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        }
         scanf("%d", i);*/      }
       for (i=-1; i<=nlstate+ndeath; i++)        
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
             freq[i][jk][m]=0;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
        /*         printf("ddd %lf ",ps[ii][jj]); */
       dateintsum=0;  /*       } */
       k2cpt=0;  /*       printf("\n "); */
       for (i=1; i<=imx; i++) {  /*        } */
         bool=1;  /*        printf("\n ");printf("%lf ",cov[2]); */
         if  (cptcovn>0) {         /*
           for (z1=1; z1<=cptcoveff; z1++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        goto end;*/
               bool=0;      return ps;
         }  }
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  /**************** Product of 2 matrices ******************/
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
               if(agev[m][i]==0) agev[m][i]=agemax+1;  {
               if(agev[m][i]==1) agev[m][i]=agemax+2;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
               if (m<lastpass) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    /* in, b, out are matrice of pointers which should have been initialized 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];       before: only the contents of out is modified. The function returns
               }       a pointer to pointers identical to out */
                  long i, j, k;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    for(i=nrl; i<= nrh; i++)
                 dateintsum=dateintsum+k2;      for(k=ncolol; k<=ncoloh; k++)
                 k2cpt++;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
               }          out[i][k] +=in[i][j]*b[j][k];
             }  
           }    return out;
         }  }
       }  
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /************* Higher Matrix Product ***************/
   
       if  (cptcovn>0) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         fprintf(ficresp, "\n#********** Variable ");  {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* Computes the transition matrix starting at age 'age' over 
         fprintf(ficresp, "**********\n#");       'nhstepm*hstepm*stepm' months (i.e. until
       }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       for(i=1; i<=nlstate;i++)       nhstepm*hstepm matrices. 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       fprintf(ficresp, "\n");       (typically every 2 years instead of every month which is too big 
             for the memory).
       for(i=(int)agemin; i <= (int)agemax+3; i++){       Model is determined by parameters x and covariates have to be 
         if(i==(int)agemax+3)       included manually here. 
           printf("Total");  
         else       */
           printf("Age %d", i);  
         for(jk=1; jk <=nlstate ; jk++){    int i, j, d, h, k;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double **out, cov[NCOVMAX];
             pp[jk] += freq[jk][m][i];    double **newm;
         }  
         for(jk=1; jk <=nlstate ; jk++){    /* Hstepm could be zero and should return the unit matrix */
           for(m=-1, pos=0; m <=0 ; m++)    for (i=1;i<=nlstate+ndeath;i++)
             pos += freq[jk][m][i];      for (j=1;j<=nlstate+ndeath;j++){
           if(pp[jk]>=1.e-10)        oldm[i][j]=(i==j ? 1.0 : 0.0);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        po[i][j][0]=(i==j ? 1.0 : 0.0);
           else      }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         }    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
         for(jk=1; jk <=nlstate ; jk++){        newm=savm;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /* Covariates have to be included here again */
             pp[jk] += freq[jk][m][i];        cov[1]=1.;
         }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for (k=1; k<=cptcovage;k++)
           pos += pp[jk];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovprod;k++)
           if(pos>=1.e-5)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           else  
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
           if( i <= (int) agemax){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
             if(pos>=1.e-5){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
               probs[i][jk][j1]= pp[jk]/pos;        savm=oldm;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        oldm=newm;
             }      }
             else      for(i=1; i<=nlstate+ndeath; i++)
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        for(j=1;j<=nlstate+ndeath;j++) {
           }          po[i][j][h]=newm[i][j];
         }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
                   */
         for(jk=-1; jk <=nlstate+ndeath; jk++)        }
           for(m=-1; m <=nlstate+ndeath; m++)    } /* end h */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    return po;
         if(i <= (int) agemax)  }
           fprintf(ficresp,"\n");  
         printf("\n");  
       }  /*************** log-likelihood *************/
     }  double func( double *x)
   }  {
   dateintmean=dateintsum/k2cpt;    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
   fclose(ficresp);    double **out;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double sw; /* Sum of weights */
   free_vector(pp,1,nlstate);    double lli; /* Individual log likelihood */
      int s1, s2;
   /* End of Freq */    double bbh, survp;
 }    long ipmx;
     /*extern weight */
 /************ Prevalence ********************/    /* We are differentiating ll according to initial status */
 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 (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 {  /* Some frequencies */    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    */
   double ***freq; /* Frequencies */    cov[1]=1.;
   double *pp;  
   double pos, k2;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   pp=vector(1,nlstate);    if(mle==1){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for(mi=1; mi<= wav[i]-1; mi++){
   j1=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   j=cptcoveff;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
  for(k1=1; k1<=j;k1++){          for(d=0; d<dh[mi][i]; d++){
     for(i1=1; i1<=ncodemax[k1];i1++){            newm=savm;
       j1++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
       for (i=-1; i<=nlstate+ndeath; i++)                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for (jk=-1; jk<=nlstate+ndeath; jk++)              }
           for(m=agemin; m <= agemax+3; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             freq[i][jk][m]=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
       for (i=1; i<=imx; i++) {            oldm=newm;
         bool=1;          } /* end mult */
         if  (cptcovn>0) {        
           for (z1=1; z1<=cptcoveff; z1++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          /* But now since version 0.9 we anticipate for bias at large stepm.
               bool=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
         if (bool==1) {           * the nearest (and in case of equal distance, to the lowest) interval but now
           for(m=firstpass; m<=lastpass; m++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             k2=anint[m][i]+(mint[m][i]/12.);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
             if ((k2>=dateprev1) && (k2<=dateprev2)) {           * probability in order to take into account the bias as a fraction of the way
               if(agev[m][i]==0) agev[m][i]=agemax+1;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
               if(agev[m][i]==1) agev[m][i]=agemax+2;           * -stepm/2 to stepm/2 .
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];           * For stepm=1 the results are the same as for previous versions of Imach.
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */           * For stepm > 1 the results are less biased than in previous versions. 
             }           */
           }          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
         for(i=(int)agemin; i <= (int)agemax+3; i++){          /* bias bh is positive if real duration
           for(jk=1; jk <=nlstate ; jk++){           * is higher than the multiple of stepm and negative otherwise.
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           */
               pp[jk] += freq[jk][m][i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           }          if( s2 > nlstate){ 
           for(jk=1; jk <=nlstate ; jk++){            /* i.e. if s2 is a death state and if the date of death is known 
             for(m=-1, pos=0; m <=0 ; m++)               then the contribution to the likelihood is the probability to 
             pos += freq[jk][m][i];               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(jk=1; jk <=nlstate ; jk++){               In version up to 0.92 likelihood was computed
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          as if date of death was unknown. Death was treated as any other
              pp[jk] += freq[jk][m][i];          health state: the date of the interview describes the actual state
          }          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,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
          for(jk=1; jk <=nlstate ; jk++){                    the contribution of an exact death to the likelihood. This new
            if( i <= (int) agemax){          contribution is smaller and very dependent of the step unit
              if(pos>=1.e-5){          stepm. It is no more the probability to die between last interview
                probs[i][jk][j1]= pp[jk]/pos;          and month of death but the probability to survive from last
              }          interview up to one month before death multiplied by the
            }          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
         }          which slows down the processing. The difference can be up to 10%
     }          lower mortality.
   }            */
              lli=log(out[s1][s2] - savm[s1][s2]);
    
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);          } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
 }  /* End of Freq */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
 /************* Waves Concatenation ***************/            lli= log(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)          
 {          else if  (s2==-4) { 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for (j=3,survp=0. ; j<=nlstate; j++)  
      Death is a valid wave (if date is known).              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            lli= log(survp); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          } 
      and mw[mi+1][i]. dh depends on stepm.  
      */          else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
   int i, mi, m;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            lli= log(survp); 
      double sum=0., jmean=0.;*/          } 
           
   int j, k=0,jk, ju, jl;          else{
   double sum=0.;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   jmin=1e+5;            /*  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 */
   jmax=-1;          } 
   jmean=0.;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for(i=1; i<=imx; i++){          /*if(lli ==000.0)*/
     mi=0;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     m=firstpass;          ipmx +=1;
     while(s[m][i] <= nlstate){          sw += weight[i];
       if(s[m][i]>=1)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         mw[++mi][i]=m;        } /* end of wave */
       if(m >=lastpass)      } /* end of individual */
         break;    }  else if(mle==2){
       else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         m++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }/* end while */        for(mi=1; mi<= wav[i]-1; mi++){
     if (s[m][i] > nlstate){          for (ii=1;ii<=nlstate+ndeath;ii++)
       mi++;     /* Death is another wave */            for (j=1;j<=nlstate+ndeath;j++){
       /* if(mi==0)  never been interviewed correctly before death */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
          /* Only death is a correct wave */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       mw[mi][i]=m;            }
     }          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
     wav[i]=mi;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if(mi==0)            for (kk=1; kk<=cptcovage;kk++) {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=1; i<=imx; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(mi=1; mi<wav[i];mi++){            savm=oldm;
       if (stepm <=0)            oldm=newm;
         dh[mi][i]=1;          } /* end mult */
       else{        
         if (s[mw[mi+1][i]][i] > nlstate) {          s1=s[mw[mi][i]][i];
           if (agedc[i] < 2*AGESUP) {          s2=s[mw[mi+1][i]][i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          bbh=(double)bh[mi][i]/(double)stepm; 
           if(j==0) j=1;  /* Survives at least one month after exam */          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 */
           k=k+1;          ipmx +=1;
           if (j >= jmax) jmax=j;          sw += weight[i];
           if (j <= jmin) jmin=j;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           sum=sum+j;        } /* end of wave */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      } /* end of individual */
           }    }  else if(mle==3){  /* exponential inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         else{        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        for(mi=1; mi<= wav[i]-1; mi++){
           k=k+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
           if (j >= jmax) jmax=j;            for (j=1;j<=nlstate+ndeath;j++){
           else if (j <= jmin)jmin=j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           sum=sum+j;            }
         }          for(d=0; d<dh[mi][i]; d++){
         jk= j/stepm;            newm=savm;
         jl= j -jk*stepm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         ju= j -(jk+1)*stepm;            for (kk=1; kk<=cptcovage;kk++) {
         if(jl <= -ju)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           dh[mi][i]=jk;            }
         else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           dh[mi][i]=jk+1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(dh[mi][i]==0)            savm=oldm;
           dh[mi][i]=1; /* At least one step */            oldm=newm;
       }          } /* end mult */
     }        
   }          s1=s[mw[mi][i]][i];
   jmean=sum/k;          s2=s[mw[mi+1][i]][i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          bbh=(double)bh[mi][i]/(double)stepm; 
  }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 /*********** Tricode ****************************/          ipmx +=1;
 void tricode(int *Tvar, int **nbcode, int imx)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int Ndum[20],ij=1, k, j, i;        } /* end of wave */
   int cptcode=0;      } /* end of individual */
   cptcoveff=0;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (k=0; k<19; k++) Ndum[k]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for (j=1;j<=nlstate+ndeath;j++){
     for (i=1; i<=imx; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=(int)(covar[Tvar[j]][i]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       Ndum[ij]++;            }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(d=0; d<dh[mi][i]; d++){
       if (ij > cptcode) cptcode=ij;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for (i=0; i<=cptcode; i++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if(Ndum[i]!=0) ncodemax[j]++;            }
     }          
     ij=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for (i=1; i<=ncodemax[j]; i++) {            oldm=newm;
       for (k=0; k<=19; k++) {          } /* end mult */
         if (Ndum[k] != 0) {        
           nbcode[Tvar[j]][ij]=k;          s1=s[mw[mi][i]][i];
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/          s2=s[mw[mi+1][i]][i];
           ij++;          if( s2 > nlstate){ 
         }            lli=log(out[s1][s2] - savm[s1][s2]);
         if (ij > ncodemax[j]) break;          }else{
       }              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     }          }
   }            ipmx +=1;
           sw += weight[i];
  for (k=0; k<19; k++) Ndum[k]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
  for (i=1; i<=ncovmodel-2; i++) {        } /* end of wave */
       ij=Tvar[i];      } /* end of individual */
       Ndum[ij]++;    }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];
  ij=1;        for(mi=1; mi<= wav[i]-1; mi++){
  for (i=1; i<=10; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
    if((Ndum[i]!=0) && (i<=ncovcol)){            for (j=1;j<=nlstate+ndeath;j++){
      Tvaraff[ij]=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      ij++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    }            }
  }          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
     cptcoveff=ij-1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /*********** Health Expectancies ****************/            }
           
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Health expectancies */            savm=oldm;
   int i, j, nhstepm, hstepm, h, nstepm;            oldm=newm;
   double age, agelim, hf;          } /* end mult */
   double ***p3mat;        
            s1=s[mw[mi][i]][i];
   fprintf(ficreseij,"# Health expectancies\n");          s2=s[mw[mi+1][i]][i];
   fprintf(ficreseij,"# Age");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for(i=1; i<=nlstate;i++)          ipmx +=1;
     for(j=1; j<=nlstate;j++)          sw += weight[i];
       fprintf(ficreseij," %1d-%1d",i,j);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficreseij,"\n");          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
   if(estepm < stepm){      } /* end of individual */
     printf ("Problem %d lower than %d\n",estepm, stepm);    } /* End of if */
   }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   else  hstepm=estepm;      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /* We compute the life expectancy from trapezoids spaced every estepm months    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
    * This is mainly to measure the difference between two models: for example    return -l;
    * if stepm=24 months pijx are given only every 2 years and by summing them  }
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  /*************** log-likelihood *************/
    * to the curvature of the survival function. If, for the same date, we  double funcone( double *x)
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  {
    * to compare the new estimate of Life expectancy with the same linear    /* Same as likeli but slower because of a lot of printf and if */
    * hypothesis. A more precise result, taking into account a more precise    int i, ii, j, k, mi, d, kk;
    * curvature will be obtained if estepm is as small as stepm. */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   /* For example we decided to compute the life expectancy with the smallest unit */    double lli; /* Individual log likelihood */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double llt;
      nhstepm is the number of hstepm from age to agelim    int s1, s2;
      nstepm is the number of stepm from age to agelin.    double bbh, survp;
      Look at hpijx to understand the reason of that which relies in memory size    /*extern weight */
      and note for a fixed period like estepm months */    /* We are differentiating ll according to initial status */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      survival function given by stepm (the optimization length). Unfortunately it    /*for(i=1;i<imx;i++) 
      means that if the survival funtion is printed only each two years of age and if      printf(" %d\n",s[4][i]);
      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.    cov[1]=1.;
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   agelim=AGESUP;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     /* nhstepm age range expressed in number of stepm */      for(mi=1; mi<= wav[i]-1; mi++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        for (ii=1;ii<=nlstate+ndeath;ii++)
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          for (j=1;j<=nlstate+ndeath;j++){
     /* if (stepm >= YEARM) hstepm=1;*/            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        for(d=0; d<dh[mi][i]; d++){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          newm=savm;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          for (kk=1; kk<=cptcovage;kk++) {
     for(i=1; i<=nlstate;i++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)          }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* 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]);*/          savm=oldm;
         }          oldm=newm;
     fprintf(ficreseij,"%3.0f",age );        } /* end mult */
     for(i=1; i<=nlstate;i++)        
       for(j=1; j<=nlstate;j++){        s1=s[mw[mi][i]][i];
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
     fprintf(ficreseij,"\n");        /* bias is positive if real duration
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         * is higher than the multiple of stepm and negative otherwise.
   }         */
 }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
 /************ Variance ******************/        } else if  (s2==-2) {
 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, int estepm)          for (j=1,survp=0. ; j<=nlstate; j++) 
 {            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* Variance of health expectancies */          lli= log(survp);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }else if (mle==1){
   double **newm;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **dnewm,**doldm;        } else if(mle==2){
   int i, j, nhstepm, hstepm, h, nstepm ;          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 */
   int k, cptcode;        } else if(mle==3){  /* exponential inter-extrapolation */
   double *xp;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   double **gp, **gm;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double ***gradg, ***trgradg;          lli=log(out[s1][s2]); /* Original formula */
   double ***p3mat;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   double age,agelim, hf;          lli=log(out[s1][s2]); /* Original formula */
   int theta;        } /* End of if */
         ipmx +=1;
    fprintf(ficresvij,"# Covariances of life expectancies\n");        sw += weight[i];
   fprintf(ficresvij,"# Age");        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for(i=1; i<=nlstate;i++)  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(j=1; j<=nlstate;j++)        if(globpr){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   fprintf(ficresvij,"\n");   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   xp=vector(1,npar);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   dnewm=matrix(1,nlstate,1,npar);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   doldm=matrix(1,nlstate,1,nlstate);            llt +=ll[k]*gipmx/gsw;
              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);          fprintf(ficresilk," %10.6f\n", -llt);
   }        }
   else  hstepm=estepm;        } /* end of wave */
   /* For example we decided to compute the life expectancy with the smallest unit */    } /* end of individual */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      nhstepm is the number of hstepm from age to agelim    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      nstepm is the number of stepm from age to agelin.    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      Look at hpijx to understand the reason of that which relies in memory size    if(globpr==0){ /* First time we count the contributions and weights */
      and note for a fixed period like k years */      gipmx=ipmx;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      gsw=sw;
      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    return -l;
      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.  
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  /*************** function likelione ***********/
   agelim = AGESUP;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* This routine should help understanding what is done with 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */       the selection of individuals/waves and
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       to check the exact contribution to the likelihood.
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);       Plotting could be done.
     gp=matrix(0,nhstepm,1,nlstate);     */
     gm=matrix(0,nhstepm,1,nlstate);    int k;
   
     for(theta=1; theta <=npar; theta++){    if(*globpri !=0){ /* Just counts and sums, no printings */
       for(i=1; i<=npar; i++){ /* Computes gradient */      strcpy(fileresilk,"ilk"); 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      strcat(fileresilk,fileres);
       }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          printf("Problem with resultfile: %s\n", fileresilk);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
       if (popbased==1) {      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(i=1; i<=nlstate;i++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           prlim[i][i]=probs[(int)age][i][ij];      /*  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(k=1; k<=nlstate; k++) 
          fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       for(j=1; j<= nlstate; j++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         for(h=0; h<=nhstepm; h++){    }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
       }      fclose(ficresilk);
          fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       for(i=1; i<=npar; i++) /* Computes gradient */      fflush(fichtm); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
    
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  /*********** Maximum Likelihood Estimation ***************/
           prlim[i][i]=probs[(int)age][i][ij];  
       }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
       for(j=1; j<= nlstate; j++){    int i,j, iter;
         for(h=0; h<=nhstepm; h++){    double **xi;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    double fret;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double fretone; /* Only one call to likelihood */
         }    /*  char filerespow[FILENAMELENGTH];*/
       }    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
       for(j=1; j<= nlstate; j++)      for (j=1;j<=npar;j++)
         for(h=0; h<=nhstepm; h++){        xi[i][j]=(i==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         }    strcpy(filerespow,"pow"); 
     } /* End theta */    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(h=0; h<=nhstepm; h++)    }
       for(j=1; j<=nlstate;j++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         for(theta=1; theta <=npar; theta++)    for (i=1;i<=nlstate;i++)
           trgradg[h][j][theta]=gradg[h][theta][j];      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    fprintf(ficrespow,"\n");
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)    powell(p,xi,npar,ftol,&iter,&fret,func);
         vareij[i][j][(int)age] =0.;  
     free_matrix(xi,1,npar,1,npar);
     for(h=0;h<=nhstepm;h++){    fclose(ficrespow);
       for(k=0;k<=nhstepm;k++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)  }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }  /**** Computes Hessian and covariance matrix ***/
     }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
     fprintf(ficresvij,"%.0f ",age );    double  **a,**y,*x,pd;
     for(i=1; i<=nlstate;i++)    double **hess;
       for(j=1; j<=nlstate;j++){    int i, j,jk;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    int *indx;
       }  
     fprintf(ficresvij,"\n");    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     free_matrix(gp,0,nhstepm,1,nlstate);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     free_matrix(gm,0,nhstepm,1,nlstate);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double gompertz(double p[]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hess=matrix(1,npar,1,npar);
   } /* End age */  
      printf("\nCalculation of the hessian matrix. Wait...\n");
   free_vector(xp,1,npar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   free_matrix(doldm,1,nlstate,1,npar);    for (i=1;i<=npar;i++){
   free_matrix(dnewm,1,nlstate,1,nlstate);      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
 }     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
 /************ Variance of prevlim ******************/      
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      /*  printf(" %f ",p[i]);
 {          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   /* Variance of prevalence limit */    }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    
   double **newm;    for (i=1;i<=npar;i++) {
   double **dnewm,**doldm;      for (j=1;j<=npar;j++)  {
   int i, j, nhstepm, hstepm;        if (j>i) { 
   int k, cptcode;          printf(".%d%d",i,j);fflush(stdout);
   double *xp;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double *gp, *gm;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   double **gradg, **trgradg;          
   double age,agelim;          hess[j][i]=hess[i][j];    
   int theta;          /*printf(" %lf ",hess[i][j]);*/
            }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      }
   fprintf(ficresvpl,"# Age");    }
   for(i=1; i<=nlstate;i++)    printf("\n");
       fprintf(ficresvpl," %1d-%1d",i,i);    fprintf(ficlog,"\n");
   fprintf(ficresvpl,"\n");  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   xp=vector(1,npar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
   hstepm=1*YEARM; /* Every year of age */    x=vector(1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    indx=ivector(1,npar);
   agelim = AGESUP;    for (i=1;i<=npar;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    ludcmp(a,npar,indx,&pd);
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for (j=1;j<=npar;j++) {
     gradg=matrix(1,npar,1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
     gp=vector(1,nlstate);      x[j]=1;
     gm=vector(1,nlstate);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
     for(theta=1; theta <=npar; theta++){        matcov[i][j]=x[i];
       for(i=1; i<=npar; i++){ /* Computes gradient */      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    printf("\n#Hessian matrix#\n");
       for(i=1;i<=nlstate;i++)    fprintf(ficlog,"\n#Hessian matrix#\n");
         gp[i] = prlim[i][i];    for (i=1;i<=npar;i++) { 
          for (j=1;j<=npar;j++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */        printf("%.3e ",hess[i][j]);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        fprintf(ficlog,"%.3e ",hess[i][j]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      }
       for(i=1;i<=nlstate;i++)      printf("\n");
         gm[i] = prlim[i][i];      fprintf(ficlog,"\n");
     }
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    /* Recompute Inverse */
     } /* End theta */    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     trgradg =matrix(1,nlstate,1,npar);    ludcmp(a,npar,indx,&pd);
   
     for(j=1; j<=nlstate;j++)    /*  printf("\n#Hessian matrix recomputed#\n");
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
     for(i=1;i<=nlstate;i++)      x[j]=1;
       varpl[i][(int)age] =0.;      lubksb(a,npar,indx,x);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      for (i=1;i<=npar;i++){ 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        y[i][j]=x[i];
     for(i=1;i<=nlstate;i++)        printf("%.3e ",y[i][j]);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        fprintf(ficlog,"%.3e ",y[i][j]);
       }
     fprintf(ficresvpl,"%.0f ",age );      printf("\n");
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    }
     fprintf(ficresvpl,"\n");    */
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);    free_matrix(a,1,npar,1,npar);
     free_matrix(gradg,1,npar,1,nlstate);    free_matrix(y,1,npar,1,npar);
     free_matrix(trgradg,1,nlstate,1,npar);    free_vector(x,1,npar);
   } /* End age */    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  }
   
 }  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 /************ Variance of one-step probabilities  ******************/  {
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    int i;
 {    int l=1, lmax=20;
   int i, j;    double k1,k2;
   int k=0, cptcode;    double p2[NPARMAX+1];
   double **dnewm,**doldm;    double res;
   double *xp;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double *gp, *gm;    double fx;
   double **gradg, **trgradg;    int k=0,kmax=10;
   double age,agelim, cov[NCOVMAX];    double l1;
   int theta;  
   char fileresprob[FILENAMELENGTH];    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
   strcpy(fileresprob,"prob");    for(l=0 ; l <=lmax; l++){
   strcat(fileresprob,fileres);      l1=pow(10,l);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      delts=delt;
     printf("Problem with resultfile: %s\n", fileresprob);      for(k=1 ; k <kmax; k=k+1){
   }        delt = delta*(l1*k);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        p2[theta]=x[theta] +delt;
          k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
   xp=vector(1,npar);        k2=func(p2)-fx;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          
   cov[1]=1;  #ifdef DEBUG
   for (age=bage; age<=fage; age ++){        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);
     cov[2]=age;        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);
     gradg=matrix(1,npar,1,9);  #endif
     trgradg=matrix(1,9,1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          k=kmax;
            }
     for(theta=1; theta <=npar; theta++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(i=1; i<=npar; i++)          k=kmax; l=lmax*10.;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
              else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          delts=delt;
            }
       k=0;      }
       for(i=1; i<= (nlstate+ndeath); i++){    }
         for(j=1; j<=(nlstate+ndeath);j++){    delti[theta]=delts;
            k=k+1;    return res; 
           gp[k]=pmmij[i][j];    
         }  }
       }  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       for(i=1; i<=npar; i++)  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i;
        int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double p2[NPARMAX+1];
       k=0;    int k;
       for(i=1; i<=(nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){    fx=func(x);
           k=k+1;    for (k=1; k<=2; k++) {
           gm[k]=pmmij[i][j];      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;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        p2[thetai]=x[thetai]+delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    
       for(theta=1; theta <=npar; theta++)      p2[thetai]=x[thetai]-delti[thetai]/k;
       trgradg[j][theta]=gradg[theta][j];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k3=func(p2)-fx;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      pmij(pmmij,cov,ncovmodel,x,nlstate);      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      k=0;  #ifdef DEBUG
      for(i=1; i<=(nlstate+ndeath); i++){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        for(j=1; j<=(nlstate+ndeath);j++){      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);
          k=k+1;  #endif
          gm[k]=pmmij[i][j];    }
         }    return res;
      }  }
        
      /*printf("\n%d ",(int)age);  /************** Inverse of matrix **************/
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  void ludcmp(double **a, int n, int *indx, double *d) 
          { 
     int i,imax,j,k; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double big,dum,sum,temp; 
      }*/    double *vv; 
    
   fprintf(ficresprob,"\n%d ",(int)age);    vv=vector(1,n); 
     *d=1.0; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for (i=1;i<=n;i++) { 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      big=0.0; 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      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"); 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      vv[i]=1.0/big; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    } 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (j=1;j<=n;j++) { 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (i=1;i<j;i++) { 
 }        sum=a[i][j]; 
  free_vector(xp,1,npar);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 fclose(ficresprob);        a[i][j]=sum; 
       } 
 }      big=0.0; 
       for (i=j;i<=n;i++) { 
 /******************* Printing html file ***********/        sum=a[i][j]; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        for (k=1;k<j;k++) 
  int lastpass, int stepm, int weightopt, char model[],\          sum -= a[i][k]*a[k][j]; 
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        a[i][j]=sum; 
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\        if ( (dum=vv[i]*fabs(sum)) >= big) { 
  char version[], int popforecast, int estepm ){          big=dum; 
   int jj1, k1, i1, cpt;          imax=i; 
   FILE *fichtm;        } 
   /*char optionfilehtm[FILENAMELENGTH];*/      } 
       if (j != imax) { 
   strcpy(optionfilehtm,optionfile);        for (k=1;k<=n;k++) { 
   strcat(optionfilehtm,".htm");          dum=a[imax][k]; 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          a[imax][k]=a[j][k]; 
     printf("Problem with %s \n",optionfilehtm), exit(0);          a[j][k]=dum; 
   }        } 
         *d = -(*d); 
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        vv[imax]=vv[j]; 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      } 
 \n      indx[j]=imax; 
 Total number of observations=%d <br>\n      if (a[j][j] == 0.0) a[j][j]=TINY; 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      if (j != n) { 
 <hr  size=\"2\" color=\"#EC5E5E\">        dum=1.0/(a[j][j]); 
  <ul><li>Outputs files<br>\n        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      } 
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    } 
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    free_vector(vv,1,n);  /* Doesn't work */
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n  ;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n  } 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);  
   void lubksb(double **a, int n, int *indx, double b[]) 
  fprintf(fichtm,"\n  { 
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    int i,ii=0,ip,j; 
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    double sum; 
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n   
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
  if(popforecast==1) fprintf(fichtm,"\n      sum=b[ip]; 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      b[ip]=b[i]; 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      if (ii) 
         <br>",fileres,fileres,fileres,fileres);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
  else      else if (sum) ii=i; 
    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);      b[i]=sum; 
 fprintf(fichtm," <li>Graphs</li><p>");    } 
     for (i=n;i>=1;i--) { 
  m=cptcoveff;      sum=b[i]; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
  jj1=0;    } 
  for(k1=1; k1<=m;k1++){  } 
    for(i1=1; i1<=ncodemax[k1];i1++){  
        jj1++;  void pstamp(FILE *fichier)
        if (cptcovn > 0) {  {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
          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\">");  /************ Frequencies ********************/
        }  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[])
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  {  /* Some frequencies */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        
        for(cpt=1; cpt<nlstate;cpt++){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    int first;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double ***freq; /* Frequencies */
        }    double *pp, **prop;
     for(cpt=1; cpt<=nlstate;cpt++) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    char fileresp[FILENAMELENGTH];
 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);      pp=vector(1,nlstate);
      }    prop=matrix(1,nlstate,iagemin,iagemax+3);
      for(cpt=1; cpt<=nlstate;cpt++) {    strcpy(fileresp,"p");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    strcat(fileresp,fileres);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if((ficresp=fopen(fileresp,"w"))==NULL) {
      }      printf("Problem with prevalence resultfile: %s\n", fileresp);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 health expectancies in states (1) and (2): e%s%d.gif<br>      exit(0);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
 fprintf(fichtm,"\n</body>");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    }    j1=0;
    }    
 fclose(fichtm);    j=cptcoveff;
 }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
 /******************* Gnuplot file **************/    first=1;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
     for(k1=1; k1<=j;k1++){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   strcpy(optionfilegnuplot,optionfilefiname);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   strcat(optionfilegnuplot,".gp.txt");          scanf("%d", i);*/
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for (i=-5; i<=nlstate+ndeath; i++)  
     printf("Problem with file %s",optionfilegnuplot);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   }            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);      for (i=1; i<=nlstate; i++)  
 #endif        for(m=iagemin; m <= iagemax+3; m++)
 m=pow(2,cptcoveff);          prop[i][m]=0;
          
  /* 1eme*/        dateintsum=0;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        k2cpt=0;
    for (k1=1; k1<= m ; k1 ++) {        for (i=1; i<=imx; i++) {
           bool=1;
 #ifdef windows          if  (cptcovn>0) {
     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",ageminpar,fage,fileres,k1-1,k1-1);            for (z1=1; z1<=cptcoveff; z1++) 
 #endif              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 #ifdef unix                bool=0;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          }
 #endif          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
 for (i=1; i<= nlstate ; i ++) {              k2=anint[m][i]+(mint[m][i]/12.);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for (i=1; i<= nlstate ; i ++) {                if (m<lastpass) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 }                }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                
      for (i=1; i<= nlstate ; i ++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  dateintsum=dateintsum+k2;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  k2cpt++;
 }                  }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                /*}*/
 #ifdef unix            }
 fprintf(ficgp,"\nset ter gif small size 400,300");          }
 #endif        }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);         
    }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   }        pstamp(ficresp);
   /*2 eme*/        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   for (k1=1; k1<= m ; k1 ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);          fprintf(ficresp, "**********\n#");
            }
     for (i=1; i<= nlstate+1 ; i ++) {        for(i=1; i<=nlstate;i++) 
       k=2*i;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresp, "\n");
       for (j=1; j<= nlstate+1 ; j ++) {        
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=iagemin; i <= iagemax+3; i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(i==iagemax+3){
 }              fprintf(ficlog,"Total");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          }else{
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            if(first==1){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              first=0;
       for (j=1; j<= nlstate+1 ; j ++) {              printf("See log file for details...\n");
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
         else fprintf(ficgp," \%%*lf (\%%*lf)");            fprintf(ficlog,"Age %d", i);
 }            }
       fprintf(ficgp,"\" t\"\" w l 0,");          for(jk=1; jk <=nlstate ; jk++){
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       for (j=1; j<= nlstate+1 ; j ++) {              pp[jk] += freq[jk][m][i]; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){
 }              for(m=-1, pos=0; m <=0 ; m++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              pos += freq[jk][m][i];
       else fprintf(ficgp,"\" t\"\" w l 0,");            if(pp[jk]>=1.e-10){
     }              if(first==1){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /*3eme*/            }else{
               if(first==1)
   for (k1=1; k1<= m ; k1 ++) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for (cpt=1; cpt<= nlstate ; cpt ++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       k=2+nlstate*(cpt-1);            }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          }
       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);          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              pp[jk] += freq[jk][m][i];
     }          }       
     }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
              pos += pp[jk];
   /* CV preval stat */            posprop += prop[jk][i];
     for (k1=1; k1<= m ; k1 ++) {          }
     for (cpt=1; cpt<nlstate ; cpt ++) {          for(jk=1; jk <=nlstate ; jk++){
       k=3;            if(pos>=1.e-5){
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for (i=1; i< nlstate ; i ++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         fprintf(ficgp,"+$%d",k+i+1);            }else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              if(first==1)
                      printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       l=3+(nlstate+ndeath)*cpt;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            }
       for (i=1; i< nlstate ; i ++) {            if( i <= iagemax){
         l=3+(nlstate+ndeath)*cpt;              if(pos>=1.e-5){
         fprintf(ficgp,"+$%d",l+i+1);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       }                /*probs[i][jk][j1]= pp[jk]/pos;*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
     }              else
   }                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
              }
   /* proba elementaires */          }
    for(i=1,jk=1; i <=nlstate; i++){          
     for(k=1; k <=(nlstate+ndeath); k++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
       if (k != i) {            for(m=-1; m <=nlstate+ndeath; m++)
         for(j=1; j <=ncovmodel; j++){              if(freq[jk][m][i] !=0 ) {
                      if(first==1)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           jk++;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           fprintf(ficgp,"\n");              }
         }          if(i <= iagemax)
       }            fprintf(ficresp,"\n");
     }          if(first==1)
     }            printf("Others in log...\n");
           fprintf(ficlog,"\n");
     for(jk=1; jk <=m; jk++) {        }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      }
    i=1;    }
    for(k2=1; k2<=nlstate; k2++) {    dateintmean=dateintsum/k2cpt; 
      k3=i;   
      for(k=1; k<=(nlstate+ndeath); k++) {    fclose(ficresp);
        if (k != k2){    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    free_vector(pp,1,nlstate);
 ij=1;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         for(j=3; j <=ncovmodel; j++) {    /* End of Freq */
           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++;  /************ Prevalence ********************/
           }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
           else  {  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         }       in each health status at the date of interview (if between dateprev1 and dateprev2).
           fprintf(ficgp,")/(1");       We still use firstpass and lastpass as another selection.
            */
         for(k1=1; k1 <=nlstate; k1++){     
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 ij=1;    double ***freq; /* Frequencies */
           for(j=3; j <=ncovmodel; j++){    double *pp, **prop;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double pos,posprop; 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double  y2; /* in fractional years */
             ij++;    int iagemin, iagemax;
           }  
           else    iagemin= (int) agemin;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    iagemax= (int) agemax;
           }    /*pp=vector(1,nlstate);*/
           fprintf(ficgp,")");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    j1=0;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    
         i=i+ncovmodel;    j=cptcoveff;
        }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      }    
    }    for(k1=1; k1<=j;k1++){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for(i1=1; i1<=ncodemax[k1];i1++){
    }        j1++;
            
   fclose(ficgp);        for (i=1; i<=nlstate; i++)  
 }  /* end gnuplot */          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
        
 /*************** Moving average **************/        for (i=1; i<=imx; i++) { /* Each individual */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          bool=1;
           if  (cptcovn>0) {
   int i, cpt, cptcod;            for (z1=1; z1<=cptcoveff; z1++) 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for (i=1; i<=nlstate;i++)                bool=0;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          } 
           mobaverage[(int)agedeb][i][cptcod]=0.;          if (bool==1) { 
                for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for (i=1; i<=nlstate;i++){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           for (cpt=0;cpt<=4;cpt++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
           }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                  prop[s[m][i]][iagemax+3] += weight[i]; 
     }                } 
                  }
 }            } /* end selection of waves */
           }
         }
 /************** Forecasting ******************/        for(i=iagemin; i <= iagemax+3; i++){  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          
            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            posprop += prop[jk][i]; 
   int *popage;          } 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;          for(jk=1; jk <=nlstate ; jk++){     
   double ***p3mat;            if( i <=  iagemax){ 
   char fileresf[FILENAMELENGTH];              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
  agelim=AGESUP;              } 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            } 
           }/* end jk */ 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }/* end i */ 
        } /* end i1 */
      } /* end k1 */
   strcpy(fileresf,"f");    
   strcat(fileresf,fileres);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /*free_vector(pp,1,nlstate);*/
     printf("Problem with forecast resultfile: %s\n", fileresf);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  }  /* End of prevalence */
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   /************* Waves Concatenation ***************/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   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)
   if (mobilav==1) {  {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     movingaverage(agedeb, fage, ageminpar, mobaverage);       Death is a valid wave (if date is known).
   }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   stepsize=(int) (stepm+YEARM-1)/YEARM;       and mw[mi+1][i]. dh depends on stepm.
   if (stepm<=12) stepsize=1;       */
    
   agelim=AGESUP;    int i, mi, m;
      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   hstepm=1;       double sum=0., jmean=0.;*/
   hstepm=hstepm/stepm;    int first;
   yp1=modf(dateintmean,&yp);    int j, k=0,jk, ju, jl;
   anprojmean=yp;    double sum=0.;
   yp2=modf((yp1*12),&yp);    first=0;
   mprojmean=yp;    jmin=1e+5;
   yp1=modf((yp2*30.5),&yp);    jmax=-1;
   jprojmean=yp;    jmean=0.;
   if(jprojmean==0) jprojmean=1;    for(i=1; i<=imx; i++){
   if(mprojmean==0) jprojmean=1;      mi=0;
        m=firstpass;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      while(s[m][i] <= nlstate){
          if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   for(cptcov=1;cptcov<=i2;cptcov++){          mw[++mi][i]=m;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        if(m >=lastpass)
       k=k+1;          break;
       fprintf(ficresf,"\n#******");        else
       for(j=1;j<=cptcoveff;j++) {          m++;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }/* end while */
       }      if (s[m][i] > nlstate){
       fprintf(ficresf,"******\n");        mi++;     /* Death is another wave */
       fprintf(ficresf,"# StartingAge FinalAge");        /* if(mi==0)  never been interviewed correctly before death */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);           /* Only death is a correct wave */
              mw[mi][i]=m;
            }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");      wav[i]=mi;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        if(mi==0){
         nbwarn++;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        if(first==0){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           nhstepm = nhstepm/hstepm;          first=1;
                  }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if(first==1){
           oldm=oldms;savm=savms;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
              } /* end mi==0 */
           for (h=0; h<=nhstepm; h++){    } /* End individuals */
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    for(i=1; i<=imx; i++){
             }      for(mi=1; mi<wav[i];mi++){
             for(j=1; j<=nlstate+ndeath;j++) {        if (stepm <=0)
               kk1=0.;kk2=0;          dh[mi][i]=1;
               for(i=1; i<=nlstate;i++) {                      else{
                 if (mobilav==1)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            if (agedc[i] < 2*AGESUP) {
                 else {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              if(j==0) j=1;  /* Survives at least one month after exam */
                 }              else if(j<0){
                                nberr++;
               }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               if (h==(int)(calagedate+12*cpt)){                j=1; /* Temporary Dangerous patch */
                 fprintf(ficresf," %.3f", kk1);                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);
                                        fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }              }
           }              k=k+1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if (j >= jmax){
         }                jmax=j;
       }                ijmax=i;
     }              }
   }              if (j <= jmin){
                        jmin=j;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                ijmin=i;
               }
   fclose(ficresf);              sum=sum+j;
 }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 /************** Forecasting ******************/              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 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;          else{
   int *popage;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  /*        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]); */
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;            k=k+1;
   char filerespop[FILENAMELENGTH];            if (j >= jmax) {
               jmax=j;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              ijmax=i;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
   agelim=AGESUP;            else if (j <= jmin){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              jmin=j;
                ijmin=i;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            }
              /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
              /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   strcpy(filerespop,"pop");            if(j<0){
   strcat(filerespop,fileres);              nberr++;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              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]);
     printf("Problem with forecast resultfile: %s\n", filerespop);              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]);
   }            }
   printf("Computing forecasting: result on file '%s' \n", filerespop);            sum=sum+j;
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          jk= j/stepm;
           jl= j -jk*stepm;
   if (mobilav==1) {          ju= j -(jk+1)*stepm;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     movingaverage(agedeb, fage, ageminpar, mobaverage);            if(jl==0){
   }              dh[mi][i]=jk;
               bh[mi][i]=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;            }else{ /* We want a negative bias in order to only have interpolation ie
   if (stepm<=12) stepsize=1;                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   agelim=AGESUP;              bh[mi][i]=ju;
              }
   hstepm=1;          }else{
   hstepm=hstepm/stepm;            if(jl <= -ju){
                dh[mi][i]=jk;
   if (popforecast==1) {              bh[mi][i]=jl;       /* bias is positive if real duration
     if((ficpop=fopen(popfile,"r"))==NULL) {                                   * is higher than the multiple of stepm and negative otherwise.
       printf("Problem with population file : %s\n",popfile);exit(0);                                   */
     }            }
     popage=ivector(0,AGESUP);            else{
     popeffectif=vector(0,AGESUP);              dh[mi][i]=jk+1;
     popcount=vector(0,AGESUP);              bh[mi][i]=ju;
                }
     i=1;              if(dh[mi][i]==0){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              dh[mi][i]=1; /* At least one step */
                  bh[mi][i]=ju; /* At least one step */
     imx=i;              /*  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<imx;i++) popeffectif[popage[i]]=popcount[i];            }
   }          } /* end if mle */
         }
   for(cptcov=1;cptcov<=i2;cptcov++){      } /* end wave */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
       k=k+1;    jmean=sum/k;
       fprintf(ficrespop,"\n#******");    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);
       for(j=1;j<=cptcoveff;j++) {    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);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   }
       }  
       fprintf(ficrespop,"******\n");  /*********** Tricode ****************************/
       fprintf(ficrespop,"# Age");  void tricode(int *Tvar, int **nbcode, int imx)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  {
       if (popforecast==1)  fprintf(ficrespop," [Population]");    
          int Ndum[20],ij=1, k, j, i, maxncov=19;
       for (cpt=0; cpt<=0;cpt++) {    int cptcode=0;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      cptcoveff=0; 
           
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for (k=0; k<maxncov; k++) Ndum[k]=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for (k=1; k<=7; k++) ncodemax[k]=0;
           nhstepm = nhstepm/hstepm;  
              for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           oldm=oldms;savm=savms;                                 modality*/ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                Ndum[ij]++; /*store the modality */
           for (h=0; h<=nhstepm; h++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             if (h==(int) (calagedate+YEARM*cpt)) {        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                                         Tvar[j]. If V=sex and male is 0 and 
             }                                         female is 1, then  cptcode=1.*/
             for(j=1; j<=nlstate+ndeath;j++) {      }
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                    for (i=0; i<=cptcode; i++) {
                 if (mobilav==1)        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 */
                   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];      ij=1; 
                 }      for (i=1; i<=ncodemax[j]; i++) {
               }        for (k=0; k<= maxncov; k++) {
               if (h==(int)(calagedate+12*cpt)){          if (Ndum[k] != 0) {
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            nbcode[Tvar[j]][ij]=k; 
                   /*fprintf(ficrespop," %.3f", kk1);            /* 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; */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/            
               }            ij++;
             }          }
             for(i=1; i<=nlstate;i++){          if (ij > ncodemax[j]) break; 
               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+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];   for (k=0; k< maxncov; k++) Ndum[k]=0;
             }  
    for (i=1; i<=ncovmodel-2; i++) { 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);     ij=Tvar[i];
           }     Ndum[ij]++;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   }
         }  
       }   ij=1;
     for (i=1; i<= maxncov; i++) {
   /******/     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {       ij++;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);       }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){   }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   
           nhstepm = nhstepm/hstepm;   cptcoveff=ij-1; /*Number of simple covariates*/
            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /*********** Health Expectancies ****************/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           for (h=0; h<=nhstepm; h++){  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[] )
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  {
             }    /* Health expectancies, no variances */
             for(j=1; j<=nlstate+ndeath;j++) {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
               kk1=0.;kk2=0;    double age, agelim, hf;
               for(i=1; i<=nlstate;i++) {                  double ***p3mat;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        double eip;
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    pstamp(ficreseij);
             }    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");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=nlstate;i++){
         }      for(j=1; j<=nlstate;j++){
       }        fprintf(ficreseij," e%1d%1d ",i,j);
    }      }
   }      fprintf(ficreseij," e%1d. ",i);
      }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficreseij,"\n");
   
   if (popforecast==1) {    
     free_ivector(popage,0,AGESUP);    if(estepm < stepm){
     free_vector(popeffectif,0,AGESUP);      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_vector(popcount,0,AGESUP);    }
   }    else  hstepm=estepm;   
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* We compute the life expectancy from trapezoids spaced every estepm months
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * This is mainly to measure the difference between two models: for example
   fclose(ficrespop);     * if stepm=24 months pijx are given only every 2 years and by summing them
 }     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
 /***********************************************/     * to the curvature of the survival function. If, for the same date, we 
 /**************** Main Program *****************/     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 /***********************************************/     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 int main(int argc, char *argv[])     * curvature will be obtained if estepm is as small as stepm. */
 {  
     /* For example we decided to compute the life expectancy with the smallest unit */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double agedeb, agefin,hf;       nhstepm is the number of hstepm from age to agelim 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   double fret;       and note for a fixed period like estepm months */
   double **xi,tmp,delta;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   double dum; /* Dummy variable */       means that if the survival funtion is printed only each two years of age and if
   double ***p3mat;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   int *indx;       results. So we changed our mind and took the option of the best precision.
   char line[MAXLINE], linepar[MAXLINE];    */
   char title[MAXLINE];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    agelim=AGESUP;
      /* nhstepm age range expressed in number of stepm */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   char filerest[FILENAMELENGTH];    /* if (stepm >= YEARM) hstepm=1;*/
   char fileregp[FILENAMELENGTH];    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char popfile[FILENAMELENGTH];    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   int sdeb, sfin; /* Status at beginning and end */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   int c,  h , cpt,l;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   int ju,jl, mi;      
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      
   int mobilav=0,popforecast=0;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   int hstepm, nhstepm;      
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   double bage, fage, age, agelim, agebase;      
   double ftolpl=FTOL;      /* Computing expectancies */
   double **prlim;      for(i=1; i<=nlstate;i++)
   double *severity;        for(j=1; j<=nlstate;j++)
   double ***param; /* Matrix of parameters */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   double  *p;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   double **matcov; /* Matrix of covariance */            
   double ***delti3; /* Scale */            /* 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]);*/
   double *delti; /* Scale */  
   double ***eij, ***vareij;          }
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;      fprintf(ficreseij,"%3.0f",age );
   double kk1, kk2;      for(i=1; i<=nlstate;i++){
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        eip=0;
          for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   char *alph[]={"a","a","b","c","d","e"}, str[4];        }
         fprintf(ficreseij,"%9.4f", eip );
       }
   char z[1]="c", occ;      fprintf(ficreseij,"\n");
 #include <sys/time.h>      
 #include <time.h>    }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      printf("\n");
   /* long total_usecs;    fprintf(ficlog,"\n");
   struct timeval start_time, end_time;    
    }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);  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[] )
   
   printf("\n%s",version);  {
   if(argc <=1){    /* Covariances of health expectancies eij and of total life expectancies according
     printf("\nEnter the parameter file name: ");     to initial status i, ei. .
     scanf("%s",pathtot);    */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   else{    double age, agelim, hf;
     strcpy(pathtot,argv[1]);    double ***p3matp, ***p3matm, ***varhe;
   }    double **dnewm,**doldm;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    double *xp, *xm;
   /*cygwin_split_path(pathtot,path,optionfile);    double **gp, **gm;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double ***gradg, ***trgradg;
   /* cutv(path,optionfile,pathtot,'\\');*/    int theta;
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    double eip, vip;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   replace(pathc,path);    xp=vector(1,npar);
     xm=vector(1,npar);
 /*-------- arguments in the command line --------*/    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   strcpy(fileres,"r");    
   strcat(fileres, optionfilefiname);    pstamp(ficresstdeij);
   strcat(fileres,".txt");    /* Other files have txt extension */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
   /*---------arguments file --------*/    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     printf("Problem with optionfile %s\n",optionfile);      fprintf(ficresstdeij," e%1d. ",i);
     goto end;    }
   }    fprintf(ficresstdeij,"\n");
   
   strcpy(filereso,"o");    pstamp(ficrescveij);
   strcat(filereso,fileres);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   if((ficparo=fopen(filereso,"w"))==NULL) {    fprintf(ficrescveij,"# Age");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
   /* Reads comments: lines beginning with '#' */        for(i2=1; i2<=nlstate;i2++)
   while((c=getc(ficpar))=='#' && c!= EOF){          for(j2=1; j2<=nlstate;j2++){
     ungetc(c,ficpar);            cptj2= (j2-1)*nlstate+i2;
     fgets(line, MAXLINE, ficpar);            if(cptj2 <= cptj)
     puts(line);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     fputs(line,ficparo);          }
   }      }
   ungetc(c,ficpar);    fprintf(ficrescveij,"\n");
     
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    if(estepm < stepm){
   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);      printf ("Problem %d lower than %d\n",estepm, stepm);
   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);    }
 while((c=getc(ficpar))=='#' && c!= EOF){    else  hstepm=estepm;   
     ungetc(c,ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
     fgets(line, MAXLINE, ficpar);     * This is mainly to measure the difference between two models: for example
     puts(line);     * if stepm=24 months pijx are given only every 2 years and by summing them
     fputs(line,ficparo);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }     * progression in between and thus overestimating or underestimating according
   ungetc(c,ficpar);     * to the curvature of the survival function. If, for the same date, we 
       * estimate the model with stepm=1 month, we can keep estepm to 24 months
         * to compare the new estimate of Life expectancy with the same linear 
   covar=matrix(0,NCOVMAX,1,n);     * hypothesis. A more precise result, taking into account a more precise
   cptcovn=0;     * curvature will be obtained if estepm is as small as stepm. */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
     /* For example we decided to compute the life expectancy with the smallest unit */
   ncovmodel=2+cptcovn;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   /* Read guess parameters */       Look at hpijx to understand the reason of that which relies in memory size
   /* Reads comments: lines beginning with '#' */       and note for a fixed period like estepm months */
   while((c=getc(ficpar))=='#' && c!= EOF){    /* 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
     fgets(line, MAXLINE, ficpar);       means that if the survival funtion is printed only each two years of age and if
     puts(line);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fputs(line,ficparo);       results. So we changed our mind and took the option of the best precision.
   }    */
   ungetc(c,ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* If stepm=6 months */
     for(i=1; i <=nlstate; i++)    /* nhstepm age range expressed in number of stepm */
     for(j=1; j <=nlstate+ndeath-1; j++){    agelim=AGESUP;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       fprintf(ficparo,"%1d%1d",i1,j1);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       printf("%1d%1d",i,j);    /* if (stepm >= YEARM) hstepm=1;*/
       for(k=1; k<=ncovmodel;k++){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fscanf(ficpar," %lf",&param[i][j][k]);    
         printf(" %lf",param[i][j][k]);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficparo," %lf",param[i][j][k]);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       fscanf(ficpar,"\n");    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       printf("\n");    gp=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficparo,"\n");    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     }  
      for (age=bage; age<=fage; age ++){ 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
   p=param[1][1];         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     
   /* Reads comments: lines beginning with '#' */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      /* Computing  Variances of health expectancies */
     fgets(line, MAXLINE, ficpar);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     puts(line);         decrease memory allocation */
     fputs(line,ficparo);      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ 
   ungetc(c,ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   for(i=1; i <=nlstate; i++){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     for(j=1; j <=nlstate+ndeath-1; j++){    
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(j=1; j<= nlstate; j++){
       printf("%1d%1d",i,j);          for(i=1; i<=nlstate; i++){
       fprintf(ficparo,"%1d%1d",i1,j1);            for(h=0; h<=nhstepm-1; h++){
       for(k=1; k<=ncovmodel;k++){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
         fscanf(ficpar,"%le",&delti3[i][j][k]);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
         printf(" %le",delti3[i][j][k]);            }
         fprintf(ficparo," %le",delti3[i][j][k]);          }
       }        }
       fscanf(ficpar,"\n");       
       printf("\n");        for(ij=1; ij<= nlstate*nlstate; ij++)
       fprintf(ficparo,"\n");          for(h=0; h<=nhstepm-1; h++){
     }            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   }          }
   delti=delti3[1][1];      }/* End theta */
        
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){      for(h=0; h<=nhstepm-1; h++)
     ungetc(c,ficpar);        for(j=1; j<=nlstate*nlstate;j++)
     fgets(line, MAXLINE, ficpar);          for(theta=1; theta <=npar; theta++)
     puts(line);            trgradg[h][j][theta]=gradg[h][theta][j];
     fputs(line,ficparo);      
   }  
   ungetc(c,ficpar);       for(ij=1;ij<=nlstate*nlstate;ij++)
          for(ji=1;ji<=nlstate*nlstate;ji++)
   matcov=matrix(1,npar,1,npar);          varhe[ij][ji][(int)age] =0.;
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);       printf("%d|",(int)age);fflush(stdout);
     printf("%s",str);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     fprintf(ficparo,"%s",str);       for(h=0;h<=nhstepm-1;h++){
     for(j=1; j <=i; j++){        for(k=0;k<=nhstepm-1;k++){
       fscanf(ficpar," %le",&matcov[i][j]);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       printf(" %.5le",matcov[i][j]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficparo," %.5le",matcov[i][j]);          for(ij=1;ij<=nlstate*nlstate;ij++)
     }            for(ji=1;ji<=nlstate*nlstate;ji++)
     fscanf(ficpar,"\n");              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     printf("\n");        }
     fprintf(ficparo,"\n");      }
   }      /* Computing expectancies */
   for(i=1; i <=npar; i++)      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     for(j=i+1;j<=npar;j++)      for(i=1; i<=nlstate;i++)
       matcov[i][j]=matcov[j][i];        for(j=1; j<=nlstate;j++)
              for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   printf("\n");            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* 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]);*/
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */          }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
      strcat(rfileres,".");    /* */      fprintf(ficresstdeij,"%3.0f",age );
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      for(i=1; i<=nlstate;i++){
     if((ficres =fopen(rfileres,"w"))==NULL) {        eip=0.;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;        vip=0.;
     }        for(j=1; j<=nlstate;j++){
     fprintf(ficres,"#%s\n",version);          eip += eij[i][j][(int)age];
              for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     /*-------- data file ----------*/            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     if((fic=fopen(datafile,"r"))==NULL)    {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       printf("Problem with datafile: %s\n", datafile);goto end;        }
     }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
     n= lastobs;      fprintf(ficresstdeij,"\n");
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);      fprintf(ficrescveij,"%3.0f",age );
     num=ivector(1,n);      for(i=1; i<=nlstate;i++)
     moisnais=vector(1,n);        for(j=1; j<=nlstate;j++){
     annais=vector(1,n);          cptj= (j-1)*nlstate+i;
     moisdc=vector(1,n);          for(i2=1; i2<=nlstate;i2++)
     andc=vector(1,n);            for(j2=1; j2<=nlstate;j2++){
     agedc=vector(1,n);              cptj2= (j2-1)*nlstate+i2;
     cod=ivector(1,n);              if(cptj2 <= cptj)
     weight=vector(1,n);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     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);      fprintf(ficrescveij,"\n");
     s=imatrix(1,maxwav+1,1,n);     
     adl=imatrix(1,maxwav+1,1,n);        }
     tab=ivector(1,NCOVMAX);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     ncodemax=ivector(1,8);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     i=1;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     while (fgets(line, MAXLINE, fic) != NULL)    {    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if ((i >= firstobs) && (i <=lastobs)) {    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            printf("\n");
         for (j=maxwav;j>=1;j--){    fprintf(ficlog,"\n");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);    free_vector(xm,1,npar);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(xp,1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
            free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
   /************ Variance ******************/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  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[])
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  {
     /* Variance of health expectancies */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         for (j=ncovcol;j>=1;j--){    /* double **newm;*/
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **dnewm,**doldm;
         }    double **dnewmp,**doldmp;
         num[i]=atol(stra);    int i, j, nhstepm, hstepm, h, nstepm ;
            int k, cptcode;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double *xp;
           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;}*/    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
         i=i+1;    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 */
     /* printf("ii=%d", ij);    double ***p3mat;
        scanf("%d",i);*/    double age,agelim, hf;
   imx=i-1; /* Number of individuals */    double ***mobaverage;
     int theta;
   /* for (i=1; i<=imx; i++){    char digit[4];
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    char digitp[25];
     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;    char fileresprobmorprev[FILENAMELENGTH];
     }*/  
      if(popbased==1){
   /* for (i=1; i<=imx; i++){      if(mobilav!=0)
      if (s[4][i]==9)  s[4][i]=-1;        strcpy(digitp,"-populbased-mobilav-");
      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]));}      else strcpy(digitp,"-populbased-nomobil-");
   */    }
      else 
   /* Calculation of the number of parameter from char model*/      strcpy(digitp,"-stablbased-");
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);    if (mobilav!=0) {
   Tvaraff=ivector(1,15);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   Tvard=imatrix(1,15,1,2);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   Tage=ivector(1,15);              fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if (strlen(model) >1){      }
     j=0, j1=0, k1=1, k2=1;    }
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');    strcpy(fileresprobmorprev,"prmorprev"); 
     cptcovn=j+1;    sprintf(digit,"%-d",ij);
     cptcovprod=j1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcpy(modelsav,model);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    strcat(fileresprobmorprev,fileres);
       printf("Error. Non available option model=%s ",model);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       goto end;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        }
     for(i=(j+1); i>=1;i--){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       cutv(stra,strb,modelsav,'+');   
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    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);
       if (strchr(strb,'*')) {    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         cutv(strd,strc,strb,'*');    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         if (strcmp(strc,"age")==0) {      fprintf(ficresprobmorprev," p.%-d SE",j);
           cptcovprod--;      for(i=1; i<=nlstate;i++)
           cutv(strb,stre,strd,'V');        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           Tvar[i]=atoi(stre);    }  
           cptcovage++;    fprintf(ficresprobmorprev,"\n");
             Tage[cptcovage]=i;    fprintf(ficgp,"\n# Routine varevsij");
             /*printf("stre=%s ", stre);*/    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         }    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");
         else if (strcmp(strd,"age")==0) {    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           cptcovprod--;  /*   } */
           cutv(strb,stre,strc,'V');    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           Tvar[i]=atoi(stre);    pstamp(ficresvij);
           cptcovage++;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           Tage[cptcovage]=i;    if(popbased==1)
         }      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
         else {    else
           cutv(strb,stre,strc,'V');      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
           Tvar[i]=ncovcol+k1;    fprintf(ficresvij,"# Age");
           cutv(strb,strc,strd,'V');    for(i=1; i<=nlstate;i++)
           Tprod[k1]=i;      for(j=1; j<=nlstate;j++)
           Tvard[k1][1]=atoi(strc);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
           Tvard[k1][2]=atoi(stre);    fprintf(ficresvij,"\n");
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    xp=vector(1,npar);
           for (k=1; k<=lastobs;k++)    dnewm=matrix(1,nlstate,1,npar);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    doldm=matrix(1,nlstate,1,nlstate);
           k1++;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           k2=k2+2;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
       }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       else {    gpp=vector(nlstate+1,nlstate+ndeath);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    gmp=vector(nlstate+1,nlstate+ndeath);
        /*  scanf("%d",i);*/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       cutv(strd,strc,strb,'V');    
       Tvar[i]=atoi(strc);    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
       strcpy(modelsav,stra);      }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    else  hstepm=estepm;   
         scanf("%d",i);*/    /* 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 
         nstepm is the number of stepm from age to agelin. 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);       Look at hpijx to understand the reason of that which relies in memory size
   printf("cptcovprod=%d ", cptcovprod);       and note for a fixed period like k years */
   scanf("%d ",i);*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fclose(fic);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
     /*  if(mle==1){*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     if (weightopt != 1) { /* Maximisation without weights*/       results. So we changed our mind and took the option of the best precision.
       for(i=1;i<=n;i++) weight[i]=1.0;    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     /*-calculation of age at interview from date of interview and age at death -*/    agelim = AGESUP;
     agev=matrix(1,maxwav,1,imx);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     for (i=1; i<=imx; i++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(m=2; (m<= maxwav); m++) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          anint[m][i]=9999;      gp=matrix(0,nhstepm,1,nlstate);
          s[m][i]=-1;      gm=matrix(0,nhstepm,1,nlstate);
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }      for(theta=1; theta <=npar; theta++){
     }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for (i=1; i<=imx; i++)  {        }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(m=1; (m<= maxwav); m++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {        if (popbased==1) {
             if(agedc[i]>0)          if(mobilav ==0){
               if(moisdc[i]!=99 && andc[i]!=9999)            for(i=1; i<=nlstate;i++)
                 agev[m][i]=agedc[i];              prlim[i][i]=probs[(int)age][i][ij];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          }else{ /* mobilav */ 
            else {            for(i=1; i<=nlstate;i++)
               if (andc[i]!=9999){              prlim[i][i]=mobaverage[(int)age][i][ij];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          }
               agev[m][i]=-1;        }
               }    
             }        for(j=1; j<= nlstate; j++){
           }          for(h=0; h<=nhstepm; h++){
           else if(s[m][i] !=9){ /* Should no more exist */            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
             if(mint[m][i]==99 || anint[m][i]==9999)          }
               agev[m][i]=1;        }
             else if(agev[m][i] <agemin){        /* This for computing probability of death (h=1 means
               agemin=agev[m][i];           computed over hstepm matrices product = hstepm*stepm months) 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/           as a weighted average of prlim.
             }        */
             else if(agev[m][i] >agemax){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
               agemax=agev[m][i];          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            gpp[j] += prlim[i][i]*p3mat[i][j][1];
             }        }    
             /*agev[m][i]=anint[m][i]-annais[i];*/        /* end probability of death */
             /*   agev[m][i] = age[i]+2*m;*/  
           }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           else { /* =9 */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             agev[m][i]=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             s[m][i]=-1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }   
         }        if (popbased==1) {
         else /*= 0 Unknown */          if(mobilav ==0){
           agev[m][i]=1;            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     for (i=1; i<=imx; i++)  {              prlim[i][i]=mobaverage[(int)age][i][ij];
       for(m=1; (m<= maxwav); m++){          }
         if (s[m][i] > (nlstate+ndeath)) {        }
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;        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];
           }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        }
         /* This for computing probability of death (h=1 means
     free_vector(severity,1,maxwav);           computed over hstepm matrices product = hstepm*stepm months) 
     free_imatrix(outcome,1,maxwav+1,1,n);           as a weighted average of prlim.
     free_vector(moisnais,1,n);        */
     free_vector(annais,1,n);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     /* free_matrix(mint,1,maxwav,1,n);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
        free_matrix(anint,1,maxwav,1,n);*/           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     free_vector(moisdc,1,n);        }    
     free_vector(andc,1,n);        /* end probability of death */
   
            for(j=1; j<= nlstate; j++) /* vareij */
     wav=ivector(1,imx);          for(h=0; h<=nhstepm; h++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          }
      
     /* Concatenates waves */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       Tcode=ivector(1,100);      } /* End theta */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
            for(h=0; h<=nhstepm; h++) /* veij */
    codtab=imatrix(1,100,1,10);        for(j=1; j<=nlstate;j++)
    h=0;          for(theta=1; theta <=npar; theta++)
    m=pow(2,cptcoveff);            trgradg[h][j][theta]=gradg[h][theta][j];
    
    for(k=1;k<=cptcoveff; k++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
      for(i=1; i <=(m/pow(2,k));i++){        for(theta=1; theta <=npar; theta++)
        for(j=1; j <= ncodemax[k]; j++){          trgradgp[j][theta]=gradgp[theta][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;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      for(i=1;i<=nlstate;i++)
          }        for(j=1;j<=nlstate;j++)
        }          vareij[i][j][(int)age] =0.;
      }  
    }      for(h=0;h<=nhstepm;h++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);        for(k=0;k<=nhstepm;k++){
       codtab[1][2]=1;codtab[2][2]=2; */          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
    /* for(i=1; i <=m ;i++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       for(k=1; k <=cptcovn; k++){          for(i=1;i<=nlstate;i++)
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            for(j=1;j<=nlstate;j++)
       }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       printf("\n");        }
       }      }
       scanf("%d",i);*/    
          /* pptj */
    /* Calculates basic frequencies. Computes observed prevalence at single age      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        and prints on file fileres'p'. */      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
            for(i=nlstate+1;i<=nlstate+ndeath;i++)
              varppt[j][i]=doldmp[j][i];
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* end ppptj */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /*  x centered again */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   
            if (popbased==1) {
     /* For Powell, parameters are in a vector p[] starting at p[1]        if(mobilav ==0){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          for(i=1; i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
     if(mle==1){          for(i=1; i<=nlstate;i++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            prlim[i][i]=mobaverage[(int)age][i][ij];
     }        }
          }
     /*--------- 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);      /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
    jk=1;      */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++){
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
    for(i=1,jk=1; i <=nlstate; i++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
      for(k=1; k <=(nlstate+ndeath); k++){      }    
        if (k != i)      /* end probability of death */
          {  
            printf("%d%d ",i,k);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
            fprintf(ficres,"%1d%1d ",i,k);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
            for(j=1; j <=ncovmodel; j++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
              printf("%f ",p[jk]);        for(i=1; i<=nlstate;i++){
              fprintf(ficres,"%f ",p[jk]);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
              jk++;        }
            }      } 
            printf("\n");      fprintf(ficresprobmorprev,"\n");
            fprintf(ficres,"\n");  
          }      fprintf(ficresvij,"%.0f ",age );
      }      for(i=1; i<=nlstate;i++)
    }        for(j=1; j<=nlstate;j++){
  if(mle==1){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     /* Computing hessian and covariance matrix */        }
     ftolhess=ftol; /* Usually correct */      fprintf(ficresvij,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);      free_matrix(gp,0,nhstepm,1,nlstate);
  }      free_matrix(gm,0,nhstepm,1,nlstate);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     printf("# Scales (for hessian or gradient estimation)\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
      for(i=1,jk=1; i <=nlstate; i++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j <=nlstate+ndeath; j++){    } /* End age */
         if (j!=i) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
           fprintf(ficres,"%1d%1d",i,j);    free_vector(gmp,nlstate+1,nlstate+ndeath);
           printf("%1d%1d",i,j);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           for(k=1; k<=ncovmodel;k++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             printf(" %.5e",delti[jk]);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
             fprintf(ficres," %.5e",delti[jk]);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
             jk++;    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); */
           printf("\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,"\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
      }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
        fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     k=1;    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     fprintf(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");    /*  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);
     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");  */
     for(i=1;i<=npar;i++){  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       /*  if (k>nlstate) k=1;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    free_vector(xp,1,npar);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    free_matrix(doldm,1,nlstate,1,nlstate);
       fprintf(ficres,"%3d",i);    free_matrix(dnewm,1,nlstate,1,npar);
       printf("%3d",i);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(j=1; j<=i;j++){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         fprintf(ficres," %.5e",matcov[i][j]);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         printf(" %.5e",matcov[i][j]);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }    fclose(ficresprobmorprev);
       fprintf(ficres,"\n");    fflush(ficgp);
       printf("\n");    fflush(fichtm); 
       k++;  }  /* end varevsij */
     }  
      /************ Variance of prevlim ******************/
     while((c=getc(ficpar))=='#' && c!= EOF){  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[])
       ungetc(c,ficpar);  {
       fgets(line, MAXLINE, ficpar);    /* Variance of prevalence limit */
       puts(line);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       fputs(line,ficparo);    double **newm;
     }    double **dnewm,**doldm;
     ungetc(c,ficpar);    int i, j, nhstepm, hstepm;
     estepm=0;    int k, cptcode;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    double *xp;
     if (estepm==0 || estepm < stepm) estepm=stepm;    double *gp, *gm;
     if (fage <= 2) {    double **gradg, **trgradg;
       bage = ageminpar;    double age,agelim;
       fage = agemaxpar;    int theta;
     }    
        pstamp(ficresvpl);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    fprintf(ficresvpl,"# Age");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %1d-%1d",i,i);
     while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresvpl,"\n");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    xp=vector(1,npar);
     puts(line);    dnewm=matrix(1,nlstate,1,npar);
     fputs(line,ficparo);    doldm=matrix(1,nlstate,1,nlstate);
   }    
   ungetc(c,ficpar);    hstepm=1*YEARM; /* Every year of age */
      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    agelim = AGESUP;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
            if (stepm >= YEARM) hstepm=1;
   while((c=getc(ficpar))=='#' && c!= EOF){      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     ungetc(c,ficpar);      gradg=matrix(1,npar,1,nlstate);
     fgets(line, MAXLINE, ficpar);      gp=vector(1,nlstate);
     puts(line);      gm=vector(1,nlstate);
     fputs(line,ficparo);  
   }      for(theta=1; theta <=npar; theta++){
   ungetc(c,ficpar);        for(i=1; i<=npar; i++){ /* Computes gradient */
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
   fscanf(ficpar,"pop_based=%d\n",&popbased);      
   fprintf(ficparo,"pop_based=%d\n",popbased);          for(i=1; i<=npar; i++) /* Computes gradient */
   fprintf(ficres,"pop_based=%d\n",popbased);            xp[i] = x[i] - (i==theta ?delti[theta]:0);
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);          gm[i] = prlim[i][i];
     fgets(line, MAXLINE, ficpar);  
     puts(line);        for(i=1;i<=nlstate;i++)
     fputs(line,ficparo);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   }      } /* End theta */
   ungetc(c,ficpar);  
       trgradg =matrix(1,nlstate,1,npar);
   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(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      for(j=1; j<=nlstate;j++)
 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(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
 while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);        varpl[i][(int)age] =0.;
     fgets(line, MAXLINE, ficpar);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     puts(line);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     fputs(line,ficparo);      for(i=1;i<=nlstate;i++)
   }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   ungetc(c,ficpar);  
       fprintf(ficresvpl,"%.0f ",age );
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      for(i=1; i<=nlstate;i++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
 /*------------ gnuplot -------------*/      free_matrix(trgradg,1,nlstate,1,npar);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    } /* End age */
    
 /*------------ free_vector  -------------*/    free_vector(xp,1,npar);
  chdir(path);    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);  /************ Variance of one-step probabilities  ******************/
  free_vector(agedc,1,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[])
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  {
  fclose(ficparo);    int i, j=0,  i1, k1, l1, t, tj;
  fclose(ficres);    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
 /*--------- index.htm --------*/    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    double **dnewm,**doldm;
     double *xp;
      double *gp, *gm;
   /*--------------- Prevalence limit --------------*/    double **gradg, **trgradg;
      double **mu;
   strcpy(filerespl,"pl");    double age,agelim, cov[NCOVMAX];
   strcat(filerespl,fileres);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    int theta;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    char fileresprob[FILENAMELENGTH];
   }    char fileresprobcov[FILENAMELENGTH];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    char fileresprobcor[FILENAMELENGTH];
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");    double ***varpij;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");    strcpy(fileresprob,"prob"); 
      strcat(fileresprob,fileres);
   prlim=matrix(1,nlstate,1,nlstate);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with resultfile: %s\n", fileresprob);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(fileresprobcov,"probcov"); 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    strcat(fileresprobcov,fileres);
   k=0;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   agebase=ageminpar;      printf("Problem with resultfile: %s\n", fileresprobcov);
   agelim=agemaxpar;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   ftolpl=1.e-10;    }
   i1=cptcoveff;    strcpy(fileresprobcor,"probcor"); 
   if (cptcovn < 1){i1=1;}    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   for(cptcov=1;cptcov<=i1;cptcov++){      printf("Problem with resultfile: %s\n", fileresprobcor);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         k=k+1;    }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         fprintf(ficrespl,"\n#******");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         for(j=1;j<=cptcoveff;j++)    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(ficrespl,"******\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
            fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         for (age=agebase; age<=agelim; age++){    pstamp(ficresprob);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           fprintf(ficrespl,"%.0f",age );    fprintf(ficresprob,"# Age");
           for(i=1; i<=nlstate;i++)    pstamp(ficresprobcov);
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           fprintf(ficrespl,"\n");    fprintf(ficresprobcov,"# Age");
         }    pstamp(ficresprobcor);
       }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     }    fprintf(ficresprobcor,"# Age");
   fclose(ficrespl);  
   
   /*------------- h Pij x at various ages ------------*/    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   }      }  
   printf("Computing pij: result on file '%s' \n", filerespij);   /* fprintf(ficresprob,"\n");
      fprintf(ficresprobcov,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficresprobcor,"\n");
   /*if (stepm<=24) stepsize=2;*/   */
    xp=vector(1,npar);
   agelim=AGESUP;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   hstepm=stepsize*YEARM; /* Every year of age */    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
      varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   k=0;    first=1;
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficgp,"\n# Routine varprob");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       k=k+1;    fprintf(fichtm,"\n");
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
         fprintf(ficrespij,"******\n");    file %s<br>\n",optionfilehtmcov);
            fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  and drawn. It helps understanding how is the covariance between two incidences.\
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    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. \
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
           oldm=oldms;savm=savms;  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    standard deviations wide on each axis. <br>\
           fprintf(ficrespij,"# Age");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
           for(i=1; i<=nlstate;i++)   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
             for(j=1; j<=nlstate+ndeath;j++)  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");    cov[1]=1;
           for (h=0; h<=nhstepm; h++){    tj=cptcoveff;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
             for(i=1; i<=nlstate;i++)    j1=0;
               for(j=1; j<=nlstate+ndeath;j++)    for(t=1; t<=tj;t++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      for(i1=1; i1<=ncodemax[t];i1++){ 
             fprintf(ficrespij,"\n");        j1++;
           }        if  (cptcovn>0) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprob, "\n#********** Variable "); 
           fprintf(ficrespij,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprob, "**********\n#\n");
     }          fprintf(ficresprobcov, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          
           fprintf(ficgp, "\n#********** Variable "); 
   fclose(ficrespij);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
   /*---------- Forecasting ------------------*/          
   if((stepm == 1) && (strcmp(model,".")==0)){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     free_matrix(mint,1,maxwav,1,n);          
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficresprobcor, "\n#********** Variable ");    
     free_vector(weight,1,n);}          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   else{          fprintf(ficresprobcor, "**********\n#");    
     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);        
   }        for (age=bage; age<=fage; age ++){ 
            cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
   /*---------- Health expectancies and variances ------------*/            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
   strcpy(filerest,"t");          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   strcat(filerest,fileres);          for (k=1; k<=cptcovprod;k++)
   if((ficrest=fopen(filerest,"w"))==NULL) {            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          
   }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
   strcpy(filerese,"e");      
   strcat(filerese,fileres);          for(theta=1; theta <=npar; theta++){
   if((ficreseij=fopen(filerese,"w"))==NULL) {            for(i=1; i<=npar; i++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   }            
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
  strcpy(fileresv,"v");            k=0;
   strcat(fileresv,fileres);            for(i=1; i<= (nlstate); i++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {              for(j=1; j<=(nlstate+ndeath);j++){
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                k=k+1;
   }                gp[k]=pmmij[i][j];
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);              }
             }
   k=0;            
   for(cptcov=1;cptcov<=i1;cptcov++){            for(i=1; i<=npar; i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       k=k+1;      
       fprintf(ficrest,"\n#****** ");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       for(j=1;j<=cptcoveff;j++)            k=0;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(i=1; i<=(nlstate); i++){
       fprintf(ficrest,"******\n");              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
       fprintf(ficreseij,"\n#****** ");                gm[k]=pmmij[i][j];
       for(j=1;j<=cptcoveff;j++)              }
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
       fprintf(ficreseij,"******\n");       
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       fprintf(ficresvij,"\n#****** ");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       for(j=1;j<=cptcoveff;j++)          }
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              trgradg[j][theta]=gradg[theta][j];
       oldm=oldms;savm=savms;          
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       oldm=oldms;savm=savms;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
              free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          pmij(pmmij,cov,ncovmodel,x,nlstate);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          
       fprintf(ficrest,"\n");          k=0;
           for(i=1; i<=(nlstate); i++){
       epj=vector(1,nlstate+1);            for(j=1; j<=(nlstate+ndeath);j++){
       for(age=bage; age <=fage ;age++){              k=k+1;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              mu[k][(int) age]=pmmij[i][j];
         if (popbased==1) {            }
           for(i=1; i<=nlstate;i++)          }
             prlim[i][i]=probs[(int)age][i][k];          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                      varpij[i][j][(int)age] = doldm[i][j];
         fprintf(ficrest," %4.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          /*printf("\n%d ",(int)age);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           epj[nlstate+1] +=epj[j];            }*/
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)          fprintf(ficresprob,"\n%d ",(int)age);
           for(j=1;j <=nlstate;j++)          fprintf(ficresprobcov,"\n%d ",(int)age);
             vepp += vareij[i][j][(int)age];          fprintf(ficresprobcor,"\n%d ",(int)age);
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
         }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         fprintf(ficrest,"\n");            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     }          }
   }          i=0;
           for (k=1; k<=(nlstate);k++){
   fclose(ficreseij);            for (l=1; l<=(nlstate+ndeath);l++){ 
   fclose(ficresvij);              i=i++;
   fclose(ficrest);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   fclose(ficpar);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   free_vector(epj,1,nlstate+1);              for (j=1; j<=i;j++){
                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /*------- Variance limit prevalence------*/                  fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
   strcpy(fileresvpl,"vpl");            }
   strcat(fileresvpl,fileres);          }/* end of loop for state */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        } /* end of loop for age */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);        /* Confidence intervalle of pij  */
   }        /*
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   k=0;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       k=k+1;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficresvpl,"\n#****** ");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       for(j=1;j<=cptcoveff;j++)        */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
              first1=1;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        for (k2=1; k2<=(nlstate);k2++){
       oldm=oldms;savm=savms;          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            if(l2==k2) continue;
     }            j=(k2-1)*(nlstate+ndeath)+l2;
  }            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   fclose(ficresvpl);                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
   /*---------- End : free ----------------*/                if(i<=j) continue;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                for (age=bage; age<=fage; age ++){ 
                    if ((int)age %5==0){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      mu1=mu[i][(int) age]/stepm*YEARM ;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                    mu2=mu[j][(int) age]/stepm*YEARM;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                    c12=cv12/sqrt(v1*v2);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                    /* Computing eigen value of matrix of covariance */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                    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.;
   free_matrix(matcov,1,npar,1,npar);                    /* Eigen vectors */
   free_vector(delti,1,npar);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   free_matrix(agev,1,maxwav,1,imx);                    /*v21=sqrt(1.-v11*v11); *//* error */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
   if(erreur >0)                    v22=v11;
     printf("End of Imach with error or warning %d\n",erreur);                    tnalp=v21/v11;
   else   printf("End of Imach\n");                    if(first1==1){
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                      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);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/                    }
   /*printf("Total time was %d uSec.\n", total_usecs);*/                    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);
   /*------ End -----------*/                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
  end:                    if(first==1){
 #ifdef windows                      first=0;
   /* chdir(pathcd);*/                      fprintf(ficgp,"\nset parametric;unset label");
 #endif                      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);
  /*system("wgnuplot graph.plt");*/                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
  /*system("../gp37mgw/wgnuplot graph.plt");*/                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  /*system("cd ../gp37mgw");*/   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
  strcpy(plotcmd,GNUPLOTPROGRAM);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
  strcat(plotcmd," ");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  strcat(plotcmd,optionfilegnuplot);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  system(plotcmd);                      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);
 #ifdef windows                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   while (z[0] != 'q') {                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     /* chdir(path); */                      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",\
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     scanf("%s",z);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     if (z[0] == 'c') system("./imach");                    }else{
     else if (z[0] == 'e') system(optionfilehtm);                      first=0;
     else if (z[0] == 'g') system(plotcmd);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
     else if (z[0] == 'q') exit(0);                      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);
 #endif                      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; /* Dirty */
       }
     }
     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); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     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 while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening 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,pathcd); /* 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,pathcd); /* 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\n# Age ( 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 -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*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.1.36  
changed lines
  Added in v.1.120


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