Diff for /imach/src/imach.c between versions 1.28 and 1.109

version 1.28, 2002/03/01 17:56:23 version 1.109, 2006/01/24 19:37:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.109  2006/01/24 19:37:15  brouard
      (Module): Comments (lines starting with a #) are allowed in data.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.108  2006/01/19 18:05:42  lievre
   first survey ("cross") where individuals from different ages are    Gnuplot problem appeared...
   interviewed on their health status or degree of disability (in the    To be fixed
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.107  2006/01/19 16:20:37  brouard
   (if any) in individual health status.  Health expectancies are    Test existence of gnuplot in imach path
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.106  2006/01/19 13:24:36  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Some cleaning and links added in html output
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.105  2006/01/05 20:23:19  lievre
   conditional to be observed in state i at the first wave. Therefore    *** empty log message ***
   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 1.104  2005/09/30 16:11:43  lievre
   complex model than "constant and age", you should modify the program    (Module): sump fixed, loop imx fixed, and simplifications.
   where the markup *Covariates have to be included here again* invites    (Module): If the status is missing at the last wave but we know
   you to do it.  More covariates you add, slower the    that the person is alive, then we can code his/her status as -2
   convergence.    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
   The advantage of this computer programme, compared to a simple    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   multinomial logistic model, is clear when the delay between waves is not    the healthy state at last known wave). Version is 0.98
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.103  2005/09/30 15:54:49  lievre
   account using an interpolation or extrapolation.      (Module): sump fixed, loop imx fixed, and simplifications.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.102  2004/09/15 17:31:30  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Add the possibility to read data file including tab characters.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.101  2004/09/15 10:38:38  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Fix on curr_time
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.100  2004/07/12 18:29:06  brouard
   hPijx.    Add version for Mac OS X. Just define UNIX in Makefile
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.99  2004/06/05 08:57:40  brouard
   of the life expectancies. It also computes the prevalence limits.    *** empty log message ***
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.98  2004/05/16 15:05:56  brouard
            Institut national d'études démographiques, Paris.    New version 0.97 . First attempt to estimate force of mortality
   This software have been partly granted by Euro-REVES, a concerted action    directly from the data i.e. without the need of knowing the health
   from the European Union.    state at each age, but using a Gompertz model: log u =a + b*age .
   It is copyrighted identically to a GNU software product, ie programme and    This is the basic analysis of mortality and should be done before any
   software can be distributed freely for non commercial use. Latest version    other analysis, in order to test if the mortality estimated from the
   can be accessed at http://euroreves.ined.fr/imach .    cross-longitudinal survey is different from the mortality estimated
   **********************************************************************/    from other sources like vital statistic data.
    
 #include <math.h>    The same imach parameter file can be used but the option for mle should be -3.
 #include <stdio.h>  
 #include <stdlib.h>    Agnès, who wrote this part of the code, tried to keep most of the
 #include <unistd.h>    former routines in order to include the new code within the former code.
   
 #define MAXLINE 256    The output is very simple: only an estimate of the intercept and of
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    the slope with 95% confident intervals.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Current limitations:
 #define windows    A) Even if you enter covariates, i.e. with the
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    B) There is no computation of Life Expectancy nor Life Table.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.97  2004/02/20 13:25:42  lievre
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.96  2003/07/15 15:38:55  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define NCOVMAX 8 /* Maximum number of covariates */    rewritten within the same printf. Workaround: many printfs.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.95  2003/07/08 07:54:34  brouard
 #define AGESUP 130    * imach.c (Repository):
 #define AGEBASE 40    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
   
 int erreur; /* Error number */    Revision 1.94  2003/06/27 13:00:02  brouard
 int nvar;    Just cleaning
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.93  2003/06/25 16:33:55  brouard
 int nlstate=2; /* Number of live states */    (Module): On windows (cygwin) function asctime_r doesn't
 int ndeath=1; /* Number of dead states */    exist so I changed back to asctime which exists.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): Version 0.96b
 int popbased=0;  
     Revision 1.92  2003/06/25 16:30:45  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): On windows (cygwin) function asctime_r doesn't
 int maxwav; /* Maxim number of waves */    exist so I changed back to asctime which exists.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.91  2003/06/25 15:30:29  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    * imach.c (Repository): Duplicated warning errors corrected.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Repository): Elapsed time after each iteration is now output. It
 double jmean; /* Mean space between 2 waves */    helps to forecast when convergence will be reached. Elapsed time
 double **oldm, **newm, **savm; /* Working pointers to matrices */    is stamped in powell.  We created a new html file for the graphs
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    concerning matrix of covariance. It has extension -cov.htm.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.90  2003/06/24 12:34:15  brouard
 FILE *ficreseij;    (Module): Some bugs corrected for windows. Also, when
   char filerese[FILENAMELENGTH];    mle=-1 a template is output in file "or"mypar.txt with the design
  FILE  *ficresvij;    of the covariance matrix to be input.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.89  2003/06/24 12:30:52  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define NR_END 1    of the covariance matrix to be input.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 #define NRANSI  
 #define ITMAX 200    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 #define TOL 2.0e-4  
     Revision 1.86  2003/06/17 20:04:08  brouard
 #define CGOLD 0.3819660    (Module): Change position of html and gnuplot routines and added
 #define ZEPS 1.0e-10    routine fileappend.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.85  2003/06/17 13:12:43  brouard
 #define GOLD 1.618034    * imach.c (Repository): Check when date of death was earlier that
 #define GLIMIT 100.0    current date of interview. It may happen when the death was just
 #define TINY 1.0e-20    prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 static double maxarg1,maxarg2;    assuming that the date of death was just one stepm after the
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    interview.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Repository): Because some people have very long ID (first column)
      we changed int to long in num[] and we added a new lvector for
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    memory allocation. But we also truncated to 8 characters (left
 #define rint(a) floor(a+0.5)    truncation)
     (Repository): No more line truncation errors.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.84  2003/06/13 21:44:43  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 int imx;    many times. Probs is memory consuming and must be used with
 int stepm;    parcimony.
 /* Stepm, step in month: minimum step interpolation*/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 int m,nb;    Revision 1.83  2003/06/10 13:39:11  lievre
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    *** empty log message ***
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.82  2003/06/05 15:57:20  brouard
 double dateintmean=0;    Add log in  imach.c and  fullversion number is now printed.
   
 double *weight;  */
 int **s; /* Status */  /*
 double *agedc, **covar, idx;     Interpolated Markov Chain
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Short summary of the programme:
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    
 double ftolhess; /* Tolerance for computing hessian */    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /**************** split *************************/    first survey ("cross") where individuals from different ages are
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    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
    char *s;                             /* pointer */    second wave of interviews ("longitudinal") which measure each change
    int  l1, l2;                         /* length counters */    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
    l1 = strlen( path );                 /* length of path */    model. More health states you consider, more time is necessary to reach the
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Maximum Likelihood of the parameters involved in the model.  The
 #ifdef windows    simplest model is the multinomial logistic model where pij is the
    s = strrchr( path, '\\' );           /* find last / */    probability to be observed in state j at the second wave
 #else    conditional to be observed in state i at the first wave. Therefore
    s = strrchr( path, '/' );            /* find last / */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #endif    'age' is age and 'sex' is a covariate. If you want to have a more
    if ( s == NULL ) {                   /* no directory, so use current */    complex model than "constant and age", you should modify the program
 #if     defined(__bsd__)                /* get current working directory */    where the markup *Covariates have to be included here again* invites
       extern char       *getwd( );    you to do it.  More covariates you add, slower the
     convergence.
       if ( getwd( dirc ) == NULL ) {  
 #else    The advantage of this computer programme, compared to a simple
       extern char       *getcwd( );    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    intermediate interview, the information is lost, but taken into
 #endif    account using an interpolation or extrapolation.  
          return( GLOCK_ERROR_GETCWD );  
       }    hPijx is the probability to be observed in state i at age x+h
       strcpy( name, path );             /* we've got it */    conditional to the observed state i at age x. The delay 'h' can be
    } else {                             /* strip direcotry from path */    split into an exact number (nh*stepm) of unobserved intermediate
       s++;                              /* after this, the filename */    states. This elementary transition (by month, quarter,
       l2 = strlen( s );                 /* length of filename */    semester or year) is modelled as a multinomial logistic.  The hPx
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    matrix is simply the matrix product of nh*stepm elementary matrices
       strcpy( name, s );                /* save file name */    and the contribution of each individual to the likelihood is simply
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    hPijx.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Also this programme outputs the covariance matrix of the parameters but also
    l1 = strlen( dirc );                 /* length of directory */    of the life expectancies. It also computes the stable prevalence. 
 #ifdef windows    
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #else             Institut national d'études démographiques, Paris.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    This software have been partly granted by Euro-REVES, a concerted action
 #endif    from the European Union.
    s = strrchr( name, '.' );            /* find last / */    It is copyrighted identically to a GNU software product, ie programme and
    s++;    software can be distributed freely for non commercial use. Latest version
    strcpy(ext,s);                       /* save extension */    can be accessed at http://euroreves.ined.fr/imach .
    l1= strlen( name);  
    l2= strlen( s)+1;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    strncpy( finame, name, l1-l2);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    finame[l1-l2]= 0;    
    return( 0 );                         /* we're done */    **********************************************************************/
 }  /*
     main
     read parameterfile
 /******************************************/    read datafile
     concatwav
 void replace(char *s, char*t)    freqsummary
 {    if (mle >= 1)
   int i;      mlikeli
   int lg=20;    print results files
   i=0;    if mle==1 
   lg=strlen(t);       computes hessian
   for(i=0; i<= lg; i++) {    read end of parameter file: agemin, agemax, bage, fage, estepm
     (s[i] = t[i]);        begin-prev-date,...
     if (t[i]== '\\') s[i]='/';    open gnuplot file
   }    open html file
 }    stable prevalence
      for age prevalim()
 int nbocc(char *s, char occ)    h Pij x
 {    variance of p varprob
   int i,j=0;    forecasting if prevfcast==1 prevforecast call prevalence()
   int lg=20;    health expectancies
   i=0;    Variance-covariance of DFLE
   lg=strlen(s);    prevalence()
   for(i=0; i<= lg; i++) {     movingaverage()
   if  (s[i] == occ ) j++;    varevsij() 
   }    if popbased==1 varevsij(,popbased)
   return j;    total life expectancies
 }    Variance of stable prevalence
    end
 void cutv(char *u,char *v, char*t, char occ)  */
 {  
   int i,lg,j,p=0;  
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {   
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #include <math.h>
   }  #include <stdio.h>
   #include <stdlib.h>
   lg=strlen(t);  #include <string.h>
   for(j=0; j<p; j++) {  #include <unistd.h>
     (u[j] = t[j]);  
   }  #include <limits.h>
      u[p]='\0';  #include <sys/types.h>
   #include <sys/stat.h>
    for(j=0; j<= lg; j++) {  #include <errno.h>
     if (j>=(p+1))(v[j-p-1] = t[j]);  extern int errno;
   }  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /********************** nrerror ********************/  #include "timeval.h"
   
 void nrerror(char error_text[])  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  #define MAXLINE 256
   exit(1);  
 }  #define GNUPLOTPROGRAM "gnuplot"
 /*********************** vector *******************/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double *vector(int nl, int nh)  #define FILENAMELENGTH 132
 {  
   double *v;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 /************************ free vector ******************/  #define NINTERVMAX 8
 void free_vector(double*v, int nl, int nh)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   free((FREE_ARG)(v+nl-NR_END));  #define NCOVMAX 8 /* Maximum number of covariates */
 }  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 /************************ivector *******************************/  #define AGESUP 130
 int *ivector(long nl,long nh)  #define AGEBASE 40
 {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   int *v;  #ifdef UNIX
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define DIRSEPARATOR '/'
   if (!v) nrerror("allocation failure in ivector");  #define CHARSEPARATOR "/"
   return v-nl+NR_END;  #define ODIRSEPARATOR '\\'
 }  #else
   #define DIRSEPARATOR '\\'
 /******************free ivector **************************/  #define CHARSEPARATOR "\\"
 void free_ivector(int *v, long nl, long nh)  #define ODIRSEPARATOR '/'
 {  #endif
   free((FREE_ARG)(v+nl-NR_END));  
 }  /* $Id$ */
   /* $State$ */
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char fullversion[]="$Revision$ $Date$"; 
 {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int nvar;
   int **m;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    int npar=NPARMAX;
   /* allocate pointers to rows */  int nlstate=2; /* Number of live states */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int ndeath=1; /* Number of dead states */
   if (!m) nrerror("allocation failure 1 in matrix()");  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m += NR_END;  int popbased=0;
   m -= nrl;  
    int *wav; /* Number of waves for this individuual 0 is possible */
    int maxwav; /* Maxim number of waves */
   /* allocate rows and set pointers to them */  int jmin, jmax; /* min, max spacing between 2 waves */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int gipmx, gsw; /* Global variables on the number of contributions 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");                     to the likelihood and the sum of weights (done by funcone)*/
   m[nrl] += NR_END;  int mle, weightopt;
   m[nrl] -= ncl;  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 */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
   /* return pointer to array of pointers to rows */  double jmean; /* Mean space between 2 waves */
   return m;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 /****************** free_imatrix *************************/  FILE *ficlog, *ficrespow;
 void free_imatrix(m,nrl,nrh,ncl,nch)  int globpr; /* Global variable for printing or not */
       int **m;  double fretone; /* Only one call to likelihood */
       long nch,ncl,nrh,nrl;  long ipmx; /* Number of contributions */
      /* free an int matrix allocated by imatrix() */  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG) (m+nrl-NR_END));  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /******************* matrix *******************************/  FILE *fichtm, *fichtmcov; /* Html File */
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  FILE  *ficresvij;
   double **m;  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileresvpl[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char title[MAXLINE];
   m += NR_END;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m -= nrl;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char command[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int  outcmd=0;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char filelog[FILENAMELENGTH]; /* Log file */
   return m;  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   free((FREE_ARG)(m+nrl-NR_END));  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /******************* ma3x *******************************/  long time_value;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  extern long time();
 {  char strcurr[80], strfor[80];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  char *endptr;
   long lval;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NR_END 1
   m += NR_END;  #define FREE_ARG char*
   m -= nrl;  #define FTOL 1.0e-10
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define NRANSI 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define ITMAX 200 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #define TOL 2.0e-4 
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  #define GOLD 1.618034 
   m[nrl][ncl] -= nll;  #define GLIMIT 100.0 
   for (j=ncl+1; j<=nch; j++)  #define TINY 1.0e-20 
     m[nrl][j]=m[nrl][j-1]+nlay;  
    static double maxarg1,maxarg2;
   for (i=nrl+1; i<=nrh; i++) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     for (j=ncl+1; j<=nch; j++)    
       m[i][j]=m[i][j-1]+nlay;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   }  #define rint(a) floor(a+0.5)
   return m;  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /*************************free ma3x ************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int agegomp= AGEGOMP;
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int imx; 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int stepm=1;
   free((FREE_ARG)(m+nrl-NR_END));  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /***************** f1dim *************************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 extern int ncom;  
 extern double *pcom,*xicom;  int m,nb;
 extern double (*nrfunc)(double []);  long *num;
    int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double f1dim(double x)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 {  double **pmmij, ***probs;
   int j;  double *ageexmed,*agecens;
   double f;  double dateintmean=0;
   double *xt;  
    double *weight;
   xt=vector(1,ncom);  int **s; /* Status */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double *agedc, **covar, idx;
   f=(*nrfunc)(xt);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free_vector(xt,1,ncom);  double *lsurv, *lpop, *tpop;
   return f;  
 }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int iter;  {
   double a,b,d,etemp;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double fu,fv,fw,fx;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double ftemp;    */ 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    char  *ss;                            /* pointer */
   double e=0.0;    int   l1, l2;                         /* length counters */
    
   a=(ax < cx ? ax : cx);    l1 = strlen(path );                   /* length of path */
   b=(ax > cx ? ax : cx);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   x=w=v=bx;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   fw=fv=fx=(*f)(x);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for (iter=1;iter<=ITMAX;iter++) {      strcpy( name, path );               /* we got the fullname name because no directory */
     xm=0.5*(a+b);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      /* get current working directory */
     printf(".");fflush(stdout);      /*    extern  char* getcwd ( char *buf , int len);*/
 #ifdef DEBUG      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);        return( GLOCK_ERROR_GETCWD );
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      }
 #endif      /* got dirc from getcwd*/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      printf(" DIRC = %s \n",dirc);
       *xmin=x;    } else {                              /* strip direcotry from path */
       return fx;      ss++;                               /* after this, the filename */
     }      l2 = strlen( ss );                  /* length of filename */
     ftemp=fu;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if (fabs(e) > tol1) {      strcpy( name, ss );         /* save file name */
       r=(x-w)*(fx-fv);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       q=(x-v)*(fx-fw);      dirc[l1-l2] = 0;                    /* add zero */
       p=(x-v)*q-(x-w)*r;      printf(" DIRC2 = %s \n",dirc);
       q=2.0*(q-r);    }
       if (q > 0.0) p = -p;    /* We add a separator at the end of dirc if not exists */
       q=fabs(q);    l1 = strlen( dirc );                  /* length of directory */
       etemp=e;    if( dirc[l1-1] != DIRSEPARATOR ){
       e=d;      dirc[l1] =  DIRSEPARATOR;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))      dirc[l1+1] = 0; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      printf(" DIRC3 = %s \n",dirc);
       else {    }
         d=p/q;    ss = strrchr( name, '.' );            /* find last / */
         u=x+d;    if (ss >0){
         if (u-a < tol2 || b-u < tol2)      ss++;
           d=SIGN(tol1,xm-x);      strcpy(ext,ss);                     /* save extension */
       }      l1= strlen( name);
     } else {      l2= strlen(ss)+1;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      strncpy( finame, name, l1-l2);
     }      finame[l1-l2]= 0;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    }
     fu=(*f)(u);  
     if (fu <= fx) {    return( 0 );                          /* we're done */
       if (u >= x) a=x; else b=x;  }
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  
         } else {  /******************************************/
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  void replace_back_to_slash(char *s, char*t)
             v=w;  {
             w=u;    int i;
             fv=fw;    int lg=0;
             fw=fu;    i=0;
           } else if (fu <= fv || v == x || v == w) {    lg=strlen(t);
             v=u;    for(i=0; i<= lg; i++) {
             fv=fu;      (s[i] = t[i]);
           }      if (t[i]== '\\') s[i]='/';
         }    }
   }  }
   nrerror("Too many iterations in brent");  
   *xmin=x;  int nbocc(char *s, char occ)
   return fx;  {
 }    int i,j=0;
     int lg=20;
 /****************** mnbrak ***********************/    i=0;
     lg=strlen(s);
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    for(i=0; i<= lg; i++) {
             double (*func)(double))    if  (s[i] == occ ) j++;
 {    }
   double ulim,u,r,q, dum;    return j;
   double fu;  }
    
   *fa=(*func)(*ax);  void cutv(char *u,char *v, char*t, char occ)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     SHFT(dum,*ax,*bx,dum)       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       SHFT(dum,*fb,*fa,dum)       gives u="abcedf" and v="ghi2j" */
       }    int i,lg,j,p=0;
   *cx=(*bx)+GOLD*(*bx-*ax);    i=0;
   *fc=(*func)(*cx);    for(j=0; j<=strlen(t)-1; j++) {
   while (*fb > *fc) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     r=(*bx-*ax)*(*fb-*fc);    }
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    lg=strlen(t);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    for(j=0; j<p; j++) {
     ulim=(*bx)+GLIMIT*(*cx-*bx);      (u[j] = t[j]);
     if ((*bx-u)*(u-*cx) > 0.0) {    }
       fu=(*func)(u);       u[p]='\0';
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);     for(j=0; j<= lg; j++) {
       if (fu < *fc) {      if (j>=(p+1))(v[j-p-1] = t[j]);
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    }
           SHFT(*fb,*fc,fu,(*func)(u))  }
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /********************** nrerror ********************/
       u=ulim;  
       fu=(*func)(u);  void nrerror(char error_text[])
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    fprintf(stderr,"ERREUR ...\n");
       fu=(*func)(u);    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     SHFT(*ax,*bx,*cx,u)  }
       SHFT(*fa,*fb,*fc,fu)  /*********************** vector *******************/
       }  double *vector(int nl, int nh)
 }  {
     double *v;
 /*************** linmin ************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 int ncom;    return v-nl+NR_END;
 double *pcom,*xicom;  }
 double (*nrfunc)(double []);  
    /************************ free vector ******************/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  void free_vector(double*v, int nl, int nh)
 {  {
   double brent(double ax, double bx, double cx,    free((FREE_ARG)(v+nl-NR_END));
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /************************ivector *******************************/
               double *fc, double (*func)(double));  int *ivector(long nl,long nh)
   int j;  {
   double xx,xmin,bx,ax;    int *v;
   double fx,fb,fa;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
   ncom=n;    return v-nl+NR_END;
   pcom=vector(1,n);  }
   xicom=vector(1,n);  
   nrfunc=func;  /******************free ivector **************************/
   for (j=1;j<=n;j++) {  void free_ivector(int *v, long nl, long nh)
     pcom[j]=p[j];  {
     xicom[j]=xi[j];    free((FREE_ARG)(v+nl-NR_END));
   }  }
   ax=0.0;  
   xx=1.0;  /************************lvector *******************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  long *lvector(long nl,long nh)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  {
 #ifdef DEBUG    long *v;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #endif    if (!v) nrerror("allocation failure in ivector");
   for (j=1;j<=n;j++) {    return v-nl+NR_END;
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  /******************free lvector **************************/
   free_vector(xicom,1,n);  void free_lvector(long *v, long nl, long nh)
   free_vector(pcom,1,n);  {
 }    free((FREE_ARG)(v+nl-NR_END));
   }
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /******************* imatrix *******************************/
             double (*func)(double []))  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   void linmin(double p[], double xi[], int n, double *fret,  { 
               double (*func)(double []));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   int i,ibig,j;    int **m; 
   double del,t,*pt,*ptt,*xit;    
   double fp,fptt;    /* allocate pointers to rows */ 
   double *xits;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   pt=vector(1,n);    if (!m) nrerror("allocation failure 1 in matrix()"); 
   ptt=vector(1,n);    m += NR_END; 
   xit=vector(1,n);    m -= nrl; 
   xits=vector(1,n);    
   *fret=(*func)(p);    
   for (j=1;j<=n;j++) pt[j]=p[j];    /* allocate rows and set pointers to them */ 
   for (*iter=1;;++(*iter)) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     fp=(*fret);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     ibig=0;    m[nrl] += NR_END; 
     del=0.0;    m[nrl] -= ncl; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    
     for (i=1;i<=n;i++)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       printf(" %d %.12f",i, p[i]);    
     printf("\n");    /* return pointer to array of pointers to rows */ 
     for (i=1;i<=n;i++) {    return m; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  } 
       fptt=(*fret);  
 #ifdef DEBUG  /****************** free_imatrix *************************/
       printf("fret=%lf \n",*fret);  void free_imatrix(m,nrl,nrh,ncl,nch)
 #endif        int **m;
       printf("%d",i);fflush(stdout);        long nch,ncl,nrh,nrl; 
       linmin(p,xit,n,fret,func);       /* free an int matrix allocated by imatrix() */ 
       if (fabs(fptt-(*fret)) > del) {  { 
         del=fabs(fptt-(*fret));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         ibig=i;    free((FREE_ARG) (m+nrl-NR_END)); 
       }  } 
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  /******************* matrix *******************************/
       for (j=1;j<=n;j++) {  double **matrix(long nrl, long nrh, long ncl, long nch)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       }    double **m;
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       printf("\n");    if (!m) nrerror("allocation failure 1 in matrix()");
 #endif    m += NR_END;
     }    m -= nrl;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       int k[2],l;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       k[0]=1;    m[nrl] += NR_END;
       k[1]=-1;    m[nrl] -= ncl;
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         printf(" %.12e",p[j]);    return m;
       printf("\n");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       for(l=0;l<=1;l++) {     */
         for (j=1;j<=n;j++) {  }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /*************************free matrix ************************/
         }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  {
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #endif    free((FREE_ARG)(m+nrl-NR_END));
   }
   
       free_vector(xit,1,n);  /******************* ma3x *******************************/
       free_vector(xits,1,n);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       return;    double ***m;
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=1;j<=n;j++) {    if (!m) nrerror("allocation failure 1 in matrix()");
       ptt[j]=2.0*p[j]-pt[j];    m += NR_END;
       xit[j]=p[j]-pt[j];    m -= nrl;
       pt[j]=p[j];  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     fptt=(*func)(ptt);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     if (fptt < fp) {    m[nrl] += NR_END;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m[nrl] -= ncl;
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
           xi[j][n]=xit[j];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         }    m[nrl][ncl] += NR_END;
 #ifdef DEBUG    m[nrl][ncl] -= nll;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    for (j=ncl+1; j<=nch; j++) 
         for(j=1;j<=n;j++)      m[nrl][j]=m[nrl][j-1]+nlay;
           printf(" %.12e",xit[j]);    
         printf("\n");    for (i=nrl+1; i<=nrh; i++) {
 #endif      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
   }    }
 }    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 /**** Prevalence limit ****************/             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  }
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /*************************free ma3x ************************/
      matrix by transitions matrix until convergence is reached */  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
   int i, ii,j,k;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double min, max, maxmin, maxmax,sumnew=0.;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double **matprod2();    free((FREE_ARG)(m+nrl-NR_END));
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
   for (ii=1;ii<=nlstate+ndeath;ii++)  {
     for (j=1;j<=nlstate+ndeath;j++){    /* Caution optionfilefiname is hidden */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
    cov[1]=1.;    return tmpout;
    }
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /*************** function subdirf2 ***********/
     newm=savm;  char *subdirf2(char fileres[], char *preop)
     /* Covariates have to be included here again */  {
      cov[2]=agefin;    
      /* Caution optionfilefiname is hidden */
       for (k=1; k<=cptcovn;k++) {    strcpy(tmpout,optionfilefiname);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    strcat(tmpout,"/");
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    strcat(tmpout,preop);
       }    strcat(tmpout,fileres);
       for (k=1; k<=cptcovage;k++)    return tmpout;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  }
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    
     /* Caution optionfilefiname is hidden */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     savm=oldm;    strcat(tmpout,preop);
     oldm=newm;    strcat(tmpout,preop2);
     maxmax=0.;    strcat(tmpout,fileres);
     for(j=1;j<=nlstate;j++){    return tmpout;
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /***************** f1dim *************************/
         sumnew=0;  extern int ncom; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  extern double *pcom,*xicom;
         prlim[i][j]= newm[i][j]/(1-sumnew);  extern double (*nrfunc)(double []); 
         max=FMAX(max,prlim[i][j]);   
         min=FMIN(min,prlim[i][j]);  double f1dim(double x) 
       }  { 
       maxmin=max-min;    int j; 
       maxmax=FMAX(maxmax,maxmin);    double f;
     }    double *xt; 
     if(maxmax < ftolpl){   
       return prlim;    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   }    f=(*nrfunc)(xt); 
 }    free_vector(xt,1,ncom); 
     return f; 
 /*************** transition probabilities ***************/  } 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /*****************brent *************************/
 {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double s1, s2;  { 
   /*double t34;*/    int iter; 
   int i,j,j1, nc, ii, jj;    double a,b,d,etemp;
     double fu,fv,fw,fx;
     for(i=1; i<= nlstate; i++){    double ftemp;
     for(j=1; j<i;j++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double e=0.0; 
         /*s2 += param[i][j][nc]*cov[nc];*/   
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    a=(ax < cx ? ax : cx); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    b=(ax > cx ? ax : cx); 
       }    x=w=v=bx; 
       ps[i][j]=s2;    fw=fv=fx=(*f)(x); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    for (iter=1;iter<=ITMAX;iter++) { 
     }      xm=0.5*(a+b); 
     for(j=i+1; j<=nlstate+ndeath;j++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      printf(".");fflush(stdout);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
       ps[i][j]=s2;      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);
     }      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)))) { */
     /*ps[3][2]=1;*/  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   for(i=1; i<= nlstate; i++){        *xmin=x; 
      s1=0;        return fx; 
     for(j=1; j<i; j++)      } 
       s1+=exp(ps[i][j]);      ftemp=fu;
     for(j=i+1; j<=nlstate+ndeath; j++)      if (fabs(e) > tol1) { 
       s1+=exp(ps[i][j]);        r=(x-w)*(fx-fv); 
     ps[i][i]=1./(s1+1.);        q=(x-v)*(fx-fw); 
     for(j=1; j<i; j++)        p=(x-v)*q-(x-w)*r; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        q=2.0*(q-r); 
     for(j=i+1; j<=nlstate+ndeath; j++)        if (q > 0.0) p = -p; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        q=fabs(q); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        etemp=e; 
   } /* end i */        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){        else { 
       ps[ii][jj]=0;          d=p/q; 
       ps[ii][ii]=1;          u=x+d; 
     }          if (u-a < tol2 || b-u < tol2) 
   }            d=SIGN(tol1,xm-x); 
         } 
       } else { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      } 
      printf("%lf ",ps[ii][jj]);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
    }      fu=(*f)(u); 
     printf("\n ");      if (fu <= fx) { 
     }        if (u >= x) a=x; else b=x; 
     printf("\n ");printf("%lf ",cov[2]);*/        SHFT(v,w,x,u) 
 /*          SHFT(fv,fw,fx,fu) 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          } else { 
   goto end;*/            if (u < x) a=u; else b=u; 
     return ps;            if (fu <= fw || w == x) { 
 }              v=w; 
               w=u; 
 /**************** Product of 2 matrices ******************/              fv=fw; 
               fw=fu; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)            } else if (fu <= fv || v == x || v == w) { 
 {              v=u; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times              fv=fu; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */            } 
   /* in, b, out are matrice of pointers which should have been initialized          } 
      before: only the contents of out is modified. The function returns    } 
      a pointer to pointers identical to out */    nrerror("Too many iterations in brent"); 
   long i, j, k;    *xmin=x; 
   for(i=nrl; i<= nrh; i++)    return fx; 
     for(k=ncolol; k<=ncoloh; k++)  } 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /****************** mnbrak ***********************/
   
   return out;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 }              double (*func)(double)) 
   { 
     double ulim,u,r,q, dum;
 /************* Higher Matrix Product ***************/    double fu; 
    
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    *fa=(*func)(*ax); 
 {    *fb=(*func)(*bx); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    if (*fb > *fa) { 
      duration (i.e. until      SHFT(dum,*ax,*bx,dum) 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        SHFT(dum,*fb,*fa,dum) 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        } 
      (typically every 2 years instead of every month which is too big).    *cx=(*bx)+GOLD*(*bx-*ax); 
      Model is determined by parameters x and covariates have to be    *fc=(*func)(*cx); 
      included manually here.    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
      */      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   int i, j, d, h, k;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double **out, cov[NCOVMAX];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double **newm;      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
   /* Hstepm could be zero and should return the unit matrix */      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   for (i=1;i<=nlstate+ndeath;i++)        fu=(*func)(u); 
     for (j=1;j<=nlstate+ndeath;j++){        if (fu < *fc) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for(h=1; h <=nhstepm; h++){        u=ulim; 
     for(d=1; d <=hstepm; d++){        fu=(*func)(u); 
       newm=savm;      } else { 
       /* Covariates have to be included here again */        u=(*cx)+GOLD*(*cx-*bx); 
       cov[1]=1.;        fu=(*func)(u); 
       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]]];      SHFT(*ax,*bx,*cx,u) 
       for (k=1; k<=cptcovage;k++)        SHFT(*fa,*fb,*fc,fu) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        } 
       for (k=1; k<=cptcovprod;k++)  } 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /*************** linmin ************************/
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  int ncom; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  double *pcom,*xicom;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  double (*nrfunc)(double []); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));   
       savm=oldm;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       oldm=newm;  { 
     }    double brent(double ax, double bx, double cx, 
     for(i=1; i<=nlstate+ndeath; i++)                 double (*f)(double), double tol, double *xmin); 
       for(j=1;j<=nlstate+ndeath;j++) {    double f1dim(double x); 
         po[i][j][h]=newm[i][j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);                double *fc, double (*func)(double)); 
          */    int j; 
       }    double xx,xmin,bx,ax; 
   } /* end h */    double fx,fb,fa;
   return po;   
 }    ncom=n; 
     pcom=vector(1,n); 
     xicom=vector(1,n); 
 /*************** log-likelihood *************/    nrfunc=func; 
 double func( double *x)    for (j=1;j<=n;j++) { 
 {      pcom[j]=p[j]; 
   int i, ii, j, k, mi, d, kk;      xicom[j]=xi[j]; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    } 
   double **out;    ax=0.0; 
   double sw; /* Sum of weights */    xx=1.0; 
   double lli; /* Individual log likelihood */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   long ipmx;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   /*extern weight */  #ifdef DEBUG
   /* We are differentiating ll according to initial status */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*for(i=1;i<imx;i++)  #endif
     printf(" %d\n",s[4][i]);    for (j=1;j<=n;j++) { 
   */      xi[j] *= xmin; 
   cov[1]=1.;      p[j] += xi[j]; 
     } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    free_vector(xicom,1,n); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    free_vector(pcom,1,n); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  } 
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  char *asc_diff_time(long time_sec, char ascdiff[])
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
       for(d=0; d<dh[mi][i]; d++){    long sec_left, days, hours, minutes;
         newm=savm;    days = (time_sec) / (60*60*24);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    sec_left = (time_sec) % (60*60*24);
         for (kk=1; kk<=cptcovage;kk++) {    hours = (sec_left) / (60*60) ;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    sec_left = (sec_left) %(60*60);
         }    minutes = (sec_left) /60;
            sec_left = (sec_left) % (60);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    return ascdiff;
         savm=oldm;  }
         oldm=newm;  
          /*************** powell ************************/
          void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       } /* end mult */              double (*func)(double [])) 
        { 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    void linmin(double p[], double xi[], int n, double *fret, 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/                double (*func)(double [])); 
       ipmx +=1;    int i,ibig,j; 
       sw += weight[i];    double del,t,*pt,*ptt,*xit;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double fp,fptt;
     } /* end of wave */    double *xits;
   } /* end of individual */    int niterf, itmp;
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    pt=vector(1,n); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    ptt=vector(1,n); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    xit=vector(1,n); 
   return -l;    xits=vector(1,n); 
 }    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
 /*********** Maximum Likelihood Estimation ***************/      fp=(*fret); 
       ibig=0; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      del=0.0; 
 {      last_time=curr_time;
   int i,j, iter;      (void) gettimeofday(&curr_time,&tzp);
   double **xi,*delti;      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);
   double fret;      /*    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);
   xi=matrix(1,npar,1,npar);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   for (i=1;i<=npar;i++)      */
     for (j=1;j<=npar;j++)     for (i=1;i<=n;i++) {
       xi[i][j]=(i==j ? 1.0 : 0.0);        printf(" %d %.12f",i, p[i]);
   printf("Powell\n");        fprintf(ficlog," %d %.12lf",i, p[i]);
   powell(p,xi,npar,ftol,&iter,&fret,func);        fprintf(ficrespow," %.12lf", p[i]);
       }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      printf("\n");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
 }      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
 /**** Computes Hessian and covariance matrix ***/        strcpy(strcurr,asctime(&tm));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*       asctime_r(&tm,strcurr); */
 {        forecast_time=curr_time; 
   double  **a,**y,*x,pd;        itmp = strlen(strcurr);
   double **hess;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   int i, j,jk;          strcurr[itmp-1]='\0';
   int *indx;        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);
   double hessii(double p[], double delta, int theta, double delti[]);        for(niterf=10;niterf<=30;niterf+=10){
   double hessij(double p[], double delti[], int i, int j);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   void lubksb(double **a, int npar, int *indx, double b[]) ;          tmf = *localtime(&forecast_time.tv_sec);
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
   hess=matrix(1,npar,1,npar);          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   printf("\nCalculation of the hessian matrix. Wait...\n");          strfor[itmp-1]='\0';
   for (i=1;i<=npar;i++){          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     printf("%d",i);fflush(stdout);          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);
     hess[i][i]=hessii(p,ftolhess,i,delti);        }
     /*printf(" %f ",p[i]);*/      }
     /*printf(" %lf ",hess[i][i]);*/      for (i=1;i<=n;i++) { 
   }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
          fptt=(*fret); 
   for (i=1;i<=npar;i++) {  #ifdef DEBUG
     for (j=1;j<=npar;j++)  {        printf("fret=%lf \n",*fret);
       if (j>i) {        fprintf(ficlog,"fret=%lf \n",*fret);
         printf(".%d%d",i,j);fflush(stdout);  #endif
         hess[i][j]=hessij(p,delti,i,j);        printf("%d",i);fflush(stdout);
         hess[j][i]=hess[i][j];            fprintf(ficlog,"%d",i);fflush(ficlog);
         /*printf(" %lf ",hess[i][j]);*/        linmin(p,xit,n,fret,func); 
       }        if (fabs(fptt-(*fret)) > del) { 
     }          del=fabs(fptt-(*fret)); 
   }          ibig=i; 
   printf("\n");        } 
   #ifdef DEBUG
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        printf("%d %.12e",i,(*fret));
          fprintf(ficlog,"%d %.12e",i,(*fret));
   a=matrix(1,npar,1,npar);        for (j=1;j<=n;j++) {
   y=matrix(1,npar,1,npar);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   x=vector(1,npar);          printf(" x(%d)=%.12e",j,xit[j]);
   indx=ivector(1,npar);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for(j=1;j<=n;j++) {
   ludcmp(a,npar,indx,&pd);          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
   for (j=1;j<=npar;j++) {        }
     for (i=1;i<=npar;i++) x[i]=0;        printf("\n");
     x[j]=1;        fprintf(ficlog,"\n");
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){      } 
       matcov[i][j]=x[i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
   }        int k[2],l;
         k[0]=1;
   printf("\n#Hessian matrix#\n");        k[1]=-1;
   for (i=1;i<=npar;i++) {        printf("Max: %.12e",(*func)(p));
     for (j=1;j<=npar;j++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
       printf("%.3e ",hess[i][j]);        for (j=1;j<=n;j++) {
     }          printf(" %.12e",p[j]);
     printf("\n");          fprintf(ficlog," %.12e",p[j]);
   }        }
         printf("\n");
   /* Recompute Inverse */        fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++)        for(l=0;l<=1;l++) {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          for (j=1;j<=n;j++) {
   ludcmp(a,npar,indx,&pd);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /*  printf("\n#Hessian matrix recomputed#\n");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
   for (j=1;j<=npar;j++) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (i=1;i<=npar;i++) x[i]=0;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     x[j]=1;        }
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);        free_vector(xit,1,n); 
     }        free_vector(xits,1,n); 
     printf("\n");        free_vector(ptt,1,n); 
   }        free_vector(pt,1,n); 
   */        return; 
       } 
   free_matrix(a,1,npar,1,npar);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   free_matrix(y,1,npar,1,npar);      for (j=1;j<=n;j++) { 
   free_vector(x,1,npar);        ptt[j]=2.0*p[j]-pt[j]; 
   free_ivector(indx,1,npar);        xit[j]=p[j]-pt[j]; 
   free_matrix(hess,1,npar,1,npar);        pt[j]=p[j]; 
       } 
       fptt=(*func)(ptt); 
 }      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 /*************** hessian matrix ****************/        if (t < 0.0) { 
 double hessii( double x[], double delta, int theta, double delti[])          linmin(p,xit,n,fret,func); 
 {          for (j=1;j<=n;j++) { 
   int i;            xi[j][ibig]=xi[j][n]; 
   int l=1, lmax=20;            xi[j][n]=xit[j]; 
   double k1,k2;          }
   double p2[NPARMAX+1];  #ifdef DEBUG
   double res;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double fx;          for(j=1;j<=n;j++){
   int k=0,kmax=10;            printf(" %.12e",xit[j]);
   double l1;            fprintf(ficlog," %.12e",xit[j]);
           }
   fx=func(x);          printf("\n");
   for (i=1;i<=npar;i++) p2[i]=x[i];          fprintf(ficlog,"\n");
   for(l=0 ; l <=lmax; l++){  #endif
     l1=pow(10,l);        }
     delts=delt;      } 
     for(k=1 ; k <kmax; k=k+1){    } 
       delt = delta*(l1*k);  } 
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  /**** Prevalence limit (stable prevalence)  ****************/
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       /*res= (k1-2.0*fx+k2)/delt/delt; */  {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
             matrix by transitions matrix until convergence is reached */
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    int i, ii,j,k;
 #endif    double min, max, maxmin, maxmax,sumnew=0.;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double **matprod2();
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    double **out, cov[NCOVMAX], **pmij();
         k=kmax;    double **newm;
       }    double agefin, delaymax=50 ; /* Max number of years to converge */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;    for (ii=1;ii<=nlstate+ndeath;ii++)
       }      for (j=1;j<=nlstate+ndeath;j++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         delts=delt;      }
       }  
     }     cov[1]=1.;
   }   
   delti[theta]=delts;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   return res;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
        newm=savm;
 }      /* Covariates have to be included here again */
        cov[2]=agefin;
 double hessij( double x[], double delti[], int thetai,int thetaj)    
 {        for (k=1; k<=cptcovn;k++) {
   int i;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int l=1, l1, lmax=20;          /*      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]]);*/
   double k1,k2,k3,k4,res,fx;        }
   double p2[NPARMAX+1];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int k;        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   fx=func(x);  
   for (k=1; k<=2; k++) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for (i=1;i<=npar;i++) p2[i]=x[i];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetai]=x[thetai]+delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     k1=func(p2)-fx;  
        savm=oldm;
     p2[thetai]=x[thetai]+delti[thetai]/k;      oldm=newm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      maxmax=0.;
     k2=func(p2)-fx;      for(j=1;j<=nlstate;j++){
          min=1.;
     p2[thetai]=x[thetai]-delti[thetai]/k;        max=0.;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(i=1; i<=nlstate; i++) {
     k3=func(p2)-fx;          sumnew=0;
            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     p2[thetai]=x[thetai]-delti[thetai]/k;          prlim[i][j]= newm[i][j]/(1-sumnew);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          max=FMAX(max,prlim[i][j]);
     k4=func(p2)-fx;          min=FMIN(min,prlim[i][j]);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        }
 #ifdef DEBUG        maxmin=max-min;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        maxmax=FMAX(maxmax,maxmin);
 #endif      }
   }      if(maxmax < ftolpl){
   return res;        return prlim;
 }      }
     }
 /************** Inverse of matrix **************/  }
 void ludcmp(double **a, int n, int *indx, double *d)  
 {  /*************** transition probabilities ***************/ 
   int i,imax,j,k;  
   double big,dum,sum,temp;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   double *vv;  {
      double s1, s2;
   vv=vector(1,n);    /*double t34;*/
   *d=1.0;    int i,j,j1, nc, ii, jj;
   for (i=1;i<=n;i++) {  
     big=0.0;      for(i=1; i<= nlstate; i++){
     for (j=1;j<=n;j++)        for(j=1; j<i;j++){
       if ((temp=fabs(a[i][j])) > big) big=temp;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            /*s2 += param[i][j][nc]*cov[nc];*/
     vv[i]=1.0/big;            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); */
   for (j=1;j<=n;j++) {          }
     for (i=1;i<j;i++) {          ps[i][j]=s2;
       sum=a[i][j];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        }
       a[i][j]=sum;        for(j=i+1; j<=nlstate+ndeath;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     big=0.0;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for (i=j;i<=n;i++) {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       sum=a[i][j];          }
       for (k=1;k<j;k++)          ps[i][j]=s2;
         sum -= a[i][k]*a[k][j];        }
       a[i][j]=sum;      }
       if ( (dum=vv[i]*fabs(sum)) >= big) {      /*ps[3][2]=1;*/
         big=dum;      
         imax=i;      for(i=1; i<= nlstate; i++){
       }        s1=0;
     }        for(j=1; j<i; j++)
     if (j != imax) {          s1+=exp(ps[i][j]);
       for (k=1;k<=n;k++) {        for(j=i+1; j<=nlstate+ndeath; j++)
         dum=a[imax][k];          s1+=exp(ps[i][j]);
         a[imax][k]=a[j][k];        ps[i][i]=1./(s1+1.);
         a[j][k]=dum;        for(j=1; j<i; j++)
       }          ps[i][j]= exp(ps[i][j])*ps[i][i];
       *d = -(*d);        for(j=i+1; j<=nlstate+ndeath; j++)
       vv[imax]=vv[j];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     indx[j]=imax;      } /* end i */
     if (a[j][j] == 0.0) a[j][j]=TINY;      
     if (j != n) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       dum=1.0/(a[j][j]);        for(jj=1; jj<= nlstate+ndeath; jj++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          ps[ii][jj]=0;
     }          ps[ii][ii]=1;
   }        }
   free_vector(vv,1,n);  /* Doesn't work */      }
 ;      
 }  
   /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 void lubksb(double **a, int n, int *indx, double b[])  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 {  /*         printf("ddd %lf ",ps[ii][jj]); */
   int i,ii=0,ip,j;  /*       } */
   double sum;  /*       printf("\n "); */
    /*        } */
   for (i=1;i<=n;i++) {  /*        printf("\n ");printf("%lf ",cov[2]); */
     ip=indx[i];         /*
     sum=b[ip];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     b[ip]=b[i];        goto end;*/
     if (ii)      return ps;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  }
     else if (sum) ii=i;  
     b[i]=sum;  /**************** Product of 2 matrices ******************/
   }  
   for (i=n;i>=1;i--) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     sum=b[i];  {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     b[i]=sum/a[i][i];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   }    /* in, b, out are matrice of pointers which should have been initialized 
 }       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
 /************ Frequencies ********************/    long i, j, k;
 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(i=nrl; i<= nrh; i++)
 {  /* Some frequencies */      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          out[i][k] +=in[i][j]*b[j][k];
   double ***freq; /* Frequencies */  
   double *pp;    return out;
   double pos, k2, dateintsum=0,k2cpt=0;  }
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  
    /************* Higher Matrix Product ***************/
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   strcpy(fileresp,"p");  {
   strcat(fileresp,fileres);    /* Computes the transition matrix starting at age 'age' over 
   if((ficresp=fopen(fileresp,"w"))==NULL) {       'nhstepm*hstepm*stepm' months (i.e. until
     printf("Problem with prevalence resultfile: %s\n", fileresp);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     exit(0);       nhstepm*hstepm matrices. 
   }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       (typically every 2 years instead of every month which is too big 
   j1=0;       for the memory).
        Model is determined by parameters x and covariates have to be 
   j=cptcoveff;       included manually here. 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
        */
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    int i, j, d, h, k;
        j1++;    double **out, cov[NCOVMAX];
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    double **newm;
          scanf("%d", i);*/  
         for (i=-1; i<=nlstate+ndeath; i++)      /* Hstepm could be zero and should return the unit matrix */
          for (jk=-1; jk<=nlstate+ndeath; jk++)      for (i=1;i<=nlstate+ndeath;i++)
            for(m=agemin; m <= agemax+3; m++)      for (j=1;j<=nlstate+ndeath;j++){
              freq[i][jk][m]=0;        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
         dateintsum=0;      }
         k2cpt=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        for (i=1; i<=imx; i++) {    for(h=1; h <=nhstepm; h++){
          bool=1;      for(d=1; d <=hstepm; d++){
          if  (cptcovn>0) {        newm=savm;
            for (z1=1; z1<=cptcoveff; z1++)        /* Covariates have to be included here again */
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        cov[1]=1.;
                bool=0;        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]]];
          if (bool==1) {        for (k=1; k<=cptcovage;k++)
            for(m=firstpass; m<=lastpass; m++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovprod;k++)
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                if(agev[m][i]==0) agev[m][i]=agemax+1;  
                if(agev[m][i]==1) agev[m][i]=agemax+2;  
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                  dateintsum=dateintsum+k2;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                  k2cpt++;        savm=oldm;
                }        oldm=newm;
       }
              }      for(i=1; i<=nlstate+ndeath; i++)
            }        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]);
                   */
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
     } /* end h */
         if  (cptcovn>0) {    return po;
          fprintf(ficresp, "\n#********** Variable ");  }
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
        fprintf(ficresp, "**********\n#");  
         }  /*************** log-likelihood *************/
        for(i=1; i<=nlstate;i++)  double func( double *x)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  {
        fprintf(ficresp, "\n");    int i, ii, j, k, mi, d, kk;
            double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for(i=(int)agemin; i <= (int)agemax+3; i++){    double **out;
     if(i==(int)agemax+3)    double sw; /* Sum of weights */
       printf("Total");    double lli; /* Individual log likelihood */
     else    int s1, s2;
       printf("Age %d", i);    double bbh, survp;
     for(jk=1; jk <=nlstate ; jk++){    long ipmx;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /*extern weight */
         pp[jk] += freq[jk][m][i];    /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(jk=1; jk <=nlstate ; jk++){    /*for(i=1;i<imx;i++) 
       for(m=-1, pos=0; m <=0 ; m++)      printf(" %d\n",s[4][i]);
         pos += freq[jk][m][i];    */
       if(pp[jk]>=1.e-10)    cov[1]=1.;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
       else    for(k=1; k<=nlstate; k++) ll[k]=0.;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
     }    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        for(mi=1; mi<= wav[i]-1; mi++){
         pp[jk] += freq[jk][m][i];          for (ii=1;ii<=nlstate+ndeath;ii++)
      }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(jk=1,pos=0; jk <=nlstate ; jk++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       pos += pp[jk];            }
     for(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
       if(pos>=1.e-5)            newm=savm;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       else            for (kk=1; kk<=cptcovage;kk++) {
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if( i <= (int) agemax){            }
         if(pos>=1.e-5){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);                         1,nlstate+ndeath,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;
         }          } /* end mult */
       else        
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       }          /* But now since version 0.9 we anticipate for bias at large stepm.
     }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for(jk=-1; jk <=nlstate+ndeath; jk++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for(m=-1; m <=nlstate+ndeath; m++)           * the nearest (and in case of equal distance, to the lowest) interval but now
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if(i <= (int) agemax)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       fprintf(ficresp,"\n");           * probability in order to take into account the bias as a fraction of the way
     printf("\n");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     }           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
  }           * For stepm > 1 the results are less biased than in previous versions. 
   dateintmean=dateintsum/k2cpt;           */
            s1=s[mw[mi][i]][i];
   fclose(ficresp);          s2=s[mw[mi+1][i]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_vector(pp,1,nlstate);          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   /* End of Freq */           */
 }          /* 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){ 
 /************ Prevalence ********************/            /* i.e. if s2 is a death state and if the date of death is known 
 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)               then the contribution to the likelihood is the probability to 
 {  /* Some frequencies */               die between last step unit time and current  step unit time, 
                 which is also equal to probability to die before dh 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;               minus probability to die before dh-stepm . 
   double ***freq; /* Frequencies */               In version up to 0.92 likelihood was computed
   double *pp;          as if date of death was unknown. Death was treated as any other
   double pos, k2;          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
   pp=vector(1,nlstate);          to consider that at each interview the state was recorded
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          (healthy, disable or death) and IMaCh was corrected; but when we
            introduced the exact date of death then we should have modified
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          the contribution of an exact death to the likelihood. This new
   j1=0;          contribution is smaller and very dependent of the step unit
            stepm. It is no more the probability to die between last interview
   j=cptcoveff;          and month of death but the probability to survive from last
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
  for(k1=1; k1<=j;k1++){          Jackson for correcting this bug.  Former versions increased
     for(i1=1; i1<=ncodemax[k1];i1++){          mortality artificially. The bad side is that we add another loop
       j1++;          which slows down the processing. The difference can be up to 10%
            lower mortality.
       for (i=-1; i<=nlstate+ndeath; i++)              */
         for (jk=-1; jk<=nlstate+ndeath; jk++)              lli=log(out[s1][s2] - savm[s1][s2]);
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  
                } else if  (s2==-2) {
       for (i=1; i<=imx; i++) {            for (j=1,survp=0. ; j<=nlstate; j++) 
         bool=1;              survp += out[s1][j];
         if  (cptcovn>0) {            lli= survp;
           for (z1=1; z1<=cptcoveff; z1++)          }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          
               bool=0;          else if  (s2==-4) {
         }            for (j=3,survp=0. ; j<=nlstate; j++) 
         if (bool==1) {              survp += out[s1][j];
           for(m=firstpass; m<=lastpass; m++){            lli= survp;
             k2=anint[m][i]+(mint[m][i]/12.);          }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          
               if(agev[m][i]==0) agev[m][i]=agemax+1;          else if  (s2==-5) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=1,survp=0. ; j<=2; j++) 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              survp += out[s1][j];
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            lli= survp;
             }          }
           }  
         }  
       }          else{
         for(i=(int)agemin; i <= (int)agemax+3; i++){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for(jk=1; jk <=nlstate ; jk++){            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          } 
               pp[jk] += freq[jk][m][i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           }          /*if(lli ==000.0)*/
           for(jk=1; jk <=nlstate ; jk++){          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
             for(m=-1, pos=0; m <=0 ; m++)          ipmx +=1;
             pos += freq[jk][m][i];          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                } /* end of wave */
          for(jk=1; jk <=nlstate ; jk++){      } /* end of individual */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    }  else if(mle==2){
              pp[jk] += freq[jk][m][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                  for(mi=1; mi<= wav[i]-1; mi++){
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
          for(jk=1; jk <=nlstate ; jk++){                        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            if( i <= (int) agemax){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              if(pos>=1.e-5){            }
                probs[i][jk][j1]= pp[jk]/pos;          for(d=0; d<=dh[mi][i]; d++){
              }            newm=savm;
            }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          }            for (kk=1; kk<=cptcovage;kk++) {
                        cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
              oldm=newm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          } /* end mult */
   free_vector(pp,1,nlstate);        
            s1=s[mw[mi][i]][i];
 }  /* End of Freq */          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 /************* Waves Concatenation ***************/          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        } /* end of wave */
      Death is a valid wave (if date is known).      } /* end of individual */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    }  else if(mle==3){  /* exponential inter-extrapolation */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      and mw[mi+1][i]. dh depends on stepm.        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, mi, m;            for (j=1;j<=nlstate+ndeath;j++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      double sum=0., jmean=0.;*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   int j, k=0,jk, ju, jl;          for(d=0; d<dh[mi][i]; d++){
   double sum=0.;            newm=savm;
   jmin=1e+5;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   jmax=-1;            for (kk=1; kk<=cptcovage;kk++) {
   jmean=0.;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=imx; i++){            }
     mi=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     m=firstpass;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     while(s[m][i] <= nlstate){            savm=oldm;
       if(s[m][i]>=1)            oldm=newm;
         mw[++mi][i]=m;          } /* end mult */
       if(m >=lastpass)        
         break;          s1=s[mw[mi][i]][i];
       else          s2=s[mw[mi+1][i]][i];
         m++;          bbh=(double)bh[mi][i]/(double)stepm; 
     }/* end while */          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 */
     if (s[m][i] > nlstate){          ipmx +=1;
       mi++;     /* Death is another wave */          sw += weight[i];
       /* if(mi==0)  never been interviewed correctly before death */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          /* Only death is a correct wave */        } /* end of wave */
       mw[mi][i]=m;      } /* end of individual */
     }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     wav[i]=mi;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if(mi==0)        for(mi=1; mi<= wav[i]-1; mi++){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=imx; i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(mi=1; mi<wav[i];mi++){            }
       if (stepm <=0)          for(d=0; d<dh[mi][i]; d++){
         dh[mi][i]=1;            newm=savm;
       else{            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if (s[mw[mi+1][i]][i] > nlstate) {            for (kk=1; kk<=cptcovage;kk++) {
           if (agedc[i] < 2*AGESUP) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            }
           if(j==0) j=1;  /* Survives at least one month after exam */          
           k=k+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if (j >= jmax) jmax=j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if (j <= jmin) jmin=j;            savm=oldm;
           sum=sum+j;            oldm=newm;
           /* if (j<10) printf("j=%d num=%d ",j,i); */          } /* end mult */
           }        
         }          s1=s[mw[mi][i]][i];
         else{          s2=s[mw[mi+1][i]][i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          if( s2 > nlstate){ 
           k=k+1;            lli=log(out[s1][s2] - savm[s1][s2]);
           if (j >= jmax) jmax=j;          }else{
           else if (j <= jmin)jmin=j;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          }
           sum=sum+j;          ipmx +=1;
         }          sw += weight[i];
         jk= j/stepm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         jl= j -jk*stepm;  /*      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]); */
         ju= j -(jk+1)*stepm;        } /* end of wave */
         if(jl <= -ju)      } /* end of individual */
           dh[mi][i]=jk;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           dh[mi][i]=jk+1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if(dh[mi][i]==0)        for(mi=1; mi<= wav[i]-1; mi++){
           dh[mi][i]=1; /* At least one step */          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmean=sum/k;            }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          for(d=0; d<dh[mi][i]; d++){
  }            newm=savm;
 /*********** Tricode ****************************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void tricode(int *Tvar, int **nbcode, int imx)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int Ndum[20],ij=1, k, j, i;            }
   int cptcode=0;          
   cptcoveff=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (k=0; k<19; k++) Ndum[k]=0;            savm=oldm;
   for (k=1; k<=7; k++) ncodemax[k]=0;            oldm=newm;
           } /* end mult */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        
     for (i=1; i<=imx; i++) {          s1=s[mw[mi][i]][i];
       ij=(int)(covar[Tvar[j]][i]);          s2=s[mw[mi+1][i]][i];
       Ndum[ij]++;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          ipmx +=1;
       if (ij > cptcode) cptcode=ij;          sw += weight[i];
     }          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=0; i<=cptcode; i++) {        } /* end of wave */
       if(Ndum[i]!=0) ncodemax[j]++;      } /* end of individual */
     }    } /* End of if */
     ij=1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for (i=1; i<=ncodemax[j]; i++) {    return -l;
       for (k=0; k<=19; k++) {  }
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;  /*************** log-likelihood *************/
           ij++;  double funcone( double *x)
         }  {
         if (ij > ncodemax[j]) break;    /* Same as likeli but slower because of a lot of printf and if */
       }      int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   }      double **out;
     double lli; /* Individual log likelihood */
  for (k=0; k<19; k++) Ndum[k]=0;    double llt;
     int s1, s2;
  for (i=1; i<=ncovmodel-2; i++) {    double bbh, survp;
       ij=Tvar[i];    /*extern weight */
       Ndum[ij]++;    /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
  ij=1;      printf(" %d\n",s[4][i]);
  for (i=1; i<=10; i++) {    */
    if((Ndum[i]!=0) && (i<=ncov)){    cov[1]=1.;
      Tvaraff[ij]=i;  
      ij++;    for(k=1; k<=nlstate; k++) ll[k]=0.;
    }  
  }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     cptcoveff=ij-1;      for(mi=1; mi<= wav[i]-1; mi++){
 }        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
 /*********** Health Expectancies ****************/            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          }
 {        for(d=0; d<dh[mi][i]; d++){
   /* Health expectancies */          newm=savm;
   int i, j, nhstepm, hstepm, h;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double age, agelim,hf;          for (kk=1; kk<=cptcovage;kk++) {
   double ***p3mat;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            }
   fprintf(ficreseij,"# Health expectancies\n");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficreseij,"# Age");                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=nlstate;i++)          savm=oldm;
     for(j=1; j<=nlstate;j++)          oldm=newm;
       fprintf(ficreseij," %1d-%1d",i,j);        } /* end mult */
   fprintf(ficreseij,"\n");        
         s1=s[mw[mi][i]][i];
   hstepm=1*YEARM; /*  Every j years of age (in month) */        s2=s[mw[mi+1][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   agelim=AGESUP;         * is higher than the multiple of stepm and negative otherwise.
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */         */
     /* nhstepm age range expressed in number of stepm */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          lli=log(out[s1][s2] - savm[s1][s2]);
     /* Typically if 20 years = 20*12/6=40 stepm */        } else if (mle==1){
     if (stepm >= YEARM) hstepm=1;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        } else if(mle==2){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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 */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        } else if(mle==3){  /* exponential inter-extrapolation */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          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 */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     for(i=1; i<=nlstate;i++)          lli=log(out[s1][s2]); /* Original formula */
       for(j=1; j<=nlstate;j++)        } /* End of if */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        ipmx +=1;
           eij[i][j][(int)age] +=p3mat[i][j][h];        sw += weight[i];
         }        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]); */
     hf=1;        if(globpr){
     if (stepm >= YEARM) hf=stepm/YEARM;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     fprintf(ficreseij,"%.0f",age );   %10.6f %10.6f %10.6f ", \
     for(i=1; i<=nlstate;i++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for(j=1; j<=nlstate;j++){                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       }            llt +=ll[k]*gipmx/gsw;
     fprintf(ficreseij,"\n");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   }          fprintf(ficresilk," %10.6f\n", -llt);
 }        }
       } /* end of wave */
 /************ Variance ******************/    } /* end of individual */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /* Variance of health expectancies */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    if(globpr==0){ /* First time we count the contributions and weights */
   double **newm;      gipmx=ipmx;
   double **dnewm,**doldm;      gsw=sw;
   int i, j, nhstepm, hstepm, h;    }
   int k, cptcode;    return -l;
   double *xp;  }
   double **gp, **gm;  
   double ***gradg, ***trgradg;  
   double ***p3mat;  /*************** function likelione ***********/
   double age,agelim;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   int theta;  {
     /* This routine should help understanding what is done with 
    fprintf(ficresvij,"# Covariances of life expectancies\n");       the selection of individuals/waves and
   fprintf(ficresvij,"# Age");       to check the exact contribution to the likelihood.
   for(i=1; i<=nlstate;i++)       Plotting could be done.
     for(j=1; j<=nlstate;j++)     */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int k;
   fprintf(ficresvij,"\n");  
     if(*globpri !=0){ /* Just counts and sums, no printings */
   xp=vector(1,npar);      strcpy(fileresilk,"ilk"); 
   dnewm=matrix(1,nlstate,1,npar);      strcat(fileresilk,fileres);
   doldm=matrix(1,nlstate,1,nlstate);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresilk);
   hstepm=1*YEARM; /* Every year of age */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      }
   agelim = AGESUP;      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 (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     if (stepm >= YEARM) hstepm=1;      for(k=1; k<=nlstate; k++) 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    }
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    *fretone=(*funcone)(p);
     if(*globpri !=0){
     for(theta=1; theta <=npar; theta++){      fclose(ficresilk);
       for(i=1; i<=npar; i++){ /* Computes gradient */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fflush(fichtm); 
       }    } 
       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, gp[h][j]=0.;i<=nlstate;i++)    double fret;
             gp[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(i=1; i<=npar; i++) /* Computes gradient */      for (j=1;j<=npar;j++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        xi[i][j]=(i==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      printf("Powell\n");  fprintf(ficlog,"Powell\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcpy(filerespow,"pow"); 
      strcat(filerespow,fileres);
       if (popbased==1) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         for(i=1; i<=nlstate;i++)      printf("Problem with resultfile: %s\n", filerespow);
           prlim[i][i]=probs[(int)age][i][ij];      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
       for(j=1; j<= nlstate; j++){    for (i=1;i<=nlstate;i++)
         for(h=0; h<=nhstepm; h++){      for(j=1;j<=nlstate+ndeath;j++)
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    fprintf(ficrespow,"\n");
         }  
       }    powell(p,xi,npar,ftol,&iter,&fret,func);
   
       for(j=1; j<= nlstate; j++)    fclose(ficrespow);
         for(h=0; h<=nhstepm; h++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     } /* End theta */  
   }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
   /**** Computes Hessian and covariance matrix ***/
     for(h=0; h<=nhstepm; h++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for(j=1; j<=nlstate;j++)  {
         for(theta=1; theta <=npar; theta++)    double  **a,**y,*x,pd;
           trgradg[h][j][theta]=gradg[h][theta][j];    double **hess;
     int i, j,jk;
     for(i=1;i<=nlstate;i++)    int *indx;
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for(h=0;h<=nhstepm;h++){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       for(k=0;k<=nhstepm;k++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    void ludcmp(double **a, int npar, int *indx, double *d) ;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double gompertz(double p[]);
         for(i=1;i<=nlstate;i++)    hess=matrix(1,npar,1,npar);
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];    printf("\nCalculation of the hessian matrix. Wait...\n");
       }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     }    for (i=1;i<=npar;i++){
     h=1;      printf("%d",i);fflush(stdout);
     if (stepm >= YEARM) h=stepm/YEARM;      fprintf(ficlog,"%d",i);fflush(ficlog);
     fprintf(ficresvij,"%.0f ",age );     
     for(i=1; i<=nlstate;i++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(j=1; j<=nlstate;j++){      
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      /*  printf(" %f ",p[i]);
       }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     fprintf(ficresvij,"\n");    }
     free_matrix(gp,0,nhstepm,1,nlstate);    
     free_matrix(gm,0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      for (j=1;j<=npar;j++)  {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        if (j>i) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          printf(".%d%d",i,j);fflush(stdout);
   } /* End age */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
            hess[i][j]=hessij(p,delti,i,j,func,npar);
   free_vector(xp,1,npar);          
   free_matrix(doldm,1,nlstate,1,npar);          hess[j][i]=hess[i][j];    
   free_matrix(dnewm,1,nlstate,1,nlstate);          /*printf(" %lf ",hess[i][j]);*/
         }
 }      }
     }
 /************ Variance of prevlim ******************/    printf("\n");
 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)    fprintf(ficlog,"\n");
 {  
   /* Variance of prevalence limit */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **newm;    
   double **dnewm,**doldm;    a=matrix(1,npar,1,npar);
   int i, j, nhstepm, hstepm;    y=matrix(1,npar,1,npar);
   int k, cptcode;    x=vector(1,npar);
   double *xp;    indx=ivector(1,npar);
   double *gp, *gm;    for (i=1;i<=npar;i++)
   double **gradg, **trgradg;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double age,agelim;    ludcmp(a,npar,indx,&pd);
   int theta;  
        for (j=1;j<=npar;j++) {
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for (i=1;i<=npar;i++) x[i]=0;
   fprintf(ficresvpl,"# Age");      x[j]=1;
   for(i=1; i<=nlstate;i++)      lubksb(a,npar,indx,x);
       fprintf(ficresvpl," %1d-%1d",i,i);      for (i=1;i<=npar;i++){ 
   fprintf(ficresvpl,"\n");        matcov[i][j]=x[i];
       }
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
   hstepm=1*YEARM; /* Every year of age */    for (i=1;i<=npar;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (j=1;j<=npar;j++) { 
   agelim = AGESUP;        printf("%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        fprintf(ficlog,"%.3e ",hess[i][j]);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      }
     if (stepm >= YEARM) hstepm=1;      printf("\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficlog,"\n");
     gradg=matrix(1,npar,1,nlstate);    }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
     for(theta=1; theta <=npar; theta++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       for(i=1; i<=npar; i++){ /* Computes gradient */    ludcmp(a,npar,indx,&pd);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    /*  printf("\n#Hessian matrix recomputed#\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    for (j=1;j<=npar;j++) {
         gp[i] = prlim[i][i];      for (i=1;i<=npar;i++) x[i]=0;
          x[j]=1;
       for(i=1; i<=npar; i++) /* Computes gradient */      lubksb(a,npar,indx,x);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++){ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        y[i][j]=x[i];
       for(i=1;i<=nlstate;i++)        printf("%.3e ",y[i][j]);
         gm[i] = prlim[i][i];        fprintf(ficlog,"%.3e ",y[i][j]);
       }
       for(i=1;i<=nlstate;i++)      printf("\n");
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      fprintf(ficlog,"\n");
     } /* End theta */    }
     */
     trgradg =matrix(1,nlstate,1,npar);  
     free_matrix(a,1,npar,1,npar);
     for(j=1; j<=nlstate;j++)    free_matrix(y,1,npar,1,npar);
       for(theta=1; theta <=npar; theta++)    free_vector(x,1,npar);
         trgradg[j][theta]=gradg[theta][j];    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)  /*************** hessian matrix ****************/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
     fprintf(ficresvpl,"%.0f ",age );    int i;
     for(i=1; i<=nlstate;i++)    int l=1, lmax=20;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    double k1,k2;
     fprintf(ficresvpl,"\n");    double p2[NPARMAX+1];
     free_vector(gp,1,nlstate);    double res;
     free_vector(gm,1,nlstate);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     free_matrix(gradg,1,npar,1,nlstate);    double fx;
     free_matrix(trgradg,1,nlstate,1,npar);    int k=0,kmax=10;
   } /* End age */    double l1;
   
   free_vector(xp,1,npar);    fx=func(x);
   free_matrix(doldm,1,nlstate,1,npar);    for (i=1;i<=npar;i++) p2[i]=x[i];
   free_matrix(dnewm,1,nlstate,1,nlstate);    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
 }      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
 /************ Variance of one-step probabilities  ******************/        delt = delta*(l1*k);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        p2[theta]=x[theta] +delt;
 {        k1=func(p2)-fx;
   int i, j;        p2[theta]=x[theta]-delt;
   int k=0, cptcode;        k2=func(p2)-fx;
   double **dnewm,**doldm;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   double *xp;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double *gp, *gm;        
   double **gradg, **trgradg;  #ifdef DEBUG
   double age,agelim, cov[NCOVMAX];        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);
   int theta;        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);
   char fileresprob[FILENAMELENGTH];  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   strcpy(fileresprob,"prob");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   strcat(fileresprob,fileres);          k=kmax;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        }
     printf("Problem with resultfile: %s\n", fileresprob);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   }          k=kmax; l=lmax*10.;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   xp=vector(1,npar);        }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    }
      delti[theta]=delts;
   cov[1]=1;    return res; 
   for (age=bage; age<=fage; age ++){    
     cov[2]=age;  }
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    int i;
        int l=1, l1, lmax=20;
     for(theta=1; theta <=npar; theta++){    double k1,k2,k3,k4,res,fx;
       for(i=1; i<=npar; i++)    double p2[NPARMAX+1];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int k;
        
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    fx=func(x);
        for (k=1; k<=2; k++) {
       k=0;      for (i=1;i<=npar;i++) p2[i]=x[i];
       for(i=1; i<= (nlstate+ndeath); i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
         for(j=1; j<=(nlstate+ndeath);j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
            k=k+1;      k1=func(p2)-fx;
           gp[k]=pmmij[i][j];    
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
       for(i=1; i<=npar; i++)    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    
       k=0;      p2[thetai]=x[thetai]-delti[thetai]/k;
       for(i=1; i<=(nlstate+ndeath); i++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for(j=1; j<=(nlstate+ndeath);j++){      k4=func(p2)-fx;
           k=k+1;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           gm[k]=pmmij[i][j];  #ifdef DEBUG
         }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
        #endif
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      return res;
     }  }
   
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  /************** Inverse of matrix **************/
       for(theta=1; theta <=npar; theta++)  void ludcmp(double **a, int n, int *indx, double *d) 
       trgradg[j][theta]=gradg[theta][j];  { 
      int i,imax,j,k; 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    double big,dum,sum,temp; 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double *vv; 
    
      pmij(pmmij,cov,ncovmodel,x,nlstate);    vv=vector(1,n); 
     *d=1.0; 
      k=0;    for (i=1;i<=n;i++) { 
      for(i=1; i<=(nlstate+ndeath); i++){      big=0.0; 
        for(j=1; j<=(nlstate+ndeath);j++){      for (j=1;j<=n;j++) 
          k=k+1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
          gm[k]=pmmij[i][j];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
      }    } 
          for (j=1;j<=n;j++) { 
      /*printf("\n%d ",(int)age);      for (i=1;i<j;i++) { 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        sum=a[i][j]; 
                for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      } 
      }*/      big=0.0; 
       for (i=j;i<=n;i++) { 
   fprintf(ficresprob,"\n%d ",(int)age);        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          sum -= a[i][k]*a[k][j]; 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        a[i][j]=sum; 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   }          big=dum; 
           imax=i; 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        } 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      } 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if (j != imax) { 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for (k=1;k<=n;k++) { 
 }          dum=a[imax][k]; 
  free_vector(xp,1,npar);          a[imax][k]=a[j][k]; 
 fclose(ficresprob);          a[j][k]=dum; 
         } 
 }        *d = -(*d); 
         vv[imax]=vv[j]; 
 /******************* Printing html file ***********/      } 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){      indx[j]=imax; 
   int jj1, k1, i1, cpt;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   FILE *fichtm;      if (j != n) { 
   /*char optionfilehtm[FILENAMELENGTH];*/        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   strcpy(optionfilehtm,optionfile);      } 
   strcat(optionfilehtm,".htm");    } 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    free_vector(vv,1,n);  /* Doesn't work */
     printf("Problem with %s \n",optionfilehtm), exit(0);  ;
   }  } 
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  void lubksb(double **a, int n, int *indx, double b[]) 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  { 
     int i,ii=0,ip,j; 
 Total number of observations=%d <br>    double sum; 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>   
 <hr  size=\"2\" color=\"#EC5E5E\">    for (i=1;i<=n;i++) { 
 <li>Outputs files<br><br>\n      ip=indx[i]; 
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      sum=b[ip]; 
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>      b[ip]=b[i]; 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      if (ii) 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      else if (sum) ii=i; 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      b[i]=sum; 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    } 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    for (i=n;i>=1;i--) { 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      sum=b[i]; 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>      b[i]=sum/a[i][i]; 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    } 
    } 
 fprintf(fichtm," <li>Graphs</li><p>");  
   /************ Frequencies ********************/
  m=cptcoveff;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  {  /* Some frequencies */
     
  jj1=0;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
  for(k1=1; k1<=m;k1++){    int first;
    for(i1=1; i1<=ncodemax[k1];i1++){    double ***freq; /* Frequencies */
        jj1++;    double *pp, **prop;
        if (cptcovn > 0) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    FILE *ficresp;
          for (cpt=1; cpt<=cptcoveff;cpt++)    char fileresp[FILENAMELENGTH];
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    pp=vector(1,nlstate);
        }    prop=matrix(1,nlstate,iagemin,iagemax+3);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    strcpy(fileresp,"p");
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        strcat(fileresp,fileres);
        for(cpt=1; cpt<nlstate;cpt++){    if((ficresp=fopen(fileresp,"w"))==NULL) {
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      printf("Problem with prevalence resultfile: %s\n", fileresp);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        }      exit(0);
     for(cpt=1; cpt<=nlstate;cpt++) {    }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 interval) in state (%d): v%s%d%d.gif <br>    j1=0;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      
      }    j=cptcoveff;
      for(cpt=1; cpt<=nlstate;cpt++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    first=1;
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    for(k1=1; k1<=j;k1++){
 health expectancies in states (1) and (2): e%s%d.gif<br>      for(i1=1; i1<=ncodemax[k1];i1++){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        j1++;
 fprintf(fichtm,"\n</body>");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
    }          scanf("%d", i);*/
    }        for (i=-5; i<=nlstate+ndeath; i++)  
 fclose(fichtm);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
 }            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){      for (i=1; i<=nlstate; i++)  
         for(m=iagemin; m <= iagemax+3; m++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          prop[i][m]=0;
         
   strcpy(optionfilegnuplot,optionfilefiname);        dateintsum=0;
   strcat(optionfilegnuplot,".plt");        k2cpt=0;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for (i=1; i<=imx; i++) {
     printf("Problem with file %s",optionfilegnuplot);          bool=1;
   }          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 #ifdef windows              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fprintf(ficgp,"cd \"%s\" \n",pathc);                bool=0;
 #endif          }
 m=pow(2,cptcoveff);          if (bool==1){
              for(m=firstpass; m<=lastpass; m++){
  /* 1eme*/              k2=anint[m][i]+(mint[m][i]/12.);
   for (cpt=1; cpt<= nlstate ; cpt ++) {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
    for (k1=1; k1<= m ; k1 ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
 #ifdef windows                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);                if (m<lastpass) {
 #endif                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 #ifdef unix                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                }
 #endif                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 for (i=1; i<= nlstate ; i ++) {                  dateintsum=dateintsum+k2;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  k2cpt++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                }
 }                /*}*/
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            }
     for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");         
 }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  fprintf(ficresp, "#Local time at start: %s", strstart);
      for (i=1; i<= nlstate ; i ++) {        if  (cptcovn>0) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresp, "\n#********** Variable "); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 }            fprintf(ficresp, "**********\n#");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix        for(i=1; i<=nlstate;i++) 
 fprintf(ficgp,"\nset ter gif small size 400,300");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 #endif        fprintf(ficresp, "\n");
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        
    }        for(i=iagemin; i <= iagemax+3; i++){
   }          if(i==iagemax+3){
   /*2 eme*/            fprintf(ficlog,"Total");
           }else{
   for (k1=1; k1<= m ; k1 ++) {            if(first==1){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              first=0;
                  printf("See log file for details...\n");
     for (i=1; i<= nlstate+1 ; i ++) {            }
       k=2*i;            fprintf(ficlog,"Age %d", i);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {          for(jk=1; jk <=nlstate ; jk++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              pp[jk] += freq[jk][m][i]; 
 }            }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          for(jk=1; jk <=nlstate ; jk++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            for(m=-1, pos=0; m <=0 ; m++)
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              pos += freq[jk][m][i];
       for (j=1; j<= nlstate+1 ; j ++) {            if(pp[jk]>=1.e-10){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if(first==1){
         else fprintf(ficgp," \%%*lf (\%%*lf)");              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 }                }
       fprintf(ficgp,"\" t\"\" w l 0,");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            }else{
       for (j=1; j<= nlstate+1 ; j ++) {              if(first==1)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }              }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          }
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   }              pp[jk] += freq[jk][m][i];
            }       
   /*3eme*/          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   for (k1=1; k1<= m ; k1 ++) {            posprop += prop[jk][i];
     for (cpt=1; cpt<= nlstate ; cpt ++) {          }
       k=2+nlstate*(cpt-1);          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);            if(pos>=1.e-5){
       for (i=1; i< nlstate ; i ++) {              if(first==1)
         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);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            }else{
     }              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /* CV preval stat */            }
     for (k1=1; k1<= m ; k1 ++) {            if( i <= iagemax){
     for (cpt=1; cpt<nlstate ; cpt ++) {              if(pos>=1.e-5){
       k=3;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for (i=1; i< nlstate ; i ++)              }
         fprintf(ficgp,"+$%d",k+i+1);              else
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                  }
       l=3+(nlstate+ndeath)*cpt;          }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          
       for (i=1; i< nlstate ; i ++) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
         l=3+(nlstate+ndeath)*cpt;            for(m=-1; m <=nlstate+ndeath; m++)
         fprintf(ficgp,"+$%d",l+i+1);              if(freq[jk][m][i] !=0 ) {
       }              if(first==1)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     }              }
   }            if(i <= iagemax)
              fprintf(ficresp,"\n");
   /* proba elementaires */          if(first==1)
    for(i=1,jk=1; i <=nlstate; i++){            printf("Others in log...\n");
     for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficlog,"\n");
       if (k != i) {        }
         for(j=1; j <=ncovmodel; j++){      }
            }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    dateintmean=dateintsum/k2cpt; 
           jk++;   
           fprintf(ficgp,"\n");    fclose(ficresp);
         }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       }    free_vector(pp,1,nlstate);
     }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     }    /* End of Freq */
   }
     for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);  /************ Prevalence ********************/
    i=1;  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
    for(k2=1; k2<=nlstate; k2++) {  {  
      k3=i;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      for(k=1; k<=(nlstate+ndeath); k++) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
        if (k != k2){       We still use firstpass and lastpass as another selection.
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    */
 ij=1;   
         for(j=3; j <=ncovmodel; j++) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double ***freq; /* Frequencies */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double *pp, **prop;
             ij++;    double pos,posprop; 
           }    double  y2; /* in fractional years */
           else    int iagemin, iagemax;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         }    iagemin= (int) agemin;
           fprintf(ficgp,")/(1");    iagemax= (int) agemax;
            /*pp=vector(1,nlstate);*/
         for(k1=1; k1 <=nlstate; k1++){      prop=matrix(1,nlstate,iagemin,iagemax+3); 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 ij=1;    j1=0;
           for(j=3; j <=ncovmodel; j++){    
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    j=cptcoveff;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             ij++;    
           }    for(k1=1; k1<=j;k1++){
           else      for(i1=1; i1<=ncodemax[k1];i1++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        j1++;
           }        
           fprintf(ficgp,")");        for (i=1; i<=nlstate; i++)  
         }          for(m=iagemin; m <= iagemax+3; m++)
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            prop[i][m]=0.0;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");       
         i=i+ncovmodel;        for (i=1; i<=imx; i++) { /* Each individual */
        }          bool=1;
      }          if  (cptcovn>0) {
    }            for (z1=1; z1<=cptcoveff; z1++) 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    }                bool=0;
              } 
   fclose(ficgp);          if (bool==1) { 
 }  /* end gnuplot */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 /*************** Moving average **************/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   int i, cpt, cptcod;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for (agedeb=agemin; agedeb<=fage; agedeb++)                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       for (i=1; i<=nlstate;i++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
           mobaverage[(int)agedeb][i][cptcod]=0.;                } 
                  }
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){            } /* end selection of waves */
       for (i=1; i<=nlstate;i++){          }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
           for (cpt=0;cpt<=4;cpt++){        for(i=iagemin; i <= iagemax+3; i++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          
           }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            posprop += prop[jk][i]; 
         }          } 
       }  
     }          for(jk=1; jk <=nlstate ; jk++){     
                if( i <=  iagemax){ 
 }              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
 /************** Forecasting ******************/            } 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          }/* end jk */ 
          }/* end i */ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      } /* end i1 */
   int *popage;    } /* end k1 */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    
   double *popeffectif,*popcount;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   double ***p3mat;    /*free_vector(pp,1,nlstate);*/
   char fileresf[FILENAMELENGTH];    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  /************* Waves Concatenation ***************/
   
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
    {
      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   strcpy(fileresf,"f");       Death is a valid wave (if date is known).
   strcat(fileresf,fileres);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   if((ficresf=fopen(fileresf,"w"))==NULL) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     printf("Problem with forecast resultfile: %s\n", fileresf);       and mw[mi+1][i]. dh depends on stepm.
   }       */
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
     int i, mi, m;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
   if (mobilav==1) {    int first;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int j, k=0,jk, ju, jl;
     movingaverage(agedeb, fage, agemin, mobaverage);    double sum=0.;
   }    first=0;
     jmin=1e+5;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    jmax=-1;
   if (stepm<=12) stepsize=1;    jmean=0.;
      for(i=1; i<=imx; i++){
   agelim=AGESUP;      mi=0;
        m=firstpass;
   hstepm=1;      while(s[m][i] <= nlstate){
   hstepm=hstepm/stepm;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   yp1=modf(dateintmean,&yp);          mw[++mi][i]=m;
   anprojmean=yp;        if(m >=lastpass)
   yp2=modf((yp1*12),&yp);          break;
   mprojmean=yp;        else
   yp1=modf((yp2*30.5),&yp);          m++;
   jprojmean=yp;      }/* end while */
   if(jprojmean==0) jprojmean=1;      if (s[m][i] > nlstate){
   if(mprojmean==0) jprojmean=1;        mi++;     /* Death is another wave */
          /* if(mi==0)  never been interviewed correctly before death */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);           /* Only death is a correct wave */
          mw[mi][i]=m;
   for(cptcov=1;cptcov<=i2;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;      wav[i]=mi;
       fprintf(ficresf,"\n#******");      if(mi==0){
       for(j=1;j<=cptcoveff;j++) {        nbwarn++;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if(first==0){
       }          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fprintf(ficresf,"******\n");          first=1;
       fprintf(ficresf,"# StartingAge FinalAge");        }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        if(first==1){
                fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
              }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      } /* end mi==0 */
         fprintf(ficresf,"\n");    } /* End individuals */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
     for(i=1; i<=imx; i++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      for(mi=1; mi<wav[i];mi++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        if (stepm <=0)
           nhstepm = nhstepm/hstepm;          dh[mi][i]=1;
                  else{
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           oldm=oldms;savm=savms;            if (agedc[i] < 2*AGESUP) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                      if(j==0) j=1;  /* Survives at least one month after exam */
           for (h=0; h<=nhstepm; h++){              else if(j<0){
             if (h==(int) (calagedate+YEARM*cpt)) {                nberr++;
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }                j=1; /* Temporary Dangerous patch */
             for(j=1; j<=nlstate+ndeath;j++) {                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);
               kk1=0.;kk2=0;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               for(i=1; i<=nlstate;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);
                 if (mobilav==1)              }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              k=k+1;
                 else {              if (j >= jmax) jmax=j;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              if (j <= jmin) jmin=j;
                 }              sum=sum+j;
                              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
               if (h==(int)(calagedate+12*cpt)){            }
                 fprintf(ficresf," %.3f", kk1);          }
                                  else{
               }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             }  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            k=k+1;
         }            if (j >= jmax) jmax=j;
       }            else if (j <= jmin)jmin=j;
     }            /*        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]);*/
                    if(j<0){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   fclose(ficresf);              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]);
 }            }
 /************** Forecasting ******************/            sum=sum+j;
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){          }
            jk= j/stepm;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          jl= j -jk*stepm;
   int *popage;          ju= j -(jk+1)*stepm;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   double *popeffectif,*popcount;            if(jl==0){
   double ***p3mat,***tabpop,***tabpopprev;              dh[mi][i]=jk;
   char filerespop[FILENAMELENGTH];              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    * at the price of an extra matrix product in likelihood */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              dh[mi][i]=jk+1;
   agelim=AGESUP;              bh[mi][i]=ju;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            }
            }else{
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            if(jl <= -ju){
                dh[mi][i]=jk;
                bh[mi][i]=jl;       /* bias is positive if real duration
   strcpy(filerespop,"pop");                                   * is higher than the multiple of stepm and negative otherwise.
   strcat(filerespop,fileres);                                   */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {            }
     printf("Problem with forecast resultfile: %s\n", filerespop);            else{
   }              dh[mi][i]=jk+1;
   printf("Computing forecasting: result on file '%s' \n", filerespop);              bh[mi][i]=ju;
             }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
   if (mobilav==1) {              bh[mi][i]=ju; /* At least one step */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              /*  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);*/
     movingaverage(agedeb, fage, agemin, mobaverage);            }
   }          } /* end if mle */
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      } /* end wave */
   if (stepm<=12) stepsize=1;    }
      jmean=sum/k;
   agelim=AGESUP;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   hstepm=1;   }
   hstepm=hstepm/stepm;  
    /*********** Tricode ****************************/
   if (popforecast==1) {  void tricode(int *Tvar, int **nbcode, int imx)
     if((ficpop=fopen(popfile,"r"))==NULL) {  {
       printf("Problem with population file : %s\n",popfile);exit(0);    
     }    int Ndum[20],ij=1, k, j, i, maxncov=19;
     popage=ivector(0,AGESUP);    int cptcode=0;
     popeffectif=vector(0,AGESUP);    cptcoveff=0; 
     popcount=vector(0,AGESUP);   
        for (k=0; k<maxncov; k++) Ndum[k]=0;
     i=1;      for (k=1; k<=7; k++) ncodemax[k]=0;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
        for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     imx=i;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                                 modality*/ 
   }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
   for(cptcov=1;cptcov<=i2;cptcov++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       k=k+1;                                         Tvar[j]. If V=sex and male is 0 and 
       fprintf(ficrespop,"\n#******");                                         female is 1, then  cptcode=1.*/
       for(j=1;j<=cptcoveff;j++) {      }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }      for (i=0; i<=cptcode; i++) {
       fprintf(ficrespop,"******\n");        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       fprintf(ficrespop,"# Age");      }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");      ij=1; 
            for (i=1; i<=ncodemax[j]; i++) {
       for (cpt=0; cpt<=0;cpt++) {        for (k=0; k<= maxncov; k++) {
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            if (Ndum[k] != 0) {
                    nbcode[Tvar[j]][ij]=k; 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            /* 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; */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            
           nhstepm = nhstepm/hstepm;            ij++;
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (ij > ncodemax[j]) break; 
           oldm=oldms;savm=savms;        }  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        } 
            }  
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {   for (k=0; k< maxncov; k++) Ndum[k]=0;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }   for (i=1; i<=ncovmodel-2; i++) { 
             for(j=1; j<=nlstate+ndeath;j++) {     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
               kk1=0.;kk2=0;     ij=Tvar[i];
               for(i=1; i<=nlstate;i++) {                   Ndum[ij]++;
                 if (mobilav==1)   }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {   ij=1;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   for (i=1; i<= maxncov; i++) {
                 }     if((Ndum[i]!=0) && (i<=ncovcol)){
               }       Tvaraff[ij]=i; /*For printing */
               if (h==(int)(calagedate+12*cpt)){       ij++;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;     }
                   /*fprintf(ficrespop," %.3f", kk1);   }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/   
               }   cptcoveff=ij-1; /*Number of simple covariates*/
             }  }
             for(i=1; i<=nlstate;i++){  
               kk1=0.;  /*********** Health Expectancies ****************/
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
                 }  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  {
             }    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    double age, agelim, hf;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    double ***p3mat,***varhe;
           }    double **dnewm,**doldm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *xp;
         }    double **gp, **gm;
       }    double ***gradg, ***trgradg;
      int theta;
   /******/  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    xp=vector(1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      dnewm=matrix(1,nlstate*nlstate,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    
           nhstepm = nhstepm/hstepm;    fprintf(ficreseij,"# Local time at start: %s", strstart);
              fprintf(ficreseij,"# Health expectancies\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficreseij,"# Age");
           oldm=oldms;savm=savms;    for(i=1; i<=nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(j=1; j<=nlstate;j++)
           for (h=0; h<=nhstepm; h++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficreseij,"\n");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    if(estepm < stepm){
             for(j=1; j<=nlstate+ndeath;j++) {      printf ("Problem %d lower than %d\n",estepm, stepm);
               kk1=0.;kk2=0;    }
               for(i=1; i<=nlstate;i++) {                  else  hstepm=estepm;   
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        /* We compute the life expectancy from trapezoids spaced every estepm months
               }     * This is mainly to measure the difference between two models: for example
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);     * 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
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * 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 
    }     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* 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. 
   if (popforecast==1) {       nhstepm is the number of hstepm from age to agelim 
     free_ivector(popage,0,AGESUP);       nstepm is the number of stepm from age to agelin. 
     free_vector(popeffectif,0,AGESUP);       Look at hpijx to understand the reason of that which relies in memory size
     free_vector(popcount,0,AGESUP);       and note for a fixed period like estepm months */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       survival function given by stepm (the optimization length). Unfortunately it
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       means that if the survival funtion is printed only each two years of age and if
   fclose(ficrespop);       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 */ 
 /**************** Main Program *****************/  
 /***********************************************/    agelim=AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 int main(int argc, char *argv[])      /* nhstepm age range expressed in number of stepm */
 {      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      /* if (stepm >= YEARM) hstepm=1;*/
   double agedeb, agefin,hf;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   double fret;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   double **xi,tmp,delta;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   double dum; /* Dummy variable */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   double ***p3mat;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   int *indx;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   char line[MAXLINE], linepar[MAXLINE];   
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
        /* Computing  Variances of health expectancies */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];  
        for(theta=1; theta <=npar; theta++){
   char filerest[FILENAMELENGTH];        for(i=1; i<=npar; i++){ 
   char fileregp[FILENAMELENGTH];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char popfile[FILENAMELENGTH];        }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int firstobs=1, lastobs=10;    
   int sdeb, sfin; /* Status at beginning and end */        cptj=0;
   int c,  h , cpt,l;        for(j=1; j<= nlstate; j++){
   int ju,jl, mi;          for(i=1; i<=nlstate; i++){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            cptj=cptj+1;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   int mobilav=0,popforecast=0;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   int hstepm, nhstepm;            }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;          }
         }
   double bage, fage, age, agelim, agebase;       
   double ftolpl=FTOL;       
   double **prlim;        for(i=1; i<=npar; i++) 
   double *severity;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double ***param; /* Matrix of parameters */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double  *p;        
   double **matcov; /* Matrix of covariance */        cptj=0;
   double ***delti3; /* Scale */        for(j=1; j<= nlstate; j++){
   double *delti; /* Scale */          for(i=1;i<=nlstate;i++){
   double ***eij, ***vareij;            cptj=cptj+1;
   double **varpl; /* Variances of prevalence limits by age */            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   double *epj, vepp;  
   double kk1, kk2;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            }
            }
         }
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";        for(j=1; j<= nlstate*nlstate; j++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   char z[1]="c", occ;       } 
 #include <sys/time.h>     
 #include <time.h>  /* End theta */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
         trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   /* long total_usecs;  
   struct timeval start_time, end_time;       for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
        
   printf("\n%s",version);  
   if(argc <=1){       for(i=1;i<=nlstate*nlstate;i++)
     printf("\nEnter the parameter file name: ");        for(j=1;j<=nlstate*nlstate;j++)
     scanf("%s",pathtot);          varhe[i][j][(int)age] =0.;
   }  
   else{       printf("%d|",(int)age);fflush(stdout);
     strcpy(pathtot,argv[1]);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   }       for(h=0;h<=nhstepm-1;h++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        for(k=0;k<=nhstepm-1;k++){
   /*cygwin_split_path(pathtot,path,optionfile);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   /* cutv(path,optionfile,pathtot,'\\');*/          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1;j<=nlstate*nlstate;j++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        }
   chdir(path);      }
   replace(pathc,path);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
 /*-------- arguments in the command line --------*/        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   strcpy(fileres,"r");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   strcat(fileres, optionfilefiname);            
   strcat(fileres,".txt");    /* Other files have txt extension */  /* 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]);*/
   
   /*---------arguments file --------*/          }
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      fprintf(ficreseij,"%3.0f",age );
     printf("Problem with optionfile %s\n",optionfile);      cptj=0;
     goto end;      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
           cptj++;
   strcpy(filereso,"o");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   strcat(filereso,fileres);        }
   if((ficparo=fopen(filereso,"w"))==NULL) {      fprintf(ficreseij,"\n");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;     
   }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   /* Reads comments: lines beginning with '#' */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     ungetc(c,ficpar);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    printf("\n");
     fputs(line,ficparo);    fprintf(ficlog,"\n");
   }  
   ungetc(c,ficpar);    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);  }
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /************ Variance ******************/
     fgets(line, MAXLINE, ficpar);  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[])
     puts(line);  {
     fputs(line,ficparo);    /* Variance of health expectancies */
   }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   ungetc(c,ficpar);    /* double **newm;*/
      double **dnewm,**doldm;
        double **dnewmp,**doldmp;
   covar=matrix(0,NCOVMAX,1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
   cptcovn=0;    int k, cptcode;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    double *xp;
     double **gp, **gm;  /* for var eij */
   ncovmodel=2+cptcovn;    double ***gradg, ***trgradg; /*for var eij */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double **gradgp, **trgradgp; /* for var p point j */
      double *gpp, *gmp; /* for var p point j */
   /* Read guess parameters */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   /* Reads comments: lines beginning with '#' */    double ***p3mat;
   while((c=getc(ficpar))=='#' && c!= EOF){    double age,agelim, hf;
     ungetc(c,ficpar);    double ***mobaverage;
     fgets(line, MAXLINE, ficpar);    int theta;
     puts(line);    char digit[4];
     fputs(line,ficparo);    char digitp[25];
   }  
   ungetc(c,ficpar);    char fileresprobmorprev[FILENAMELENGTH];
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    if(popbased==1){
     for(i=1; i <=nlstate; i++)      if(mobilav!=0)
     for(j=1; j <=nlstate+ndeath-1; j++){        strcpy(digitp,"-populbased-mobilav-");
       fscanf(ficpar,"%1d%1d",&i1,&j1);      else strcpy(digitp,"-populbased-nomobil-");
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       printf("%1d%1d",i,j);    else 
       for(k=1; k<=ncovmodel;k++){      strcpy(digitp,"-stablbased-");
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);    if (mobilav!=0) {
         fprintf(ficparo," %lf",param[i][j][k]);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fscanf(ficpar,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       printf("\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficparo,"\n");      }
     }    }
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   p=param[1][1];    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
   /* Reads comments: lines beginning with '#' */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   while((c=getc(ficpar))=='#' && c!= EOF){    strcat(fileresprobmorprev,fileres);
     ungetc(c,ficpar);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     puts(line);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     fputs(line,ficparo);    }
   }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   ungetc(c,ficpar);   
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    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);
   for(i=1; i <=nlstate; i++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=1; j <=nlstate+ndeath-1; j++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficresprobmorprev," p.%-d SE",j);
       printf("%1d%1d",i,j);      for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       for(k=1; k<=ncovmodel;k++){    }  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    fprintf(ficresprobmorprev,"\n");
         printf(" %le",delti3[i][j][k]);    fprintf(ficgp,"\n# Routine varevsij");
         fprintf(ficparo," %le",delti3[i][j][k]);    /* 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");
       fscanf(ficpar,"\n");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       printf("\n");  /*   } */
       fprintf(ficparo,"\n");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }   fprintf(ficresvij, "#Local time at start: %s", strstart);
   }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   delti=delti3[1][1];    fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */      for(j=1; j<=nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     ungetc(c,ficpar);    fprintf(ficresvij,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    xp=vector(1,npar);
     fputs(line,ficparo);    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
   ungetc(c,ficpar);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     fscanf(ficpar,"%s",&str);    gpp=vector(nlstate+1,nlstate+ndeath);
     printf("%s",str);    gmp=vector(nlstate+1,nlstate+ndeath);
     fprintf(ficparo,"%s",str);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for(j=1; j <=i; j++){    
       fscanf(ficpar," %le",&matcov[i][j]);    if(estepm < stepm){
       printf(" %.5le",matcov[i][j]);      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficparo," %.5le",matcov[i][j]);    }
     }    else  hstepm=estepm;   
     fscanf(ficpar,"\n");    /* For example we decided to compute the life expectancy with the smallest unit */
     printf("\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fprintf(ficparo,"\n");       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   for(i=1; i <=npar; i++)       Look at hpijx to understand the reason of that which relies in memory size
     for(j=i+1;j<=npar;j++)       and note for a fixed period like k years */
       matcov[i][j]=matcov[j][i];    /* 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
   printf("\n");       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     /*-------- data file ----------*/    */
     if((ficres =fopen(fileres,"w"))==NULL) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       printf("Problem with resultfile: %s\n", fileres);goto end;    agelim = AGESUP;
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fprintf(ficres,"#%s\n",version);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     if((fic=fopen(datafile,"r"))==NULL)    {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("Problem with datafile: %s\n", datafile);goto end;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     }      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
     n= lastobs;  
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);      for(theta=1; theta <=npar; theta++){
     num=ivector(1,n);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     moisnais=vector(1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     annais=vector(1,n);        }
     moisdc=vector(1,n);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     andc=vector(1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     agedc=vector(1,n);  
     cod=ivector(1,n);        if (popbased==1) {
     weight=vector(1,n);          if(mobilav ==0){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            for(i=1; i<=nlstate;i++)
     mint=matrix(1,maxwav,1,n);              prlim[i][i]=probs[(int)age][i][ij];
     anint=matrix(1,maxwav,1,n);          }else{ /* mobilav */ 
     s=imatrix(1,maxwav+1,1,n);            for(i=1; i<=nlstate;i++)
     adl=imatrix(1,maxwav+1,1,n);                  prlim[i][i]=mobaverage[(int)age][i][ij];
     tab=ivector(1,NCOVMAX);          }
     ncodemax=ivector(1,8);        }
     
     i=1;        for(j=1; j<= nlstate; j++){
     while (fgets(line, MAXLINE, fic) != NULL)    {          for(h=0; h<=nhstepm; h++){
       if ((i >= firstobs) && (i <=lastobs)) {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                      gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         for (j=maxwav;j>=1;j--){          }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        }
           strcpy(line,stra);        /* This for computing probability of death (h=1 means
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);           computed over hstepm matrices product = hstepm*stepm months) 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);           as a weighted average of prlim.
         }        */
                for(j=nlstate+1;j<=nlstate+ndeath;j++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        /* end probability of death */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (j=ncov;j>=1;j--){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         }   
         num[i]=atol(stra);        if (popbased==1) {
                  if(mobilav ==0){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            for(i=1; i<=nlstate;i++)
           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;}*/              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
         i=i+1;            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=mobaverage[(int)age][i][ij];
     }          }
     /* printf("ii=%d", ij);        }
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   /* for (i=1; i<=imx; i++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     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;        }
     }        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
     for (i=1; i<=imx; i++)           as a weighted average of prlim.
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /* Calculation of the number of parameter from char model*/          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   Tvar=ivector(1,15);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   Tprod=ivector(1,15);        }    
   Tvaraff=ivector(1,15);        /* end probability of death */
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);              for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
   if (strlen(model) >1){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     j=0, j1=0, k1=1, k2=1;          }
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     cptcovn=j+1;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     cptcovprod=j1;        }
      
          } /* End theta */
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       printf("Error. Non available option model=%s ",model);  
       goto end;      for(h=0; h<=nhstepm; h++) /* veij */
     }        for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
     for(i=(j+1); i>=1;i--){            trgradg[h][j][theta]=gradg[h][theta][j];
       cutv(stra,strb,modelsav,'+');  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        for(theta=1; theta <=npar; theta++)
       /*scanf("%d",i);*/          trgradgp[j][theta]=gradgp[theta][j];
       if (strchr(strb,'*')) {    
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           cptcovprod--;      for(i=1;i<=nlstate;i++)
           cutv(strb,stre,strd,'V');        for(j=1;j<=nlstate;j++)
           Tvar[i]=atoi(stre);          vareij[i][j][(int)age] =0.;
           cptcovage++;  
             Tage[cptcovage]=i;      for(h=0;h<=nhstepm;h++){
             /*printf("stre=%s ", stre);*/        for(k=0;k<=nhstepm;k++){
         }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         else if (strcmp(strd,"age")==0) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           cptcovprod--;          for(i=1;i<=nlstate;i++)
           cutv(strb,stre,strc,'V');            for(j=1;j<=nlstate;j++)
           Tvar[i]=atoi(stre);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           cptcovage++;        }
           Tage[cptcovage]=i;      }
         }    
         else {      /* pptj */
           cutv(strb,stre,strc,'V');      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           Tvar[i]=ncov+k1;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           cutv(strb,strc,strd,'V');      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           Tprod[k1]=i;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           Tvard[k1][1]=atoi(strc);          varppt[j][i]=doldmp[j][i];
           Tvard[k1][2]=atoi(stre);      /* end ppptj */
           Tvar[cptcovn+k2]=Tvard[k1][1];      /*  x centered again */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           for (k=1; k<=lastobs;k++)      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   
           k1++;      if (popbased==1) {
           k2=k2+2;        if(mobilav ==0){
         }          for(i=1; i<=nlstate;i++)
       }            prlim[i][i]=probs[(int)age][i][ij];
       else {        }else{ /* mobilav */ 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          for(i=1; i<=nlstate;i++)
        /*  scanf("%d",i);*/            prlim[i][i]=mobaverage[(int)age][i][ij];
       cutv(strd,strc,strb,'V');        }
       Tvar[i]=atoi(strc);      }
       }               
       strcpy(modelsav,stra);        /* This for computing probability of death (h=1 means
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         scanf("%d",i);*/         as a weighted average of prlim.
     }      */
 }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   printf("cptcovprod=%d ", cptcovprod);      }    
   scanf("%d ",i);*/      /* end probability of death */
     fclose(fic);  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     /*  if(mle==1){*/      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     if (weightopt != 1) { /* Maximisation without weights*/        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       for(i=1;i<=n;i++) weight[i]=1.0;        for(i=1; i<=nlstate;i++){
     }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     /*-calculation of age at interview from date of interview and age at death -*/        }
     agev=matrix(1,maxwav,1,imx);      } 
       fprintf(ficresprobmorprev,"\n");
    for (i=1; i<=imx; i++)  
      for(m=2; (m<= maxwav); m++)      fprintf(ficresvij,"%.0f ",age );
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      for(i=1; i<=nlstate;i++)
          anint[m][i]=9999;        for(j=1; j<=nlstate;j++){
          s[m][i]=-1;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
        }        }
          fprintf(ficresvij,"\n");
     for (i=1; i<=imx; i++)  {      free_matrix(gp,0,nhstepm,1,nlstate);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      free_matrix(gm,0,nhstepm,1,nlstate);
       for(m=1; (m<= maxwav); m++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         if(s[m][i] >0){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           if (s[m][i] == nlstate+1) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             if(agedc[i]>0)    } /* End age */
               if(moisdc[i]!=99 && andc[i]!=9999)    free_vector(gpp,nlstate+1,nlstate+ndeath);
               agev[m][i]=agedc[i];    free_vector(gmp,nlstate+1,nlstate+ndeath);
             else {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
               if (andc[i]!=9999){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
               agev[m][i]=-1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
               }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
             }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           else if(s[m][i] !=9){ /* Should no more exist */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
               agev[m][i]=1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
             else if(agev[m][i] <agemin){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
               agemin=agev[m][i];    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);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
             }  */
             else if(agev[m][i] >agemax){  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
               agemax=agev[m][i];    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    free_vector(xp,1,npar);
             /*agev[m][i]=anint[m][i]-annais[i];*/    free_matrix(doldm,1,nlstate,1,nlstate);
             /*   agev[m][i] = age[i]+2*m;*/    free_matrix(dnewm,1,nlstate,1,npar);
           }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           else { /* =9 */    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
             agev[m][i]=1;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             s[m][i]=-1;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           }    fclose(ficresprobmorprev);
         }    fflush(ficgp);
         else /*= 0 Unknown */    fflush(fichtm); 
           agev[m][i]=1;  }  /* end varevsij */
       }  
      /************ Variance of prevlim ******************/
     }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
     for (i=1; i<=imx; i++)  {  {
       for(m=1; (m<= maxwav); m++){    /* Variance of prevalence limit */
         if (s[m][i] > (nlstate+ndeath)) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           printf("Error: Wrong value in nlstate or ndeath\n");      double **newm;
           goto end;    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
       }    int k, cptcode;
     }    double *xp;
     double *gp, *gm;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double **gradg, **trgradg;
     double age,agelim;
     free_vector(severity,1,maxwav);    int theta;
     free_imatrix(outcome,1,maxwav+1,1,n);    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     free_vector(moisnais,1,n);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     free_vector(annais,1,n);    fprintf(ficresvpl,"# Age");
     /* free_matrix(mint,1,maxwav,1,n);    for(i=1; i<=nlstate;i++)
        free_matrix(anint,1,maxwav,1,n);*/        fprintf(ficresvpl," %1d-%1d",i,i);
     free_vector(moisdc,1,n);    fprintf(ficresvpl,"\n");
     free_vector(andc,1,n);  
     xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
     wav=ivector(1,imx);    doldm=matrix(1,nlstate,1,nlstate);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    hstepm=1*YEARM; /* Every year of age */
        hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     /* Concatenates waves */    agelim = AGESUP;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       Tcode=ivector(1,100);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      gradg=matrix(1,npar,1,nlstate);
       ncodemax[1]=1;      gp=vector(1,nlstate);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      gm=vector(1,nlstate);
        
    codtab=imatrix(1,100,1,10);      for(theta=1; theta <=npar; theta++){
    h=0;        for(i=1; i<=npar; i++){ /* Computes gradient */
    m=pow(2,cptcoveff);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
    for(k=1;k<=cptcoveff; k++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      for(i=1; i <=(m/pow(2,k));i++){        for(i=1;i<=nlstate;i++)
        for(j=1; j <= ncodemax[k]; j++){          gp[i] = prlim[i][i];
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      
            h++;        for(i=1; i<=npar; i++) /* Computes gradient */
            if (h>m) h=1;codtab[h][k]=j;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        }        for(i=1;i<=nlstate;i++)
      }          gm[i] = prlim[i][i];
    }  
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
    /*for(i=1; i <=m ;i++){      } /* End theta */
      for(k=1; k <=cptcovn; k++){  
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);      trgradg =matrix(1,nlstate,1,npar);
      }  
      printf("\n");      for(j=1; j<=nlstate;j++)
    }        for(theta=1; theta <=npar; theta++)
    scanf("%d",i);*/          trgradg[j][theta]=gradg[theta][j];
      
    /* Calculates basic frequencies. Computes observed prevalence at single age      for(i=1;i<=nlstate;i++)
        and prints on file fileres'p'. */        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
          for(i=1;i<=nlstate;i++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficresvpl,"%.0f ",age );
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
            fprintf(ficresvpl,"\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]      free_vector(gp,1,nlstate);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      free_vector(gm,1,nlstate);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     if(mle==1){    } /* End age */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,npar);
     /*--------- results files --------------*/    free_matrix(dnewm,1,nlstate,1,nlstate);
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  
    }
   
    jk=1;  /************ Variance of one-step probabilities  ******************/
    fprintf(ficres,"# Parameters\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[])
    printf("# Parameters\n");  {
    for(i=1,jk=1; i <=nlstate; i++){    int i, j=0,  i1, k1, l1, t, tj;
      for(k=1; k <=(nlstate+ndeath); k++){    int k2, l2, j1,  z1;
        if (k != i)    int k=0,l, cptcode;
          {    int first=1, first1;
            printf("%d%d ",i,k);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
            fprintf(ficres,"%1d%1d ",i,k);    double **dnewm,**doldm;
            for(j=1; j <=ncovmodel; j++){    double *xp;
              printf("%f ",p[jk]);    double *gp, *gm;
              fprintf(ficres,"%f ",p[jk]);    double **gradg, **trgradg;
              jk++;    double **mu;
            }    double age,agelim, cov[NCOVMAX];
            printf("\n");    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
            fprintf(ficres,"\n");    int theta;
          }    char fileresprob[FILENAMELENGTH];
      }    char fileresprobcov[FILENAMELENGTH];
    }    char fileresprobcor[FILENAMELENGTH];
  if(mle==1){  
     /* Computing hessian and covariance matrix */    double ***varpij;
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);    strcpy(fileresprob,"prob"); 
  }    strcat(fileresprob,fileres);
     fprintf(ficres,"# Scales\n");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     printf("# Scales\n");      printf("Problem with resultfile: %s\n", fileresprob);
      for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       for(j=1; j <=nlstate+ndeath; j++){    }
         if (j!=i) {    strcpy(fileresprobcov,"probcov"); 
           fprintf(ficres,"%1d%1d",i,j);    strcat(fileresprobcov,fileres);
           printf("%1d%1d",i,j);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
           for(k=1; k<=ncovmodel;k++){      printf("Problem with resultfile: %s\n", fileresprobcov);
             printf(" %.5e",delti[jk]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
             fprintf(ficres," %.5e",delti[jk]);    }
             jk++;    strcpy(fileresprobcor,"probcor"); 
           }    strcat(fileresprobcor,fileres);
           printf("\n");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           fprintf(ficres,"\n");      printf("Problem with resultfile: %s\n", fileresprobcor);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       }    }
      }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     k=1;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficres,"# Covariance\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("# Covariance\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     for(i=1;i<=npar;i++){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       /*  if (k>nlstate) k=1;    fprintf(ficresprob, "#Local time at start: %s", strstart);
       i1=(i-1)/(ncovmodel*nlstate)+1;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    fprintf(ficresprob,"# Age");
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
       fprintf(ficres,"%3d",i);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       printf("%3d",i);    fprintf(ficresprobcov,"# Age");
       for(j=1; j<=i;j++){    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
         fprintf(ficres," %.5e",matcov[i][j]);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
         printf(" %.5e",matcov[i][j]);    fprintf(ficresprobcov,"# Age");
       }  
       fprintf(ficres,"\n");  
       printf("\n");    for(i=1; i<=nlstate;i++)
       k++;      for(j=1; j<=(nlstate+ndeath);j++){
     }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
            fprintf(ficresprobcov," p%1d-%1d ",i,j);
     while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       ungetc(c,ficpar);      }  
       fgets(line, MAXLINE, ficpar);   /* fprintf(ficresprob,"\n");
       puts(line);    fprintf(ficresprobcov,"\n");
       fputs(line,ficparo);    fprintf(ficresprobcor,"\n");
     }   */
     ungetc(c,ficpar);   xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
        mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     if (fage <= 2) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       bage = agemin;    first=1;
       fage = agemaxpar;    fprintf(ficgp,"\n# Routine varprob");
     }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
     fprintf(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\n",agemin,agemaxpar,bage,fage);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
      file %s<br>\n",optionfilehtmcov);
     while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     ungetc(c,ficpar);  and drawn. It helps understanding how is the covariance between two incidences.\
     fgets(line, MAXLINE, ficpar);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     puts(line);    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. \
     fputs(line,ficparo);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   ungetc(c,ficpar);  standard deviations wide on each axis. <br>\
     Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
          cov[1]=1;
   while((c=getc(ficpar))=='#' && c!= EOF){    tj=cptcoveff;
     ungetc(c,ficpar);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     fgets(line, MAXLINE, ficpar);    j1=0;
     puts(line);    for(t=1; t<=tj;t++){
     fputs(line,ficparo);      for(i1=1; i1<=ncodemax[t];i1++){ 
   }        j1++;
   ungetc(c,ficpar);        if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          fprintf(ficresprob, "**********\n#\n");
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fscanf(ficpar,"pop_based=%d\n",&popbased);          fprintf(ficresprobcov, "**********\n#\n");
   fprintf(ficparo,"pop_based=%d\n",popbased);            
   fprintf(ficres,"pop_based=%d\n",popbased);            fprintf(ficgp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp, "**********\n#\n");
     ungetc(c,ficpar);          
     fgets(line, MAXLINE, ficpar);          
     puts(line);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     fputs(line,ficparo);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   ungetc(c,ficpar);          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   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);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficresprobcor, "**********\n#");    
 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 (age=bage; age<=fage; age ++){ 
 while((c=getc(ficpar))=='#' && c!= EOF){          cov[2]=age;
     ungetc(c,ficpar);          for (k=1; k<=cptcovn;k++) {
     fgets(line, MAXLINE, ficpar);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     puts(line);          }
     fputs(line,ficparo);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }          for (k=1; k<=cptcovprod;k++)
   ungetc(c,ficpar);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      
           for(theta=1; theta <=npar; theta++){
 /*------------ gnuplot -------------*/            for(i=1; i<=npar; i++)
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
              
 /*------------ free_vector  -------------*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
  chdir(path);            
              k=0;
  free_ivector(wav,1,imx);            for(i=1; i<= (nlstate); i++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              for(j=1; j<=(nlstate+ndeath);j++){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                  k=k+1;
  free_ivector(num,1,n);                gp[k]=pmmij[i][j];
  free_vector(agedc,1,n);              }
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            }
  fclose(ficparo);            
  fclose(ficres);            for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
 /*--------- index.htm --------*/      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);            k=0;
             for(i=1; i<=(nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
   /*--------------- Prevalence limit --------------*/                k=k+1;
                  gm[k]=pmmij[i][j];
   strcpy(filerespl,"pl");              }
   strcat(filerespl,fileres);            }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          }
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            for(theta=1; theta <=npar; theta++)
   fprintf(ficrespl,"\n");              trgradg[j][theta]=gradg[theta][j];
            
   prlim=matrix(1,nlstate,1,nlstate);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   k=0;  
   agebase=agemin;          pmij(pmmij,cov,ncovmodel,x,nlstate);
   agelim=agemaxpar;          
   ftolpl=1.e-10;          k=0;
   i1=cptcoveff;          for(i=1; i<=(nlstate); i++){
   if (cptcovn < 1){i1=1;}            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
   for(cptcov=1;cptcov<=i1;cptcov++){              mu[k][(int) age]=pmmij[i][j];
     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]);*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         fprintf(ficrespl,"\n#******");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         for(j=1;j<=cptcoveff;j++)              varpij[i][j][(int)age] = doldm[i][j];
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");          /*printf("\n%d ",(int)age);
                    for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         for (age=agebase; age<=agelim; age++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           fprintf(ficrespl,"%.0f",age );            }*/
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficrespl,"\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
         }          fprintf(ficresprobcor,"\n%d ",(int)age);
       }  
     }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   fclose(ficrespl);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   /*------------- h Pij x at various ages ------------*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
              fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          i=0;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          for (k=1; k<=(nlstate);k++){
   }            for (l=1; l<=(nlstate+ndeath);l++){ 
   printf("Computing pij: result on file '%s' \n", filerespij);              i=i++;
                fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   stepsize=(int) (stepm+YEARM-1)/YEARM;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   /*if (stepm<=24) stepsize=2;*/              for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   agelim=AGESUP;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   hstepm=stepsize*YEARM; /* Every year of age */              }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            }
            }/* end of loop for state */
   k=0;        } /* end of loop for age */
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        /* Confidence intervalle of pij  */
       k=k+1;        /*
         fprintf(ficrespij,"\n#****** ");          fprintf(ficgp,"\nset noparametric;unset label");
         for(j=1;j<=cptcoveff;j++)          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(ficrespij,"******\n");          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
                  fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          first1=1;
           fprintf(ficrespij,"# Age");        for (k2=1; k2<=(nlstate);k2++){
           for(i=1; i<=nlstate;i++)          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             for(j=1; j<=nlstate+ndeath;j++)            if(l2==k2) continue;
               fprintf(ficrespij," %1d-%1d",i,j);            j=(k2-1)*(nlstate+ndeath)+l2;
           fprintf(ficrespij,"\n");            for (k1=1; k1<=(nlstate);k1++){
           for (h=0; h<=nhstepm; h++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                if(l1==k1) continue;
             for(i=1; i<=nlstate;i++)                i=(k1-1)*(nlstate+ndeath)+l1;
               for(j=1; j<=nlstate+ndeath;j++)                if(i<=j) continue;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                for (age=bage; age<=fage; age ++){ 
             fprintf(ficrespij,"\n");                  if ((int)age %5==0){
           }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           fprintf(ficrespij,"\n");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    mu1=mu[i][(int) age]/stepm*YEARM ;
     }                    mu2=mu[j][(int) age]/stepm*YEARM;
   }                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/                    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.;
   fclose(ficrespij);                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
   /*---------- Forecasting ------------------*/                    v21=(lc1-v1)/cv12*v11;
   if(stepm == 1) {                    v12=-v21;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                    v22=v11;
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                    tnalp=v21/v11;
     free_matrix(mint,1,maxwav,1,n);                    if(first1==1){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                      first1=0;
     free_vector(weight,1,n);}                      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);
   else{                    }
     erreur=108;                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);                    /*printf(fignu*/
   }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                      /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
   /*---------- Health expectancies and variances ------------*/                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
   strcpy(filerest,"t");                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
   strcat(filerest,fileres);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if((ficrest=fopen(filerest,"w"))==NULL) {                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   }  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   strcpy(filerese,"e");                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   strcat(filerese,fileres);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   if((ficreseij=fopen(filerese,"w"))==NULL) {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   }                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
  strcpy(fileresv,"v");                    }else{
   strcat(fileresv,fileres);                      first=0;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
     printf("Problem with variance resultfile: %s\n", fileresv);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);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                      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),\
   k=0;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   for(cptcov=1;cptcov<=i1;cptcov++){                    }/* if first */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  } /* age mod 5 */
       k=k+1;                } /* end loop age */
       fprintf(ficrest,"\n#****** ");                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       for(j=1;j<=cptcoveff;j++)                first=1;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              } /*l12 */
       fprintf(ficrest,"******\n");            } /* k12 */
           } /*l1 */
       fprintf(ficreseij,"\n#****** ");        }/* k1 */
       for(j=1;j<=cptcoveff;j++)      } /* loop covariates */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }
       fprintf(ficreseij,"******\n");    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       fprintf(ficresvij,"\n#****** ");    free_vector(xp,1,npar);
       for(j=1;j<=cptcoveff;j++)    fclose(ficresprob);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fclose(ficresprobcov);
       fprintf(ficresvij,"******\n");    fclose(ficresprobcor);
     fflush(ficgp);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fflush(fichtmcov);
       oldm=oldms;savm=savms;  }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  /******************* Printing html file ***********/
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  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 ,\
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                    double jprev1, double mprev1,double anprev1, \
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                    double jprev2, double mprev2,double anprev2){
       fprintf(ficrest,"\n");    int jj1, k1, i1, cpt;
   
       hf=1;     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
       if (stepm >= YEARM) hf=stepm/YEARM;     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
       epj=vector(1,nlstate+1);  </ul>");
       for(age=bage; age <=fage ;age++){     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
         if (popbased==1) {             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
           for(i=1; i<=nlstate;i++)     fprintf(fichtm,"\
             prlim[i][i]=probs[(int)age][i][k];   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
         }             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
             fprintf(fichtm,"\
         fprintf(ficrest," %.0f",age);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
           for(i=1, epj[j]=0.;i <=nlstate;i++) {     fprintf(fichtm,"\
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];   - Life expectancies by age and initial health status (estepm=%2d months): \
           }     <a href=\"%s\">%s</a> <br>\n</li>",
           epj[nlstate+1] +=epj[j];             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];   m=cptcoveff;
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));   jj1=0;
         }   for(k1=1; k1<=m;k1++){
         fprintf(ficrest,"\n");     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++) 
   fclose(ficreseij);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   fclose(ficresvij);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   fclose(ficrest);       }
   fclose(ficpar);       /* Pij */
   free_vector(epj,1,nlstate+1);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
    <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   /*------- Variance limit prevalence------*/         /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   strcpy(fileresvpl,"vpl");   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   strcat(fileresvpl,fileres);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {         /* Stable prevalence in each health state */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);         for(cpt=1; cpt<nlstate;cpt++){
     exit(0);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   }  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);         }
        for(cpt=1; cpt<=nlstate;cpt++) {
   k=0;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   for(cptcov=1;cptcov<=i1;cptcov++){  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       }
       k=k+1;     } /* end i1 */
       fprintf(ficresvpl,"\n#****** ");   }/* End k1 */
       for(j=1;j<=cptcoveff;j++)   fprintf(fichtm,"</ul>");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");  
         fprintf(fichtm,"\
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
       oldm=oldms;savm=savms;   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
     }   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
   fclose(ficresvpl);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   fprintf(fichtm,"\
     - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   fprintf(fichtm,"\
     - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
             estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);   fprintf(fichtm,"\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   fprintf(fichtm,"\
     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   free_matrix(matcov,1,npar,1,npar);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  /*  - 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 */
   if(erreur >0)  /*      <br>",fileres,fileres,fileres,fileres); */
     printf("End of Imach with error %d\n",erreur);  /*  else  */
   else   printf("End of Imach\n");  /*    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); */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */   fflush(fichtm);
     fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   /* 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);*/   m=cptcoveff;
   /*------ End -----------*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
  end:   for(k1=1; k1<=m;k1++){
 #ifdef windows     for(i1=1; i1<=ncodemax[k1];i1++){
   /* chdir(pathcd);*/       jj1++;
 #endif       if (cptcovn > 0) {
  /*system("wgnuplot graph.plt");*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
  /*system("../gp37mgw/wgnuplot graph.plt");*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
  /*system("cd ../gp37mgw");*/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
  strcpy(plotcmd,GNUPLOTPROGRAM);       }
  strcat(plotcmd," ");       for(cpt=1; cpt<=nlstate;cpt++) {
  strcat(plotcmd,optionfilegnuplot);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
  system(plotcmd);  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);  
 #ifdef windows       }
   while (z[0] != 'q') {       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     chdir(path);  health expectancies in states (1) and (2): %s%d.png<br>\
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     scanf("%s",z);     } /* end i1 */
     if (z[0] == 'c') system("./imach");   }/* End k1 */
     else if (z[0] == 'e') {   fprintf(fichtm,"</ul>");
       chdir(path);   fflush(fichtm);
       system(optionfilehtm);  }
     }  
     else if (z[0] == 'q') exit(0);  /******************* Gnuplot file **************/
   }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
 #endif  
 }    char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) ||((i >= firstobs) && (i <=lastobs)))    {
       linei=linei+1;
       printf("IIIII= %d linei=%d\n",i,linei);
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10);j--){;};line[j+1]=0;  /* Trims blanks at end of line */
         if(line[0]=='#'){
           fprintf(ficlog,"Comment line\n%s\n",line);
           printf("Comment line\n%s\n",line);
           continue;
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %d %s for individual %d\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n",lval, i,line,linei,j,maxwav);
             exit(1);
           }
           s[j][i]=lval;
   
           strcpy(line,stra);
           cutv(stra, strb,line,'/');
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",lval, i,line,linei,j);
             exit(1);
           }
           anint[j][i]=(double)(lval); 
   
           strcpy(line,stra);
           cutv(stra, strb,line,' ');
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of exam at wave %d.  Exiting.\n",lval, i,line, linei,j);
             exit(1);
           }
           mint[j][i]=(double)(lval); 
           strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of death.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         andc[i]=(double)(lval); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of death.  Exiting.\n",lval,i,line, linei);
           exit(1);
         }
         moisdc[i]=(double)(lval); 
   
         strcpy(line,stra);
         cutv(stra, strb,line,'/'); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of birth.  Exiting.\n",lval, i,line, linei);
           exit(1);
         }
         annais[i]=(double)(lval);
   
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of birth.  Exiting.\n",lval,i,line,linei);
           exit(1);
         }
         moisnais[i]=(double)(lval); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         weight[i]=(double)(lval); 
         strcpy(line,stra);
   
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, i,line,linei);
             exit(1);
           }
           if(lval <0 || lval >1){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,i,line,linei,j);
             exit(1);
           }
           covar[j][i]=(double)(lval);
           strcpy(line,stra);
         } 
         lstra=strlen(stra);
   
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
         printf ("num [i] %ld %d\n",i, num[i]);fflush(stdout);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
     } /* End loop reading  data */
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
      
        for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
      
         for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
    tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
          }
      
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
   #ifndef UNIX
     /*  strcpy(plotcmd,"\""); */
   #endif
     strcpy(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     /*  strcat(plotcmd,"\"");*/
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
   
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     strcat(plotcmd,"\"");
   #endif
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.28  
changed lines
  Added in v.1.109


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