Diff for /imach/src/imach.c between versions 1.19 and 1.114

version 1.19, 2002/02/20 17:19:10 version 1.114, 2006/02/26 12:57:58
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.114  2006/02/26 12:57:58  brouard
   individuals from different ages are interviewed on their health status    (Module): Some improvements in processing parameter
   or degree of  disability. At least a second wave of interviews    filename with strsep.
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.113  2006/02/24 14:20:24  brouard
   waves and are computed for each degree of severity of disability (number    (Module): Memory leaks checks with valgrind and:
   of life states). More degrees you consider, more time is necessary to    datafile was not closed, some imatrix were not freed and on matrix
   reach the Maximum Likelihood of the parameters involved in the model.    allocation too.
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.112  2006/01/30 09:55:26  brouard
   to be observed in state i at the first wave. Therefore the model is:    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   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 complex model than "constant and    Revision 1.111  2006/01/25 20:38:18  brouard
   age", you should modify the program where the markup    (Module): Lots of cleaning and bugs added (Gompertz)
     *Covariates have to be included here again* invites you to do it.    (Module): Comments can be added in data file. Missing date values
   More covariates you add, less is the speed of the convergence.    can be a simple dot '.'.
   
   The advantage that this computer programme claims, comes from that if the    Revision 1.110  2006/01/25 00:51:50  brouard
   delay between waves is not identical for each individual, or if some    (Module): Lots of cleaning and bugs added (Gompertz)
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.109  2006/01/24 19:37:15  brouard
   hPijx is the probability to be    (Module): Comments (lines starting with a #) are allowed in data.
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.108  2006/01/19 18:05:42  lievre
   unobserved intermediate  states. This elementary transition (by month or    Gnuplot problem appeared...
   quarter trimester, semester or year) is model as a multinomial logistic.    To be fixed
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.106  2006/01/19 13:24:36  brouard
      Some cleaning and links added in html output
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.105  2006/01/05 20:23:19  lievre
   This software have been partly granted by Euro-REVES, a concerted action    *** empty log message ***
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.104  2005/09/30 16:11:43  lievre
   software can be distributed freely for non commercial use. Latest version    (Module): sump fixed, loop imx fixed, and simplifications.
   can be accessed at http://euroreves.ined.fr/imach .    (Module): If the status is missing at the last wave but we know
   **********************************************************************/    that the person is alive, then we can code his/her status as -2
      (instead of missing=-1 in earlier versions) and his/her
 #include <math.h>    contributions to the likelihood is 1 - Prob of dying from last
 #include <stdio.h>    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #include <stdlib.h>    the healthy state at last known wave). Version is 0.98
 #include <unistd.h>  
     Revision 1.103  2005/09/30 15:54:49  lievre
 #define MAXLINE 256    (Module): sump fixed, loop imx fixed, and simplifications.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.102  2004/09/15 17:31:30  brouard
 #define windows    Add the possibility to read data file including tab characters.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.99  2004/06/05 08:57:40  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    *** empty log message ***
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.98  2004/05/16 15:05:56  brouard
 #define YEARM 12. /* Number of months per year */    New version 0.97 . First attempt to estimate force of mortality
 #define AGESUP 130    directly from the data i.e. without the need of knowing the health
 #define AGEBASE 40    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 int nvar;    cross-longitudinal survey is different from the mortality estimated
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    from other sources like vital statistic data.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    The same imach parameter file can be used but the option for mle should be -3.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Agnès, who wrote this part of the code, tried to keep most of the
 int popbased=0;    former routines in order to include the new code within the former code.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    The output is very simple: only an estimate of the intercept and of
 int maxwav; /* Maxim number of waves */    the slope with 95% confident intervals.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Current limitations:
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    A) Even if you enter covariates, i.e. with the
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 double jmean; /* Mean space between 2 waves */    B) There is no computation of Life Expectancy nor Life Table.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.97  2004/02/20 13:25:42  lievre
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Version 0.96d. Population forecasting command line is (temporarily)
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    suppressed.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.96  2003/07/15 15:38:55  brouard
  FILE  *ficresvij;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   char fileresv[FILENAMELENGTH];    rewritten within the same printf. Workaround: many printfs.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 #define NR_END 1    (Repository): Using imachwizard code to output a more meaningful covariance
 #define FREE_ARG char*    matrix (cov(a12,c31) instead of numbers.
 #define FTOL 1.0e-10  
     Revision 1.94  2003/06/27 13:00:02  brouard
 #define NRANSI    Just cleaning
 #define ITMAX 200  
     Revision 1.93  2003/06/25 16:33:55  brouard
 #define TOL 2.0e-4    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define CGOLD 0.3819660    (Module): Version 0.96b
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define GOLD 1.618034    exist so I changed back to asctime which exists.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 static double maxarg1,maxarg2;    (Repository): Elapsed time after each iteration is now output. It
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    helps to forecast when convergence will be reached. Elapsed time
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    is stamped in powell.  We created a new html file for the graphs
      concerning matrix of covariance. It has extension -cov.htm.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 static double sqrarg;    mle=-1 a template is output in file "or"mypar.txt with the design
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    of the covariance matrix to be input.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.89  2003/06/24 12:30:52  brouard
 int imx;    (Module): Some bugs corrected for windows. Also, when
 int stepm;    mle=-1 a template is output in file "or"mypar.txt with the design
 /* Stepm, step in month: minimum step interpolation*/    of the covariance matrix to be input.
   
 int m,nb;    Revision 1.88  2003/06/23 17:54:56  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.87  2003/06/18 12:26:01  brouard
 double dateintmean=0;    Version 0.96
   
 double *weight;    Revision 1.86  2003/06/17 20:04:08  brouard
 int **s; /* Status */    (Module): Change position of html and gnuplot routines and added
 double *agedc, **covar, idx;    routine fileappend.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.85  2003/06/17 13:12:43  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    * imach.c (Repository): Check when date of death was earlier that
 double ftolhess; /* Tolerance for computing hessian */    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 /**************** split *************************/    was wrong (infinity). We still send an "Error" but patch by
 static  int split( char *path, char *dirc, char *name )    assuming that the date of death was just one stepm after the
 {    interview.
    char *s;                             /* pointer */    (Repository): Because some people have very long ID (first column)
    int  l1, l2;                         /* length counters */    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
    l1 = strlen( path );                 /* length of path */    truncation)
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Repository): No more line truncation errors.
    s = strrchr( path, '\\' );           /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.84  2003/06/13 21:44:43  brouard
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Repository): Replace "freqsummary" at a correct
       extern char       *getwd( );    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
       if ( getwd( dirc ) == NULL ) {    parcimony.
 #else    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       extern char       *getcwd( );  
     Revision 1.83  2003/06/10 13:39:11  lievre
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    *** empty log message ***
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.82  2003/06/05 15:57:20  brouard
       }    Add log in  imach.c and  fullversion number is now printed.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */  */
       s++;                              /* after this, the filename */  /*
       l2 = strlen( s );                 /* length of filename */     Interpolated Markov Chain
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Short summary of the programme:
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    
       dirc[l1-l2] = 0;                  /* add zero */    This program computes Healthy Life Expectancies from
    }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    l1 = strlen( dirc );                 /* length of directory */    first survey ("cross") where individuals from different ages are
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    interviewed on their health status or degree of disability (in the
    return( 0 );                         /* we're done */    case of a health survey which is our main interest) -2- at least a
 }    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 /******************************************/    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 void replace(char *s, char*t)    simplest model is the multinomial logistic model where pij is the
 {    probability to be observed in state j at the second wave
   int i;    conditional to be observed in state i at the first wave. Therefore
   int lg=20;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   i=0;    'age' is age and 'sex' is a covariate. If you want to have a more
   lg=strlen(t);    complex model than "constant and age", you should modify the program
   for(i=0; i<= lg; i++) {    where the markup *Covariates have to be included here again* invites
     (s[i] = t[i]);    you to do it.  More covariates you add, slower the
     if (t[i]== '\\') s[i]='/';    convergence.
   }  
 }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 int nbocc(char *s, char occ)    identical for each individual. Also, if a individual missed an
 {    intermediate interview, the information is lost, but taken into
   int i,j=0;    account using an interpolation or extrapolation.  
   int lg=20;  
   i=0;    hPijx is the probability to be observed in state i at age x+h
   lg=strlen(s);    conditional to the observed state i at age x. The delay 'h' can be
   for(i=0; i<= lg; i++) {    split into an exact number (nh*stepm) of unobserved intermediate
   if  (s[i] == occ ) j++;    states. This elementary transition (by month, quarter,
   }    semester or year) is modelled as a multinomial logistic.  The hPx
   return j;    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Also this programme outputs the covariance matrix of the parameters but also
   int i,lg,j,p=0;    of the life expectancies. It also computes the stable prevalence. 
   i=0;    
   for(j=0; j<=strlen(t)-1; j++) {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;             Institut national d'études démographiques, Paris.
   }    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
   lg=strlen(t);    It is copyrighted identically to a GNU software product, ie programme and
   for(j=0; j<p; j++) {    software can be distributed freely for non commercial use. Latest version
     (u[j] = t[j]);    can be accessed at http://euroreves.ined.fr/imach .
   }  
      u[p]='\0';    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    for(j=0; j<= lg; j++) {    
     if (j>=(p+1))(v[j-p-1] = t[j]);    **********************************************************************/
   }  /*
 }    main
     read parameterfile
 /********************** nrerror ********************/    read datafile
     concatwav
 void nrerror(char error_text[])    freqsummary
 {    if (mle >= 1)
   fprintf(stderr,"ERREUR ...\n");      mlikeli
   fprintf(stderr,"%s\n",error_text);    print results files
   exit(1);    if mle==1 
 }       computes hessian
 /*********************** vector *******************/    read end of parameter file: agemin, agemax, bage, fage, estepm
 double *vector(int nl, int nh)        begin-prev-date,...
 {    open gnuplot file
   double *v;    open html file
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    stable prevalence
   if (!v) nrerror("allocation failure in vector");     for age prevalim()
   return v-nl+NR_END;    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /************************ free vector ******************/    health expectancies
 void free_vector(double*v, int nl, int nh)    Variance-covariance of DFLE
 {    prevalence()
   free((FREE_ARG)(v+nl-NR_END));     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 /************************ivector *******************************/    total life expectancies
 int *ivector(long nl,long nh)    Variance of stable prevalence
 {   end
   int *v;  */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  
 }   
   #include <math.h>
 /******************free ivector **************************/  #include <stdio.h>
 void free_ivector(int *v, long nl, long nh)  #include <stdlib.h>
 {  #include <string.h>
   free((FREE_ARG)(v+nl-NR_END));  #include <unistd.h>
 }  
   #include <limits.h>
 /******************* imatrix *******************************/  #include <sys/types.h>
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #include <sys/stat.h>
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #include <errno.h>
 {  extern int errno;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  /* #include <sys/time.h> */
    #include <time.h>
   /* allocate pointers to rows */  #include "timeval.h"
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /* #include <libintl.h> */
   m += NR_END;  /* #define _(String) gettext (String) */
   m -= nrl;  
    #define MAXLINE 256
    
   /* allocate rows and set pointers to them */  #define GNUPLOTPROGRAM "gnuplot"
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define FILENAMELENGTH 132
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   /* return pointer to array of pointers to rows */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   return m;  
 }  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 /****************** free_imatrix *************************/  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define NCOVMAX 8 /* Maximum number of covariates */
       int **m;  #define MAXN 20000
       long nch,ncl,nrh,nrl;  #define YEARM 12. /* Number of months per year */
      /* free an int matrix allocated by imatrix() */  #define AGESUP 130
 {  #define AGEBASE 40
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   free((FREE_ARG) (m+nrl-NR_END));  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /******************* matrix *******************************/  #define ODIRSEPARATOR '\\'
 double **matrix(long nrl, long nrh, long ncl, long nch)  #else
 {  #define DIRSEPARATOR '\\'
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define CHARSEPARATOR "\\"
   double **m;  #define ODIRSEPARATOR '/'
   #endif
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /* $Id$ */
   m += NR_END;  /* $State$ */
   m -= nrl;  
   char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fullversion[]="$Revision$ $Date$"; 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   m[nrl] += NR_END;  int nvar;
   m[nrl] -= ncl;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int nlstate=2; /* Number of live states */
   return m;  int ndeath=1; /* Number of dead states */
 }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int *wav; /* Number of waves for this individuual 0 is possible */
 {  int maxwav; /* Maxim number of waves */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int jmin, jmax; /* min, max spacing between 2 waves */
   free((FREE_ARG)(m+nrl-NR_END));  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 }  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 /******************* ma3x *******************************/  int mle, weightopt;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  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 */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double ***m;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double **oldm, **newm, **savm; /* Working pointers to matrices */
   if (!m) nrerror("allocation failure 1 in matrix()");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m += NR_END;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m -= nrl;  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double fretone; /* Only one call to likelihood */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  long ipmx; /* Number of contributions */
   m[nrl] += NR_END;  double sw; /* Sum of weights */
   m[nrl] -= ncl;  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  FILE *ficresprobmorprev;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  FILE *fichtm, *fichtmcov; /* Html File */
   m[nrl][ncl] += NR_END;  FILE *ficreseij;
   m[nrl][ncl] -= nll;  char filerese[FILENAMELENGTH];
   for (j=ncl+1; j<=nch; j++)  FILE  *ficresvij;
     m[nrl][j]=m[nrl][j-1]+nlay;  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
   for (i=nrl+1; i<=nrh; i++) {  char fileresvpl[FILENAMELENGTH];
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char title[MAXLINE];
     for (j=ncl+1; j<=nch; j++)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       m[i][j]=m[i][j-1]+nlay;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   return m;  char command[FILENAMELENGTH];
 }  int  outcmd=0;
   
 /*************************free ma3x ************************/  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  char filelog[FILENAMELENGTH]; /* Log file */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char filerest[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /***************** f1dim *************************/  
 extern int ncom;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 extern double *pcom,*xicom;  struct timezone tzp;
 extern double (*nrfunc)(double []);  extern int gettimeofday();
    struct tm tmg, tm, tmf, *gmtime(), *localtime();
 double f1dim(double x)  long time_value;
 {  extern long time();
   int j;  char strcurr[80], strfor[80];
   double f;  
   double *xt;  char *endptr;
    long lval;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define NR_END 1
   f=(*nrfunc)(xt);  #define FREE_ARG char*
   free_vector(xt,1,ncom);  #define FTOL 1.0e-10
   return f;  
 }  #define NRANSI 
   #define ITMAX 200 
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define TOL 2.0e-4 
 {  
   int iter;  #define CGOLD 0.3819660 
   double a,b,d,etemp;  #define ZEPS 1.0e-10 
   double fu,fv,fw,fx;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define GOLD 1.618034 
   double e=0.0;  #define GLIMIT 100.0 
    #define TINY 1.0e-20 
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  static double maxarg1,maxarg2;
   x=w=v=bx;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   fw=fv=fx=(*f)(x);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for (iter=1;iter<=ITMAX;iter++) {    
     xm=0.5*(a+b);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define rint(a) floor(a+0.5)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  static double sqrarg;
 #ifdef DEBUG  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  int agegomp= AGEGOMP;
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int imx; 
       *xmin=x;  int stepm=1;
       return fx;  /* Stepm, step in month: minimum step interpolation*/
     }  
     ftemp=fu;  int estepm;
     if (fabs(e) > tol1) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  int m,nb;
       p=(x-v)*q-(x-w)*r;  long *num;
       q=2.0*(q-r);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       if (q > 0.0) p = -p;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       q=fabs(q);  double **pmmij, ***probs;
       etemp=e;  double *ageexmed,*agecens;
       e=d;  double dateintmean=0;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  double *weight;
       else {  int **s; /* Status */
         d=p/q;  double *agedc, **covar, idx;
         u=x+d;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
         if (u-a < tol2 || b-u < tol2)  double *lsurv, *lpop, *tpop;
           d=SIGN(tol1,xm-x);  
       }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     } else {  double ftolhess; /* Tolerance for computing hessian */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  /**************** split *************************/
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     fu=(*f)(u);  {
     if (fu <= fx) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       if (u >= x) a=x; else b=x;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       SHFT(v,w,x,u)    */ 
         SHFT(fv,fw,fx,fu)    char  *ss;                            /* pointer */
         } else {    int   l1, l2;                         /* length counters */
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {    l1 = strlen(path );                   /* length of path */
             v=w;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
             w=u;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
             fv=fw;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
             fw=fu;      strcpy( name, path );               /* we got the fullname name because no directory */
           } else if (fu <= fv || v == x || v == w) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
             v=u;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
             fv=fu;      /* get current working directory */
           }      /*    extern  char* getcwd ( char *buf , int len);*/
         }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   }        return( GLOCK_ERROR_GETCWD );
   nrerror("Too many iterations in brent");      }
   *xmin=x;      /* got dirc from getcwd*/
   return fx;      printf(" DIRC = %s \n",dirc);
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /****************** mnbrak ***********************/      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      strcpy( name, ss );         /* save file name */
             double (*func)(double))      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   double ulim,u,r,q, dum;      printf(" DIRC2 = %s \n",dirc);
   double fu;    }
      /* We add a separator at the end of dirc if not exists */
   *fa=(*func)(*ax);    l1 = strlen( dirc );                  /* length of directory */
   *fb=(*func)(*bx);    if( dirc[l1-1] != DIRSEPARATOR ){
   if (*fb > *fa) {      dirc[l1] =  DIRSEPARATOR;
     SHFT(dum,*ax,*bx,dum)      dirc[l1+1] = 0; 
       SHFT(dum,*fb,*fa,dum)      printf(" DIRC3 = %s \n",dirc);
       }    }
   *cx=(*bx)+GOLD*(*bx-*ax);    ss = strrchr( name, '.' );            /* find last / */
   *fc=(*func)(*cx);    if (ss >0){
   while (*fb > *fc) {      ss++;
     r=(*bx-*ax)*(*fb-*fc);      strcpy(ext,ss);                     /* save extension */
     q=(*bx-*cx)*(*fb-*fa);      l1= strlen( name);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      l2= strlen(ss)+1;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      strncpy( finame, name, l1-l2);
     ulim=(*bx)+GLIMIT*(*cx-*bx);      finame[l1-l2]= 0;
     if ((*bx-u)*(u-*cx) > 0.0) {    }
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {    return( 0 );                          /* we're done */
       fu=(*func)(u);  }
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /******************************************/
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  void replace_back_to_slash(char *s, char*t)
       u=ulim;  {
       fu=(*func)(u);    int i;
     } else {    int lg=0;
       u=(*cx)+GOLD*(*cx-*bx);    i=0;
       fu=(*func)(u);    lg=strlen(t);
     }    for(i=0; i<= lg; i++) {
     SHFT(*ax,*bx,*cx,u)      (s[i] = t[i]);
       SHFT(*fa,*fb,*fc,fu)      if (t[i]== '\\') s[i]='/';
       }    }
 }  }
   
 /*************** linmin ************************/  int nbocc(char *s, char occ)
   {
 int ncom;    int i,j=0;
 double *pcom,*xicom;    int lg=20;
 double (*nrfunc)(double []);    i=0;
      lg=strlen(s);
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    for(i=0; i<= lg; i++) {
 {    if  (s[i] == occ ) j++;
   double brent(double ax, double bx, double cx,    }
                double (*f)(double), double tol, double *xmin);    return j;
   double f1dim(double x);  }
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  void cutv(char *u,char *v, char*t, char occ)
   int j;  {
   double xx,xmin,bx,ax;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   double fx,fb,fa;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
         gives u="abcedf" and v="ghi2j" */
   ncom=n;    int i,lg,j,p=0;
   pcom=vector(1,n);    i=0;
   xicom=vector(1,n);    for(j=0; j<=strlen(t)-1; j++) {
   nrfunc=func;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   for (j=1;j<=n;j++) {    }
     pcom[j]=p[j];  
     xicom[j]=xi[j];    lg=strlen(t);
   }    for(j=0; j<p; j++) {
   ax=0.0;      (u[j] = t[j]);
   xx=1.0;    }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);       u[p]='\0';
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG     for(j=0; j<= lg; j++) {
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      if (j>=(p+1))(v[j-p-1] = t[j]);
 #endif    }
   for (j=1;j<=n;j++) {  }
     xi[j] *= xmin;  
     p[j] += xi[j];  /********************** nrerror ********************/
   }  
   free_vector(xicom,1,n);  void nrerror(char error_text[])
   free_vector(pcom,1,n);  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 /*************** powell ************************/    exit(EXIT_FAILURE);
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  /*********************** vector *******************/
 {  double *vector(int nl, int nh)
   void linmin(double p[], double xi[], int n, double *fret,  {
               double (*func)(double []));    double *v;
   int i,ibig,j;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double del,t,*pt,*ptt,*xit;    if (!v) nrerror("allocation failure in vector");
   double fp,fptt;    return v-nl+NR_END;
   double *xits;  }
   pt=vector(1,n);  
   ptt=vector(1,n);  /************************ free vector ******************/
   xit=vector(1,n);  void free_vector(double*v, int nl, int nh)
   xits=vector(1,n);  {
   *fret=(*func)(p);    free((FREE_ARG)(v+nl-NR_END));
   for (j=1;j<=n;j++) pt[j]=p[j];  }
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /************************ivector *******************************/
     ibig=0;  int *ivector(long nl,long nh)
     del=0.0;  {
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    int *v;
     for (i=1;i<=n;i++)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       printf(" %d %.12f",i, p[i]);    if (!v) nrerror("allocation failure in ivector");
     printf("\n");    return v-nl+NR_END;
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /******************free ivector **************************/
 #ifdef DEBUG  void free_ivector(int *v, long nl, long nh)
       printf("fret=%lf \n",*fret);  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
       printf("%d",i);fflush(stdout);  }
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /************************lvector *******************************/
         del=fabs(fptt-(*fret));  long *lvector(long nl,long nh)
         ibig=i;  {
       }    long *v;
 #ifdef DEBUG    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       printf("%d %.12e",i,(*fret));    if (!v) nrerror("allocation failure in ivector");
       for (j=1;j<=n;j++) {    return v-nl+NR_END;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /******************free lvector **************************/
       for(j=1;j<=n;j++)  void free_lvector(long *v, long nl, long nh)
         printf(" p=%.12e",p[j]);  {
       printf("\n");    free((FREE_ARG)(v+nl-NR_END));
 #endif  }
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  /******************* imatrix *******************************/
 #ifdef DEBUG  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       int k[2],l;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       k[0]=1;  { 
       k[1]=-1;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       printf("Max: %.12e",(*func)(p));    int **m; 
       for (j=1;j<=n;j++)    
         printf(" %.12e",p[j]);    /* allocate pointers to rows */ 
       printf("\n");    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       for(l=0;l<=1;l++) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
         for (j=1;j<=n;j++) {    m += NR_END; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    m -= nrl; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    
         }    
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    /* allocate rows and set pointers to them */ 
       }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
     m[nrl] -= ncl; 
       free_vector(xit,1,n);    
       free_vector(xits,1,n);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       free_vector(ptt,1,n);    
       free_vector(pt,1,n);    /* return pointer to array of pointers to rows */ 
       return;    return m; 
     }  } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  /****************** free_imatrix *************************/
       ptt[j]=2.0*p[j]-pt[j];  void free_imatrix(m,nrl,nrh,ncl,nch)
       xit[j]=p[j]-pt[j];        int **m;
       pt[j]=p[j];        long nch,ncl,nrh,nrl; 
     }       /* free an int matrix allocated by imatrix() */ 
     fptt=(*func)(ptt);  { 
     if (fptt < fp) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    free((FREE_ARG) (m+nrl-NR_END)); 
       if (t < 0.0) {  } 
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /******************* matrix *******************************/
           xi[j][ibig]=xi[j][n];  double **matrix(long nrl, long nrh, long ncl, long nch)
           xi[j][n]=xit[j];  {
         }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 #ifdef DEBUG    double **m;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
           printf(" %.12e",xit[j]);    if (!m) nrerror("allocation failure 1 in matrix()");
         printf("\n");    m += NR_END;
 #endif    m -= nrl;
       }  
     }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /**** Prevalence limit ****************/  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    return m;
 {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit     */
      matrix by transitions matrix until convergence is reached */  }
   
   int i, ii,j,k;  /*************************free matrix ************************/
   double min, max, maxmin, maxmax,sumnew=0.;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double **matprod2();  {
   double **out, cov[NCOVMAX], **pmij();    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double **newm;    free((FREE_ARG)(m+nrl-NR_END));
   double agefin, delaymax=50 ; /* Max number of years to converge */  }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  /******************* ma3x *******************************/
     for (j=1;j<=nlstate+ndeath;j++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
    cov[1]=1.;  
      m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if (!m) nrerror("allocation failure 1 in matrix()");
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m += NR_END;
     newm=savm;    m -= nrl;
     /* Covariates have to be included here again */  
      cov[2]=agefin;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for (k=1; k<=cptcovn;k++) {    m[nrl] += NR_END;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    m[nrl] -= ncl;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       for (k=1; k<=cptcovprod;k++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    for (j=ncl+1; j<=nch; j++) 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      m[nrl][j]=m[nrl][j-1]+nlay;
     
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     savm=oldm;      for (j=ncl+1; j<=nch; j++) 
     oldm=newm;        m[i][j]=m[i][j-1]+nlay;
     maxmax=0.;    }
     for(j=1;j<=nlstate;j++){    return m; 
       min=1.;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       max=0.;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       for(i=1; i<=nlstate; i++) {    */
         sumnew=0;  }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  /*************************free ma3x ************************/
         max=FMAX(max,prlim[i][j]);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         min=FMIN(min,prlim[i][j]);  {
       }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       maxmin=max-min;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       maxmax=FMAX(maxmax,maxmin);    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     if(maxmax < ftolpl){  
       return prlim;  /*************** function subdirf ***********/
     }  char *subdirf(char fileres[])
   }  {
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 /*************** transition probabilities ***************/    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    return tmpout;
 {  }
   double s1, s2;  
   /*double t34;*/  /*************** function subdirf2 ***********/
   int i,j,j1, nc, ii, jj;  char *subdirf2(char fileres[], char *preop)
   {
     for(i=1; i<= nlstate; i++){    
     for(j=1; j<i;j++){    /* Caution optionfilefiname is hidden */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcpy(tmpout,optionfilefiname);
         /*s2 += param[i][j][nc]*cov[nc];*/    strcat(tmpout,"/");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcat(tmpout,preop);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    strcat(tmpout,fileres);
       }    return tmpout;
       ps[i][j]=s2;  }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  /*************** function subdirf3 ***********/
     for(j=i+1; j<=nlstate+ndeath;j++){  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
       ps[i][j]=(s2);    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
   }    strcat(tmpout,preop2);
     /*ps[3][2]=1;*/    strcat(tmpout,fileres);
     return tmpout;
   for(i=1; i<= nlstate; i++){  }
      s1=0;  
     for(j=1; j<i; j++)  /***************** f1dim *************************/
       s1+=exp(ps[i][j]);  extern int ncom; 
     for(j=i+1; j<=nlstate+ndeath; j++)  extern double *pcom,*xicom;
       s1+=exp(ps[i][j]);  extern double (*nrfunc)(double []); 
     ps[i][i]=1./(s1+1.);   
     for(j=1; j<i; j++)  double f1dim(double x) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  { 
     for(j=i+1; j<=nlstate+ndeath; j++)    int j; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double f;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    double *xt; 
   } /* end i */   
     xt=vector(1,ncom); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    f=(*nrfunc)(xt); 
       ps[ii][jj]=0;    free_vector(xt,1,ncom); 
       ps[ii][ii]=1;    return f; 
     }  } 
   }  
   /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  { 
     for(jj=1; jj<= nlstate+ndeath; jj++){    int iter; 
      printf("%lf ",ps[ii][jj]);    double a,b,d,etemp;
    }    double fu,fv,fw,fx;
     printf("\n ");    double ftemp;
     }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     printf("\n ");printf("%lf ",cov[2]);*/    double e=0.0; 
 /*   
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    a=(ax < cx ? ax : cx); 
   goto end;*/    b=(ax > cx ? ax : cx); 
     return ps;    x=w=v=bx; 
 }    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
 /**************** Product of 2 matrices ******************/      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 {      printf(".");fflush(stdout);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      fprintf(ficlog,".");fflush(ficlog);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #ifdef DEBUG
   /* in, b, out are matrice of pointers which should have been initialized      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);
      before: only the contents of out is modified. The function returns      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);
      a pointer to pointers identical to out */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   long i, j, k;  #endif
   for(i=nrl; i<= nrh; i++)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for(k=ncolol; k<=ncoloh; k++)        *xmin=x; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        return fx; 
         out[i][k] +=in[i][j]*b[j][k];      } 
       ftemp=fu;
   return out;      if (fabs(e) > tol1) { 
 }        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
 /************* Higher Matrix Product ***************/        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        q=fabs(q); 
 {        etemp=e; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        e=d; 
      duration (i.e. until        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        else { 
      (typically every 2 years instead of every month which is too big).          d=p/q; 
      Model is determined by parameters x and covariates have to be          u=x+d; 
      included manually here.          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
      */        } 
       } else { 
   int i, j, d, h, k;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double **out, cov[NCOVMAX];      } 
   double **newm;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
   /* Hstepm could be zero and should return the unit matrix */      if (fu <= fx) { 
   for (i=1;i<=nlstate+ndeath;i++)        if (u >= x) a=x; else b=x; 
     for (j=1;j<=nlstate+ndeath;j++){        SHFT(v,w,x,u) 
       oldm[i][j]=(i==j ? 1.0 : 0.0);          SHFT(fv,fw,fx,fu) 
       po[i][j][0]=(i==j ? 1.0 : 0.0);          } else { 
     }            if (u < x) a=u; else b=u; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */            if (fu <= fw || w == x) { 
   for(h=1; h <=nhstepm; h++){              v=w; 
     for(d=1; d <=hstepm; d++){              w=u; 
       newm=savm;              fv=fw; 
       /* Covariates have to be included here again */              fw=fu; 
       cov[1]=1.;            } else if (fu <= fv || v == x || v == w) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;              v=u; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];              fv=fu; 
       for (k=1; k<=cptcovage;k++)            } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          } 
       for (k=1; k<=cptcovprod;k++)    } 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    nrerror("Too many iterations in brent"); 
     *xmin=x; 
     return fx; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  } 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /****************** mnbrak ***********************/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       oldm=newm;              double (*func)(double)) 
     }  { 
     for(i=1; i<=nlstate+ndeath; i++)    double ulim,u,r,q, dum;
       for(j=1;j<=nlstate+ndeath;j++) {    double fu; 
         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]);    *fa=(*func)(*ax); 
          */    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
   } /* end h */      SHFT(dum,*ax,*bx,dum) 
   return po;        SHFT(dum,*fb,*fa,dum) 
 }        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /*************** log-likelihood *************/    while (*fb > *fc) { 
 double func( double *x)      r=(*bx-*ax)*(*fb-*fc); 
 {      q=(*bx-*cx)*(*fb-*fa); 
   int i, ii, j, k, mi, d, kk;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double **out;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double sw; /* Sum of weights */      if ((*bx-u)*(u-*cx) > 0.0) { 
   double lli; /* Individual log likelihood */        fu=(*func)(u); 
   long ipmx;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   /*extern weight */        fu=(*func)(u); 
   /* We are differentiating ll according to initial status */        if (fu < *fc) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   /*for(i=1;i<imx;i++)            SHFT(*fb,*fc,fu,(*func)(u)) 
     printf(" %d\n",s[4][i]);            } 
   */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   cov[1]=1.;        u=ulim; 
         fu=(*func)(u); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      } else { 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        u=(*cx)+GOLD*(*cx-*bx); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fu=(*func)(u); 
     for(mi=1; mi<= wav[i]-1; mi++){      } 
       for (ii=1;ii<=nlstate+ndeath;ii++)      SHFT(*ax,*bx,*cx,u) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        SHFT(*fa,*fb,*fc,fu) 
       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++) {  /*************** linmin ************************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  int ncom; 
          double *pcom,*xicom;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  double (*nrfunc)(double []); 
                      1,nlstate+ndeath,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, 
                         double (*f)(double), double tol, double *xmin); 
       } /* end mult */    double f1dim(double x); 
          void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);                double *fc, double (*func)(double)); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    int j; 
       ipmx +=1;    double xx,xmin,bx,ax; 
       sw += weight[i];    double fx,fb,fa;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;   
     } /* end of wave */    ncom=n; 
   } /* end of individual */    pcom=vector(1,n); 
     xicom=vector(1,n); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    nrfunc=func; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    for (j=1;j<=n;j++) { 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      pcom[j]=p[j]; 
   return -l;      xicom[j]=xi[j]; 
 }    } 
     ax=0.0; 
     xx=1.0; 
 /*********** Maximum Likelihood Estimation ***************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  #ifdef DEBUG
 {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int i,j, iter;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double **xi,*delti;  #endif
   double fret;    for (j=1;j<=n;j++) { 
   xi=matrix(1,npar,1,npar);      xi[j] *= xmin; 
   for (i=1;i<=npar;i++)      p[j] += xi[j]; 
     for (j=1;j<=npar;j++)    } 
       xi[i][j]=(i==j ? 1.0 : 0.0);    free_vector(xicom,1,n); 
   printf("Powell\n");    free_vector(pcom,1,n); 
   powell(p,xi,npar,ftol,&iter,&fret,func);  } 
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  char *asc_diff_time(long time_sec, char ascdiff[])
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  {
     long sec_left, days, hours, minutes;
 }    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
 /**** Computes Hessian and covariance matrix ***/    hours = (sec_left) / (60*60) ;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    sec_left = (sec_left) %(60*60);
 {    minutes = (sec_left) /60;
   double  **a,**y,*x,pd;    sec_left = (sec_left) % (60);
   double **hess;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   int i, j,jk;    return ascdiff;
   int *indx;  }
   
   double hessii(double p[], double delta, int theta, double delti[]);  /*************** powell ************************/
   double hessij(double p[], double delti[], int i, int j);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   void lubksb(double **a, int npar, int *indx, double b[]) ;              double (*func)(double [])) 
   void ludcmp(double **a, int npar, int *indx, double *d) ;  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   hess=matrix(1,npar,1,npar);                double (*func)(double [])); 
     int i,ibig,j; 
   printf("\nCalculation of the hessian matrix. Wait...\n");    double del,t,*pt,*ptt,*xit;
   for (i=1;i<=npar;i++){    double fp,fptt;
     printf("%d",i);fflush(stdout);    double *xits;
     hess[i][i]=hessii(p,ftolhess,i,delti);    int niterf, itmp;
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/    pt=vector(1,n); 
   }    ptt=vector(1,n); 
      xit=vector(1,n); 
   for (i=1;i<=npar;i++) {    xits=vector(1,n); 
     for (j=1;j<=npar;j++)  {    *fret=(*func)(p); 
       if (j>i) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
         printf(".%d%d",i,j);fflush(stdout);    for (*iter=1;;++(*iter)) { 
         hess[i][j]=hessij(p,delti,i,j);      fp=(*fret); 
         hess[j][i]=hess[i][j];          ibig=0; 
         /*printf(" %lf ",hess[i][j]);*/      del=0.0; 
       }      last_time=curr_time;
     }      (void) gettimeofday(&curr_time,&tzp);
   }      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);
   printf("\n");      /*    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);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      */
       for (i=1;i<=n;i++) {
   a=matrix(1,npar,1,npar);        printf(" %d %.12f",i, p[i]);
   y=matrix(1,npar,1,npar);        fprintf(ficlog," %d %.12lf",i, p[i]);
   x=vector(1,npar);        fprintf(ficrespow," %.12lf", p[i]);
   indx=ivector(1,npar);      }
   for (i=1;i<=npar;i++)      printf("\n");
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      fprintf(ficlog,"\n");
   ludcmp(a,npar,indx,&pd);      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   for (j=1;j<=npar;j++) {        tm = *localtime(&curr_time.tv_sec);
     for (i=1;i<=npar;i++) x[i]=0;        strcpy(strcurr,asctime(&tm));
     x[j]=1;  /*       asctime_r(&tm,strcurr); */
     lubksb(a,npar,indx,x);        forecast_time=curr_time; 
     for (i=1;i<=npar;i++){        itmp = strlen(strcurr);
       matcov[i][j]=x[i];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     }          strcurr[itmp-1]='\0';
   }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   printf("\n#Hessian matrix#\n");        for(niterf=10;niterf<=30;niterf+=10){
   for (i=1;i<=npar;i++) {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     for (j=1;j<=npar;j++) {          tmf = *localtime(&forecast_time.tv_sec);
       printf("%.3e ",hess[i][j]);  /*      asctime_r(&tmf,strfor); */
     }          strcpy(strfor,asctime(&tmf));
     printf("\n");          itmp = strlen(strfor);
   }          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
   /* Recompute Inverse */          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);
   for (i=1;i<=npar;i++)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        }
   ludcmp(a,npar,indx,&pd);      }
       for (i=1;i<=n;i++) { 
   /*  printf("\n#Hessian matrix recomputed#\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   for (j=1;j<=npar;j++) {  #ifdef DEBUG
     for (i=1;i<=npar;i++) x[i]=0;        printf("fret=%lf \n",*fret);
     x[j]=1;        fprintf(ficlog,"fret=%lf \n",*fret);
     lubksb(a,npar,indx,x);  #endif
     for (i=1;i<=npar;i++){        printf("%d",i);fflush(stdout);
       y[i][j]=x[i];        fprintf(ficlog,"%d",i);fflush(ficlog);
       printf("%.3e ",y[i][j]);        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
     printf("\n");          del=fabs(fptt-(*fret)); 
   }          ibig=i; 
   */        } 
   #ifdef DEBUG
   free_matrix(a,1,npar,1,npar);        printf("%d %.12e",i,(*fret));
   free_matrix(y,1,npar,1,npar);        fprintf(ficlog,"%d %.12e",i,(*fret));
   free_vector(x,1,npar);        for (j=1;j<=n;j++) {
   free_ivector(indx,1,npar);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   free_matrix(hess,1,npar,1,npar);          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
 }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
 /*************** hessian matrix ****************/          fprintf(ficlog," p=%.12e",p[j]);
 double hessii( double x[], double delta, int theta, double delti[])        }
 {        printf("\n");
   int i;        fprintf(ficlog,"\n");
   int l=1, lmax=20;  #endif
   double k1,k2;      } 
   double p2[NPARMAX+1];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double res;  #ifdef DEBUG
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        int k[2],l;
   double fx;        k[0]=1;
   int k=0,kmax=10;        k[1]=-1;
   double l1;        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   fx=func(x);        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) p2[i]=x[i];          printf(" %.12e",p[j]);
   for(l=0 ; l <=lmax; l++){          fprintf(ficlog," %.12e",p[j]);
     l1=pow(10,l);        }
     delts=delt;        printf("\n");
     for(k=1 ; k <kmax; k=k+1){        fprintf(ficlog,"\n");
       delt = delta*(l1*k);        for(l=0;l<=1;l++) {
       p2[theta]=x[theta] +delt;          for (j=1;j<=n;j++) {
       k1=func(p2)-fx;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       p2[theta]=x[theta]-delt;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       k2=func(p2)-fx;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */          }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 #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);  #endif
 #endif  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        free_vector(xit,1,n); 
         k=kmax;        free_vector(xits,1,n); 
       }        free_vector(ptt,1,n); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        free_vector(pt,1,n); 
         k=kmax; l=lmax*10.;        return; 
       }      } 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         delts=delt;      for (j=1;j<=n;j++) { 
       }        ptt[j]=2.0*p[j]-pt[j]; 
     }        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
   delti[theta]=delts;      } 
   return res;      fptt=(*func)(ptt); 
        if (fptt < fp) { 
 }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
 double hessij( double x[], double delti[], int thetai,int thetaj)          linmin(p,xit,n,fret,func); 
 {          for (j=1;j<=n;j++) { 
   int i;            xi[j][ibig]=xi[j][n]; 
   int l=1, l1, lmax=20;            xi[j][n]=xit[j]; 
   double k1,k2,k3,k4,res,fx;          }
   double p2[NPARMAX+1];  #ifdef DEBUG
   int k;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fx=func(x);          for(j=1;j<=n;j++){
   for (k=1; k<=2; k++) {            printf(" %.12e",xit[j]);
     for (i=1;i<=npar;i++) p2[i]=x[i];            fprintf(ficlog," %.12e",xit[j]);
     p2[thetai]=x[thetai]+delti[thetai]/k;          }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          printf("\n");
     k1=func(p2)-fx;          fprintf(ficlog,"\n");
    #endif
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } 
     k2=func(p2)-fx;    } 
    } 
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /**** Prevalence limit (stable prevalence)  ****************/
     k3=func(p2)-fx;  
    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     k4=func(p2)-fx;       matrix by transitions matrix until convergence is reached */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG    int i, ii,j,k;
     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);    double min, max, maxmin, maxmax,sumnew=0.;
 #endif    double **matprod2();
   }    double **out, cov[NCOVMAX], **pmij();
   return res;    double **newm;
 }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
 /************** Inverse of matrix **************/    for (ii=1;ii<=nlstate+ndeath;ii++)
 void ludcmp(double **a, int n, int *indx, double *d)      for (j=1;j<=nlstate+ndeath;j++){
 {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i,imax,j,k;      }
   double big,dum,sum,temp;  
   double *vv;     cov[1]=1.;
     
   vv=vector(1,n);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   *d=1.0;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for (i=1;i<=n;i++) {      newm=savm;
     big=0.0;      /* Covariates have to be included here again */
     for (j=1;j<=n;j++)       cov[2]=agefin;
       if ((temp=fabs(a[i][j])) > big) big=temp;    
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        for (k=1; k<=cptcovn;k++) {
     vv[i]=1.0/big;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   for (j=1;j<=n;j++) {        }
     for (i=1;i<j;i++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       sum=a[i][j];        for (k=1; k<=cptcovprod;k++)
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       a[i][j]=sum;  
     }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     big=0.0;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for (i=j;i<=n;i++) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       sum=a[i][j];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];      savm=oldm;
       a[i][j]=sum;      oldm=newm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {      maxmax=0.;
         big=dum;      for(j=1;j<=nlstate;j++){
         imax=i;        min=1.;
       }        max=0.;
     }        for(i=1; i<=nlstate; i++) {
     if (j != imax) {          sumnew=0;
       for (k=1;k<=n;k++) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         dum=a[imax][k];          prlim[i][j]= newm[i][j]/(1-sumnew);
         a[imax][k]=a[j][k];          max=FMAX(max,prlim[i][j]);
         a[j][k]=dum;          min=FMIN(min,prlim[i][j]);
       }        }
       *d = -(*d);        maxmin=max-min;
       vv[imax]=vv[j];        maxmax=FMAX(maxmax,maxmin);
     }      }
     indx[j]=imax;      if(maxmax < ftolpl){
     if (a[j][j] == 0.0) a[j][j]=TINY;        return prlim;
     if (j != n) {      }
       dum=1.0/(a[j][j]);    }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  }
     }  
   }  /*************** transition probabilities ***************/ 
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 }  {
     double s1, s2;
 void lubksb(double **a, int n, int *indx, double b[])    /*double t34;*/
 {    int i,j,j1, nc, ii, jj;
   int i,ii=0,ip,j;  
   double sum;      for(i=1; i<= nlstate; i++){
          for(j=1; j<i;j++){
   for (i=1;i<=n;i++) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     ip=indx[i];            /*s2 += param[i][j][nc]*cov[nc];*/
     sum=b[ip];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     b[ip]=b[i];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     if (ii)          }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          ps[i][j]=s2;
     else if (sum) ii=i;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     b[i]=sum;        }
   }        for(j=i+1; j<=nlstate+ndeath;j++){
   for (i=n;i>=1;i--) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     sum=b[i];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     b[i]=sum/a[i][i];          }
   }          ps[i][j]=s2;
 }        }
       }
 /************ Frequencies ********************/      /*ps[3][2]=1;*/
 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)      
 {  /* Some frequencies */      for(i=1; i<= nlstate; i++){
          s1=0;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for(j=1; j<i; j++)
   double ***freq; /* Frequencies */          s1+=exp(ps[i][j]);
   double *pp;        for(j=i+1; j<=nlstate+ndeath; j++)
   double pos, k2, dateintsum=0,k2cpt=0;          s1+=exp(ps[i][j]);
   FILE *ficresp;        ps[i][i]=1./(s1+1.);
   char fileresp[FILENAMELENGTH];        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
   pp=vector(1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   strcpy(fileresp,"p");        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   strcat(fileresp,fileres);      } /* end i */
   if((ficresp=fopen(fileresp,"w"))==NULL) {      
     printf("Problem with prevalence resultfile: %s\n", fileresp);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     exit(0);        for(jj=1; jj<= nlstate+ndeath; jj++){
   }          ps[ii][jj]=0;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          ps[ii][ii]=1;
   j1=0;        }
       }
   j=cptcoveff;      
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   for(k1=1; k1<=j;k1++){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
    for(i1=1; i1<=ncodemax[k1];i1++){  /*         printf("ddd %lf ",ps[ii][jj]); */
        j1++;  /*       } */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /*       printf("\n "); */
          scanf("%d", i);*/  /*        } */
         for (i=-1; i<=nlstate+ndeath; i++)    /*        printf("\n ");printf("%lf ",cov[2]); */
          for (jk=-1; jk<=nlstate+ndeath; jk++)           /*
            for(m=agemin; m <= agemax+3; m++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
              freq[i][jk][m]=0;        goto end;*/
       return ps;
         dateintsum=0;  }
         k2cpt=0;  
        for (i=1; i<=imx; i++) {  /**************** Product of 2 matrices ******************/
          bool=1;  
          if  (cptcovn>0) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
            for (z1=1; z1<=cptcoveff; z1++)  {
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
                bool=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
          }    /* in, b, out are matrice of pointers which should have been initialized 
          if (bool==1) {       before: only the contents of out is modified. The function returns
            for(m=firstpass; m<=lastpass; m++){       a pointer to pointers identical to out */
              k2=anint[m][i]+(mint[m][i]/12.);    long i, j, k;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    for(i=nrl; i<= nrh; i++)
                if(agev[m][i]==0) agev[m][i]=agemax+1;      for(k=ncolol; k<=ncoloh; k++)
                if(agev[m][i]==1) agev[m][i]=agemax+2;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          out[i][k] +=in[i][j]*b[j][k];
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    return out;
                  dateintsum=dateintsum+k2;  }
                  k2cpt++;  
                }  
   /************* Higher Matrix Product ***************/
              }  
            }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
          }  {
        }    /* Computes the transition matrix starting at age 'age' over 
         if  (cptcovn>0) {       'nhstepm*hstepm*stepm' months (i.e. until
          fprintf(ficresp, "\n#********** Variable ");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       nhstepm*hstepm matrices. 
        fprintf(ficresp, "**********\n#");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         }       (typically every 2 years instead of every month which is too big 
        for(i=1; i<=nlstate;i++)       for the memory).
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);       Model is determined by parameters x and covariates have to be 
        fprintf(ficresp, "\n");       included manually here. 
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){       */
     if(i==(int)agemax+3)  
       printf("Total");    int i, j, d, h, k;
     else    double **out, cov[NCOVMAX];
       printf("Age %d", i);    double **newm;
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /* Hstepm could be zero and should return the unit matrix */
         pp[jk] += freq[jk][m][i];    for (i=1;i<=nlstate+ndeath;i++)
     }      for (j=1;j<=nlstate+ndeath;j++){
     for(jk=1; jk <=nlstate ; jk++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
       for(m=-1, pos=0; m <=0 ; m++)        po[i][j][0]=(i==j ? 1.0 : 0.0);
         pos += freq[jk][m][i];      }
       if(pp[jk]>=1.e-10)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for(h=1; h <=nhstepm; h++){
       else      for(d=1; d <=hstepm; d++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        newm=savm;
     }        /* Covariates have to be included here again */
         cov[1]=1.;
      for(jk=1; jk <=nlstate ; jk++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovage;k++)
      }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
     for(jk=1,pos=0; jk <=nlstate ; jk++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       else        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       if( i <= (int) agemax){        savm=oldm;
         if(pos>=1.e-5){        oldm=newm;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      }
           probs[i][jk][j1]= pp[jk]/pos;      for(i=1; i<=nlstate+ndeath; i++)
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        for(j=1;j<=nlstate+ndeath;j++) {
         }          po[i][j][h]=newm[i][j];
       else          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           */
       }        }
     }    } /* end h */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    return po;
       for(m=-1; m <=nlstate+ndeath; m++)  }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  /*************** log-likelihood *************/
     printf("\n");  double func( double *x)
     }  {
     }    int i, ii, j, k, mi, d, kk;
  }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   dateintmean=dateintsum/k2cpt;    double **out;
      double sw; /* Sum of weights */
   fclose(ficresp);    double lli; /* Individual log likelihood */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    int s1, s2;
   free_vector(pp,1,nlstate);    double bbh, survp;
     long ipmx;
   /* End of Freq */    /*extern weight */
 }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 /************ Prevalence ********************/    /*for(i=1;i<imx;i++) 
 void prevalence(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 calagedate)      printf(" %d\n",s[4][i]);
 {  /* Some frequencies */    */
      cov[1]=1.;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double *pp;  
   double pos, k2;    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   pp=vector(1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            for (j=1;j<=nlstate+ndeath;j++){
   j1=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   j=cptcoveff;            }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
  for(k1=1; k1<=j;k1++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i1=1; i1<=ncodemax[k1];i1++){            for (kk=1; kk<=cptcovage;kk++) {
       j1++;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
       for (i=-1; i<=nlstate+ndeath; i++)              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for (jk=-1; jk<=nlstate+ndeath; jk++)                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=agemin; m <= agemax+3; m++)            savm=oldm;
             freq[i][jk][m]=0;            oldm=newm;
                } /* end mult */
       for (i=1; i<=imx; i++) {        
         bool=1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         if  (cptcovn>0) {          /* But now since version 0.9 we anticipate for bias at large stepm.
           for (z1=1; z1<=cptcoveff; z1++)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * (in months) between two waves is not a multiple of stepm, we rounded to 
               bool=0;           * the nearest (and in case of equal distance, to the lowest) interval but now
         }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         if (bool==1) {           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           for(m=firstpass; m<=lastpass; m++){           * probability in order to take into account the bias as a fraction of the way
             k2=anint[m][i]+(mint[m][i]/12.);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
             if ((k2>=dateprev1) && (k2<=dateprev2)) {           * -stepm/2 to stepm/2 .
               if(agev[m][i]==0) agev[m][i]=agemax+1;           * For stepm=1 the results are the same as for previous versions of Imach.
               if(agev[m][i]==1) agev[m][i]=agemax+2;           * For stepm > 1 the results are less biased than in previous versions. 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-1/12.)] += weight[i];           */
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            s1=s[mw[mi][i]][i];
             }          s2=s[mw[mi+1][i]][i];
           }          bbh=(double)bh[mi][i]/(double)stepm; 
         }          /* bias bh is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
                 */
         for(i=(int)agemin; i <= (int)agemax+3; i++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           for(jk=1; jk <=nlstate ; jk++){          if( s2 > nlstate){ 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            /* i.e. if s2 is a death state and if the date of death is known 
               pp[jk] += freq[jk][m][i];               then the contribution to the likelihood is the probability to 
           }               die between last step unit time and current  step unit time, 
           for(jk=1; jk <=nlstate ; jk++){               which is also equal to probability to die before dh 
             for(m=-1, pos=0; m <=0 ; m++)               minus probability to die before dh-stepm . 
             pos += freq[jk][m][i];               In version up to 0.92 likelihood was computed
         }          as if date of death was unknown. Death was treated as any other
                  health state: the date of the interview describes the actual state
          for(jk=1; jk <=nlstate ; jk++){          and not the date of a change in health state. The former idea was
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          to consider that at each interview the state was recorded
              pp[jk] += freq[jk][m][i];          (healthy, disable or death) and IMaCh was corrected; but when we
          }          introduced the exact date of death then we should have modified
                    the contribution of an exact death to the likelihood. This new
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
          for(jk=1; jk <=nlstate ; jk++){                    and month of death but the probability to survive from last
            if( i <= (int) agemax){          interview up to one month before death multiplied by the
              if(pos>=1.e-5){          probability to die within a month. Thanks to Chris
                probs[i][jk][j1]= pp[jk]/pos;          Jackson for correcting this bug.  Former versions increased
              }          mortality artificially. The bad side is that we add another loop
            }          which slows down the processing. The difference can be up to 10%
          }          lower mortality.
                      */
         }            lli=log(out[s1][s2] - savm[s1][s2]);
     }  
   }  
            } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              survp += out[s1][j];
   free_vector(pp,1,nlstate);            lli= survp;
            }
 }  /* End of Freq */          
           else if  (s2==-4) {
 /************* Waves Concatenation ***************/            for (j=3,survp=0. ; j<=nlstate; j++) 
               survp += out[s1][j];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            lli= survp;
 {          }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          
      Death is a valid wave (if date is known).          else if  (s2==-5) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            for (j=1,survp=0. ; j<=2; j++) 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              survp += out[s1][j];
      and mw[mi+1][i]. dh depends on stepm.            lli= survp;
      */          }
   
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          else{
      double sum=0., jmean=0.;*/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   int j, k=0,jk, ju, jl;          } 
   double sum=0.;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   jmin=1e+5;          /*if(lli ==000.0)*/
   jmax=-1;          /*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); */
   jmean=0.;          ipmx +=1;
   for(i=1; i<=imx; i++){          sw += weight[i];
     mi=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     m=firstpass;        } /* end of wave */
     while(s[m][i] <= nlstate){      } /* end of individual */
       if(s[m][i]>=1)    }  else if(mle==2){
         mw[++mi][i]=m;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if(m >=lastpass)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         break;        for(mi=1; mi<= wav[i]-1; mi++){
       else          for (ii=1;ii<=nlstate+ndeath;ii++)
         m++;            for (j=1;j<=nlstate+ndeath;j++){
     }/* end while */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (s[m][i] > nlstate){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       mi++;     /* Death is another wave */            }
       /* if(mi==0)  never been interviewed correctly before death */          for(d=0; d<=dh[mi][i]; d++){
          /* Only death is a correct wave */            newm=savm;
       mw[mi][i]=m;            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];
     wav[i]=mi;            }
     if(mi==0)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
             oldm=newm;
   for(i=1; i<=imx; i++){          } /* end mult */
     for(mi=1; mi<wav[i];mi++){        
       if (stepm <=0)          s1=s[mw[mi][i]][i];
         dh[mi][i]=1;          s2=s[mw[mi+1][i]][i];
       else{          bbh=(double)bh[mi][i]/(double)stepm; 
         if (s[mw[mi+1][i]][i] > nlstate) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           if (agedc[i] < 2*AGESUP) {          ipmx +=1;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          sw += weight[i];
           if(j==0) j=1;  /* Survives at least one month after exam */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           k=k+1;        } /* end of wave */
           if (j >= jmax) jmax=j;      } /* end of individual */
           if (j <= jmin) jmin=j;    }  else if(mle==3){  /* exponential inter-extrapolation */
           sum=sum+j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           /* if (j<10) printf("j=%d num=%d ",j,i); */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           }        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
         else{            for (j=1;j<=nlstate+ndeath;j++){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (j >= jmax) jmax=j;            }
           else if (j <= jmin)jmin=j;          for(d=0; d<dh[mi][i]; d++){
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            newm=savm;
           sum=sum+j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
         jk= j/stepm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         jl= j -jk*stepm;            }
         ju= j -(jk+1)*stepm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if(jl <= -ju)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           dh[mi][i]=jk;            savm=oldm;
         else            oldm=newm;
           dh[mi][i]=jk+1;          } /* end mult */
         if(dh[mi][i]==0)        
           dh[mi][i]=1; /* At least one step */          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
   }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   jmean=sum/k;          ipmx +=1;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          sw += weight[i];
  }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*********** Tricode ****************************/        } /* end of wave */
 void tricode(int *Tvar, int **nbcode, int imx)      } /* end of individual */
 {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   int Ndum[20],ij=1, k, j, i;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int cptcode=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   cptcoveff=0;        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   for (k=0; k<19; k++) Ndum[k]=0;            for (j=1;j<=nlstate+ndeath;j++){
   for (k=1; k<=7; k++) ncodemax[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            }
     for (i=1; i<=imx; i++) {          for(d=0; d<dh[mi][i]; d++){
       ij=(int)(covar[Tvar[j]][i]);            newm=savm;
       Ndum[ij]++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            for (kk=1; kk<=cptcovage;kk++) {
       if (ij > cptcode) cptcode=ij;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
           
     for (i=0; i<=cptcode; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(Ndum[i]!=0) ncodemax[j]++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     ij=1;            oldm=newm;
           } /* end mult */
         
     for (i=1; i<=ncodemax[j]; i++) {          s1=s[mw[mi][i]][i];
       for (k=0; k<=19; k++) {          s2=s[mw[mi+1][i]][i];
         if (Ndum[k] != 0) {          if( s2 > nlstate){ 
           nbcode[Tvar[j]][ij]=k;            lli=log(out[s1][s2] - savm[s1][s2]);
           ij++;          }else{
         }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         if (ij > ncodemax[j]) break;          }
       }            ipmx +=1;
     }          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 (k=0; k<19; k++) Ndum[k]=0;        } /* end of wave */
       } /* end of individual */
  for (i=1; i<=ncovmodel-2; i++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       ij=Tvar[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       Ndum[ij]++;        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++)
  ij=1;            for (j=1;j<=nlstate+ndeath;j++){
  for (i=1; i<=10; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    if((Ndum[i]!=0) && (i<=ncov)){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      Tvaraff[ij]=i;            }
      ij++;          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++) {
     cptcoveff=ij-1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
           
 /*********** Health Expectancies ****************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            savm=oldm;
 {            oldm=newm;
   /* Health expectancies */          } /* end mult */
   int i, j, nhstepm, hstepm, h;        
   double age, agelim,hf;          s1=s[mw[mi][i]][i];
   double ***p3mat;          s2=s[mw[mi+1][i]][i];
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fprintf(ficreseij,"# Health expectancies\n");          ipmx +=1;
   fprintf(ficreseij,"# Age");          sw += weight[i];
   for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(j=1; j<=nlstate;j++)          /*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]);*/
       fprintf(ficreseij," %1d-%1d",i,j);        } /* end of wave */
   fprintf(ficreseij,"\n");      } /* end of individual */
     } /* End of if */
   hstepm=1*YEARM; /*  Every j years of age (in month) */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* 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 */
   agelim=AGESUP;    return -l;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  }
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  /*************** log-likelihood *************/
     /* Typically if 20 years = 20*12/6=40 stepm */  double funcone( double *x)
     if (stepm >= YEARM) hstepm=1;  {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    /* Same as likeli but slower because of a lot of printf and if */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, ii, j, k, mi, d, kk;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double l, ll[NLSTATEMAX], cov[NCOVMAX];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double **out;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double lli; /* Individual log likelihood */
     double llt;
     int s1, s2;
     for(i=1; i<=nlstate;i++)    double bbh, survp;
       for(j=1; j<=nlstate;j++)    /*extern weight */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    /* We are differentiating ll according to initial status */
           eij[i][j][(int)age] +=p3mat[i][j][h];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         }    /*for(i=1;i<imx;i++) 
          printf(" %d\n",s[4][i]);
     hf=1;    */
     if (stepm >= YEARM) hf=stepm/YEARM;    cov[1]=1.;
     fprintf(ficreseij,"%.0f",age );  
     for(i=1; i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficreseij,"\n");      for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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);
 /************ Variance ******************/          }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for(d=0; d<dh[mi][i]; d++){
 {          newm=savm;
   /* Variance of health expectancies */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for (kk=1; kk<=cptcovage;kk++) {
   double **newm;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **dnewm,**doldm;          }
   int i, j, nhstepm, hstepm, h;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int k, cptcode;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *xp;          savm=oldm;
   double **gp, **gm;          oldm=newm;
   double ***gradg, ***trgradg;        } /* end mult */
   double ***p3mat;        
   double age,agelim;        s1=s[mw[mi][i]][i];
   int theta;        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
    fprintf(ficresvij,"# Covariances of life expectancies\n");        /* bias is positive if real duration
   fprintf(ficresvij,"# Age");         * is higher than the multiple of stepm and negative otherwise.
   for(i=1; i<=nlstate;i++)         */
     for(j=1; j<=nlstate;j++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficresvij,"\n");        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   xp=vector(1,npar);        } else if(mle==2){
   dnewm=matrix(1,nlstate,1,npar);          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 */
   doldm=matrix(1,nlstate,1,nlstate);        } else if(mle==3){  /* exponential inter-extrapolation */
            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 */
   hstepm=1*YEARM; /* Every year of age */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          lli=log(out[s1][s2]); /* Original formula */
   agelim = AGESUP;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          lli=log(out[s1][s2]); /* Original formula */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /* End of if */
     if (stepm >= YEARM) hstepm=1;        ipmx +=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        sw += weight[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     gp=matrix(0,nhstepm,1,nlstate);        if(globpr){
     gm=matrix(0,nhstepm,1,nlstate);          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
     for(theta=1; theta <=npar; theta++){                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for(i=1; i<=npar; i++){ /* Computes gradient */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       }            llt +=ll[k]*gipmx/gsw;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
           fprintf(ficresilk," %10.6f\n", -llt);
       if (popbased==1) {        }
         for(i=1; i<=nlstate;i++)      } /* end of wave */
           prlim[i][i]=probs[(int)age][i][ij];    } /* end of individual */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<= nlstate; j++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(h=0; h<=nhstepm; h++){    if(globpr==0){ /* First time we count the contributions and weights */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      gipmx=ipmx;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      gsw=sw;
         }    }
       }    return -l;
      }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /*************** function likelione ***********/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
       if (popbased==1) {    /* This routine should help understanding what is done with 
         for(i=1; i<=nlstate;i++)       the selection of individuals/waves and
           prlim[i][i]=probs[(int)age][i][ij];       to check the exact contribution to the likelihood.
       }       Plotting could be done.
      */
       for(j=1; j<= nlstate; j++){    int k;
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    if(*globpri !=0){ /* Just counts and sums, no printings */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      strcpy(fileresilk,"ilk"); 
         }      strcat(fileresilk,fileres);
       }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
       for(j=1; j<= nlstate; j++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         for(h=0; h<=nhstepm; h++){      }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      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");
         }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     } /* End theta */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for(h=0; h<=nhstepm; h++)    }
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)    *fretone=(*funcone)(p);
           trgradg[h][j][theta]=gradg[h][theta][j];    if(*globpri !=0){
       fclose(ficresilk);
     for(i=1;i<=nlstate;i++)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       for(j=1;j<=nlstate;j++)      fflush(fichtm); 
         vareij[i][j][(int)age] =0.;    } 
     for(h=0;h<=nhstepm;h++){    return;
       for(k=0;k<=nhstepm;k++){  }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)  /*********** Maximum Likelihood Estimation ***************/
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       }  {
     }    int i,j, iter;
     h=1;    double **xi;
     if (stepm >= YEARM) h=stepm/YEARM;    double fret;
     fprintf(ficresvij,"%.0f ",age );    double fretone; /* Only one call to likelihood */
     for(i=1; i<=nlstate;i++)    /*  char filerespow[FILENAMELENGTH];*/
       for(j=1; j<=nlstate;j++){    xi=matrix(1,npar,1,npar);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++)
     fprintf(ficresvij,"\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
     free_matrix(gp,0,nhstepm,1,nlstate);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     free_matrix(gm,0,nhstepm,1,nlstate);    strcpy(filerespow,"pow"); 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    strcat(filerespow,fileres);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("Problem with resultfile: %s\n", filerespow);
   } /* End age */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
   free_vector(xp,1,npar);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   free_matrix(doldm,1,nlstate,1,npar);    for (i=1;i<=nlstate;i++)
   free_matrix(dnewm,1,nlstate,1,nlstate);      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 }    fprintf(ficrespow,"\n");
   
 /************ Variance of prevlim ******************/    powell(p,xi,npar,ftol,&iter,&fret,func);
 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)  
 {    fclose(ficrespow);
   /* Variance of prevalence limit */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **newm;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;  }
   int k, cptcode;  
   double *xp;  /**** Computes Hessian and covariance matrix ***/
   double *gp, *gm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double **gradg, **trgradg;  {
   double age,agelim;    double  **a,**y,*x,pd;
   int theta;    double **hess;
        int i, j,jk;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    int *indx;
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       fprintf(ficresvpl," %1d-%1d",i,i);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   fprintf(ficresvpl,"\n");    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
   xp=vector(1,npar);    double gompertz(double p[]);
   dnewm=matrix(1,nlstate,1,npar);    hess=matrix(1,npar,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);  
      printf("\nCalculation of the hessian matrix. Wait...\n");
   hstepm=1*YEARM; /* Every year of age */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=1;i<=npar;i++){
   agelim = AGESUP;      printf("%d",i);fflush(stdout);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficlog,"%d",i);fflush(ficlog);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     
     if (stepm >= YEARM) hstepm=1;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      
     gradg=matrix(1,npar,1,nlstate);      /*  printf(" %f ",p[i]);
     gp=vector(1,nlstate);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     gm=vector(1,nlstate);    }
     
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (j=1;j<=npar;j++)  {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if (j>i) { 
       }          printf(".%d%d",i,j);fflush(stdout);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       for(i=1;i<=nlstate;i++)          hess[i][j]=hessij(p,delti,i,j,func,npar);
         gp[i] = prlim[i][i];          
              hess[j][i]=hess[i][j];    
       for(i=1; i<=npar; i++) /* Computes gradient */          /*printf(" %lf ",hess[i][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];    printf("\n");
     fprintf(ficlog,"\n");
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     } /* End theta */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
     trgradg =matrix(1,nlstate,1,npar);    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     for(j=1; j<=nlstate;j++)    x=vector(1,npar);
       for(theta=1; theta <=npar; theta++)    indx=ivector(1,npar);
         trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for(i=1;i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for (j=1;j<=npar;j++) {
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for (i=1;i<=npar;i++) x[i]=0;
     for(i=1;i<=nlstate;i++)      x[j]=1;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
     fprintf(ficresvpl,"%.0f ",age );        matcov[i][j]=x[i];
     for(i=1; i<=nlstate;i++)      }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);    printf("\n#Hessian matrix#\n");
     free_vector(gm,1,nlstate);    fprintf(ficlog,"\n#Hessian matrix#\n");
     free_matrix(gradg,1,npar,1,nlstate);    for (i=1;i<=npar;i++) { 
     free_matrix(trgradg,1,nlstate,1,npar);      for (j=1;j<=npar;j++) { 
   } /* End age */        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
   free_vector(xp,1,npar);      }
   free_matrix(doldm,1,nlstate,1,npar);      printf("\n");
   free_matrix(dnewm,1,nlstate,1,nlstate);      fprintf(ficlog,"\n");
     }
 }  
     /* Recompute Inverse */
 /************ Variance of one-step probabilities  ******************/    for (i=1;i<=npar;i++)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 {    ludcmp(a,npar,indx,&pd);
   int i, j;  
   int k=0, cptcode;    /*  printf("\n#Hessian matrix recomputed#\n");
   double **dnewm,**doldm;  
   double *xp;    for (j=1;j<=npar;j++) {
   double *gp, *gm;      for (i=1;i<=npar;i++) x[i]=0;
   double **gradg, **trgradg;      x[j]=1;
   double age,agelim, cov[NCOVMAX];      lubksb(a,npar,indx,x);
   int theta;      for (i=1;i<=npar;i++){ 
   char fileresprob[FILENAMELENGTH];        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
   strcpy(fileresprob,"prob");        fprintf(ficlog,"%.3e ",y[i][j]);
   strcat(fileresprob,fileres);      }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      printf("\n");
     printf("Problem with resultfile: %s\n", fileresprob);      fprintf(ficlog,"\n");
   }    }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    */
    
     free_matrix(a,1,npar,1,npar);
   xp=vector(1,npar);    free_matrix(y,1,npar,1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_vector(x,1,npar);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    free_ivector(indx,1,npar);
      free_matrix(hess,1,npar,1,npar);
   cov[1]=1;  
   for (age=bage; age<=fage; age ++){  
     cov[2]=age;  }
     gradg=matrix(1,npar,1,9);  
     trgradg=matrix(1,9,1,npar);  /*************** hessian matrix ****************/
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  {
        int i;
     for(theta=1; theta <=npar; theta++){    int l=1, lmax=20;
       for(i=1; i<=npar; i++)    double k1,k2;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double p2[NPARMAX+1];
          double res;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        double fx;
       k=0;    int k=0,kmax=10;
       for(i=1; i<= (nlstate+ndeath); i++){    double l1;
         for(j=1; j<=(nlstate+ndeath);j++){  
            k=k+1;    fx=func(x);
           gp[k]=pmmij[i][j];    for (i=1;i<=npar;i++) p2[i]=x[i];
         }    for(l=0 ; l <=lmax; l++){
       }      l1=pow(10,l);
       delts=delt;
       for(i=1; i<=npar; i++)      for(k=1 ; k <kmax; k=k+1){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        delt = delta*(l1*k);
            p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        p2[theta]=x[theta]-delt;
       k=0;        k2=func(p2)-fx;
       for(i=1; i<=(nlstate+ndeath); i++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(j=1; j<=(nlstate+ndeath);j++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           k=k+1;        
           gm[k]=pmmij[i][j];  #ifdef DEBUG
         }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
        #endif
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     }          k=kmax;
         }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(theta=1; theta <=npar; theta++)          k=kmax; l=lmax*10.;
       trgradg[j][theta]=gradg[theta][j];        }
          else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          delts=delt;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        }
       }
      pmij(pmmij,cov,ncovmodel,x,nlstate);    }
     delti[theta]=delts;
      k=0;    return res; 
      for(i=1; i<=(nlstate+ndeath); i++){    
        for(j=1; j<=(nlstate+ndeath);j++){  }
          k=k+1;  
          gm[k]=pmmij[i][j];  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         }  {
      }    int i;
          int l=1, l1, lmax=20;
      /*printf("\n%d ",(int)age);    double k1,k2,k3,k4,res,fx;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double p2[NPARMAX+1];
            int k;
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    fx=func(x);
      }*/    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   fprintf(ficresprob,"\n%d ",(int)age);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      k1=func(p2)-fx;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      k3=func(p2)-fx;
 }    
  free_vector(xp,1,npar);      p2[thetai]=x[thetai]-delti[thetai]/k;
 fclose(ficresprob);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  exit(0);      k4=func(p2)-fx;
 }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
 /***********************************************/      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
 /**************** Main Program *****************/      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
     }
 /*int main(int argc, char *argv[])*/    return res;
 int main()  }
 {  
   /************** Inverse of matrix **************/
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  void ludcmp(double **a, int n, int *indx, double *d) 
   double agedeb, agefin,hf;  { 
   double agemin=1.e20, agemax=-1.e20;    int i,imax,j,k; 
     double big,dum,sum,temp; 
   double fret;    double *vv; 
   double **xi,tmp,delta;   
     vv=vector(1,n); 
   double dum; /* Dummy variable */    *d=1.0; 
   double ***p3mat;    for (i=1;i<=n;i++) { 
   int *indx;      big=0.0; 
   char line[MAXLINE], linepar[MAXLINE];      for (j=1;j<=n;j++) 
   char title[MAXLINE];        if ((temp=fabs(a[i][j])) > big) big=temp; 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      vv[i]=1.0/big; 
   char filerest[FILENAMELENGTH];    } 
   char fileregp[FILENAMELENGTH];    for (j=1;j<=n;j++) { 
   char popfile[FILENAMELENGTH];      for (i=1;i<j;i++) { 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        sum=a[i][j]; 
   int firstobs=1, lastobs=10;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   int sdeb, sfin; /* Status at beginning and end */        a[i][j]=sum; 
   int c,  h , cpt,l;      } 
   int ju,jl, mi;      big=0.0; 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      for (i=j;i<=n;i++) { 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        sum=a[i][j]; 
   int mobilav=0,popforecast=0;        for (k=1;k<j;k++) 
   int hstepm, nhstepm;          sum -= a[i][k]*a[k][j]; 
   int *popage;/*boolprev=0 if date and zero if wave*/        a[i][j]=sum; 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   double bage, fage, age, agelim, agebase;          imax=i; 
   double ftolpl=FTOL;        } 
   double **prlim;      } 
   double *severity;      if (j != imax) { 
   double ***param; /* Matrix of parameters */        for (k=1;k<=n;k++) { 
   double  *p;          dum=a[imax][k]; 
   double **matcov; /* Matrix of covariance */          a[imax][k]=a[j][k]; 
   double ***delti3; /* Scale */          a[j][k]=dum; 
   double *delti; /* Scale */        } 
   double ***eij, ***vareij;        *d = -(*d); 
   double **varpl; /* Variances of prevalence limits by age */        vv[imax]=vv[j]; 
   double *epj, vepp;      } 
   double kk1, kk2;      indx[j]=imax; 
   double *popeffectif,*popcount;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;      if (j != n) { 
   double yp,yp1,yp2;        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";      } 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    } 
     free_vector(vv,1,n);  /* Doesn't work */
   ;
   char z[1]="c", occ;  } 
 #include <sys/time.h>  
 #include <time.h>  void lubksb(double **a, int n, int *indx, double b[]) 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  { 
      int i,ii=0,ip,j; 
   /* long total_usecs;    double sum; 
   struct timeval start_time, end_time;   
      for (i=1;i<=n;i++) { 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      ip=indx[i]; 
       sum=b[ip]; 
       b[ip]=b[i]; 
   printf("\nIMACH, Version 0.7");      if (ii) 
   printf("\nEnter the parameter file name: ");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
 #ifdef windows      b[i]=sum; 
   scanf("%s",pathtot);    } 
   getcwd(pathcd, size);    for (i=n;i>=1;i--) { 
   /*cygwin_split_path(pathtot,path,optionfile);      sum=b[i]; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   /* cutv(path,optionfile,pathtot,'\\');*/      b[i]=sum/a[i][i]; 
     } 
 split(pathtot, path,optionfile);  } 
   chdir(path);  
   replace(pathc,path);  /************ Frequencies ********************/
 #endif  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[])
 #ifdef unix  {  /* Some frequencies */
   scanf("%s",optionfile);    
 #endif    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
 /*-------- arguments in the command line --------*/    double ***freq; /* Frequencies */
     double *pp, **prop;
   strcpy(fileres,"r");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   strcat(fileres, optionfile);    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
   /*---------arguments file --------*/    
     pp=vector(1,nlstate);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    prop=matrix(1,nlstate,iagemin,iagemax+3);
     printf("Problem with optionfile %s\n",optionfile);    strcpy(fileresp,"p");
     goto end;    strcat(fileresp,fileres);
   }    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
   strcpy(filereso,"o");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   strcat(filereso,fileres);      exit(0);
   if((ficparo=fopen(filereso,"w"))==NULL) {    }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   }    j1=0;
     
   /* Reads comments: lines beginning with '#' */    j=cptcoveff;
   while((c=getc(ficpar))=='#' && c!= EOF){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    first=1;
     puts(line);  
     fputs(line,ficparo);    for(k1=1; k1<=j;k1++){
   }      for(i1=1; i1<=ncodemax[k1];i1++){
   ungetc(c,ficpar);        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   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);          scanf("%d", i);*/
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        for (i=-5; i<=nlstate+ndeath; i++)  
   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);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
 while((c=getc(ficpar))=='#' && c!= EOF){            for(m=iagemin; m <= iagemax+3; m++)
     ungetc(c,ficpar);              freq[i][jk][m]=0;
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for (i=1; i<=nlstate; i++)  
     fputs(line,ficparo);        for(m=iagemin; m <= iagemax+3; m++)
   }          prop[i][m]=0;
   ungetc(c,ficpar);        
          dateintsum=0;
            k2cpt=0;
   covar=matrix(0,NCOVMAX,1,n);        for (i=1; i<=imx; i++) {
   cptcovn=0;          bool=1;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   ncovmodel=2+cptcovn;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                bool=0;
            }
   /* Read guess parameters */          if (bool==1){
   /* Reads comments: lines beginning with '#' */            for(m=firstpass; m<=lastpass; m++){
   while((c=getc(ficpar))=='#' && c!= EOF){              k2=anint[m][i]+(mint[m][i]/12.);
     ungetc(c,ficpar);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fgets(line, MAXLINE, ficpar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     puts(line);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fputs(line,ficparo);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                if (m<lastpass) {
   ungetc(c,ficpar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                }
     for(i=1; i <=nlstate; i++)                
     for(j=1; j <=nlstate+ndeath-1; j++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);                  dateintsum=dateintsum+k2;
       fprintf(ficparo,"%1d%1d",i1,j1);                  k2cpt++;
       printf("%1d%1d",i,j);                }
       for(k=1; k<=ncovmodel;k++){                /*}*/
         fscanf(ficpar," %lf",&param[i][j][k]);            }
         printf(" %lf",param[i][j][k]);          }
         fprintf(ficparo," %lf",param[i][j][k]);        }
       }         
       fscanf(ficpar,"\n");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       printf("\n");  fprintf(ficresp, "#Local time at start: %s", strstart);
       fprintf(ficparo,"\n");        if  (cptcovn>0) {
     }          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          fprintf(ficresp, "**********\n#");
         }
   p=param[1][1];        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   /* Reads comments: lines beginning with '#' */        fprintf(ficresp, "\n");
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        for(i=iagemin; i <= iagemax+3; i++){
     fgets(line, MAXLINE, ficpar);          if(i==iagemax+3){
     puts(line);            fprintf(ficlog,"Total");
     fputs(line,ficparo);          }else{
   }            if(first==1){
   ungetc(c,ficpar);              first=0;
               printf("See log file for details...\n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            fprintf(ficlog,"Age %d", i);
   for(i=1; i <=nlstate; i++){          }
     for(j=1; j <=nlstate+ndeath-1; j++){          for(jk=1; jk <=nlstate ; jk++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       printf("%1d%1d",i,j);              pp[jk] += freq[jk][m][i]; 
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       for(k=1; k<=ncovmodel;k++){          for(jk=1; jk <=nlstate ; jk++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);            for(m=-1, pos=0; m <=0 ; m++)
         printf(" %le",delti3[i][j][k]);              pos += freq[jk][m][i];
         fprintf(ficparo," %le",delti3[i][j][k]);            if(pp[jk]>=1.e-10){
       }              if(first==1){
       fscanf(ficpar,"\n");              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       printf("\n");              }
       fprintf(ficparo,"\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }            }else{
   }              if(first==1)
   delti=delti3[1][1];                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);          for(jk=1; jk <=nlstate ; jk++){
     puts(line);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     fputs(line,ficparo);              pp[jk] += freq[jk][m][i];
   }          }       
   ungetc(c,ficpar);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
              pos += pp[jk];
   matcov=matrix(1,npar,1,npar);            posprop += prop[jk][i];
   for(i=1; i <=npar; i++){          }
     fscanf(ficpar,"%s",&str);          for(jk=1; jk <=nlstate ; jk++){
     printf("%s",str);            if(pos>=1.e-5){
     fprintf(ficparo,"%s",str);              if(first==1)
     for(j=1; j <=i; j++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fscanf(ficpar," %le",&matcov[i][j]);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       printf(" %.5le",matcov[i][j]);            }else{
       fprintf(ficparo," %.5le",matcov[i][j]);              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fscanf(ficpar,"\n");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("\n");            }
     fprintf(ficparo,"\n");            if( i <= iagemax){
   }              if(pos>=1.e-5){
   for(i=1; i <=npar; i++)                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     for(j=i+1;j<=npar;j++)                /*probs[i][jk][j1]= pp[jk]/pos;*/
       matcov[i][j]=matcov[j][i];                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                  }
   printf("\n");              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
     /*-------- data file ----------*/          }
     if((ficres =fopen(fileres,"w"))==NULL) {          
       printf("Problem with resultfile: %s\n", fileres);goto end;          for(jk=-1; jk <=nlstate+ndeath; jk++)
     }            for(m=-1; m <=nlstate+ndeath; m++)
     fprintf(ficres,"#%s\n",version);              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
     if((fic=fopen(datafile,"r"))==NULL)    {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       printf("Problem with datafile: %s\n", datafile);goto end;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     }              }
           if(i <= iagemax)
     n= lastobs;            fprintf(ficresp,"\n");
     severity = vector(1,maxwav);          if(first==1)
     outcome=imatrix(1,maxwav+1,1,n);            printf("Others in log...\n");
     num=ivector(1,n);          fprintf(ficlog,"\n");
     moisnais=vector(1,n);        }
     annais=vector(1,n);      }
     moisdc=vector(1,n);    }
     andc=vector(1,n);    dateintmean=dateintsum/k2cpt; 
     agedc=vector(1,n);   
     cod=ivector(1,n);    fclose(ficresp);
     weight=vector(1,n);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    free_vector(pp,1,nlstate);
     mint=matrix(1,maxwav,1,n);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     anint=matrix(1,maxwav,1,n);    /* End of Freq */
     s=imatrix(1,maxwav+1,1,n);  }
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);  /************ Prevalence ********************/
     ncodemax=ivector(1,8);  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)
   {  
     i=1;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     while (fgets(line, MAXLINE, fic) != NULL)    {       in each health status at the date of interview (if between dateprev1 and dateprev2).
       if ((i >= firstobs) && (i <=lastobs)) {       We still use firstpass and lastpass as another selection.
            */
         for (j=maxwav;j>=1;j--){   
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           strcpy(line,stra);    double ***freq; /* Frequencies */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double *pp, **prop;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double pos,posprop; 
         }    double  y2; /* in fractional years */
            int iagemin, iagemax;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    iagemin= (int) agemin;
     iagemax= (int) agemax;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*pp=vector(1,nlstate);*/
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    j1=0;
         for (j=ncov;j>=1;j--){    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         num[i]=atol(stra);    
            for(k1=1; k1<=j;k1++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      for(i1=1; i1<=ncodemax[k1];i1++){
           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;}*/        j1++;
         
         i=i+1;        for (i=1; i<=nlstate; i++)  
       }          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0.0;
     /* printf("ii=%d", ij);       
        scanf("%d",i);*/        for (i=1; i<=imx; i++) { /* Each individual */
   imx=i-1; /* Number of individuals */          bool=1;
           if  (cptcovn>0) {
   /* for (i=1; i<=imx; i++){            for (z1=1; z1<=cptcoveff; z1++) 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                bool=0;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          } 
     }          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for (i=1; i<=imx; i++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     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]));*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /* Calculation of the number of parameter from char model*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   Tvar=ivector(1,15);                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); 
   Tprod=ivector(1,15);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   Tvaraff=ivector(1,15);                  /*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]]);*/
   Tvard=imatrix(1,15,1,2);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   Tage=ivector(1,15);                        prop[s[m][i]][iagemax+3] += weight[i]; 
                    } 
   if (strlen(model) >1){              }
     j=0, j1=0, k1=1, k2=1;            } /* end selection of waves */
     j=nbocc(model,'+');          }
     j1=nbocc(model,'*');        }
     cptcovn=j+1;        for(i=iagemin; i <= iagemax+3; i++){  
     cptcovprod=j1;          
              for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                posprop += prop[jk][i]; 
     strcpy(modelsav,model);          } 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);          for(jk=1; jk <=nlstate ; jk++){     
       goto end;            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
                    probs[i][jk][j1]= prop[jk][i]/posprop;
     for(i=(j+1); i>=1;i--){              } 
       cutv(stra,strb,modelsav,'+');            } 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          }/* end jk */ 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        }/* end i */ 
       /*scanf("%d",i);*/      } /* end i1 */
       if (strchr(strb,'*')) {    } /* end k1 */
         cutv(strd,strc,strb,'*');    
         if (strcmp(strc,"age")==0) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           cptcovprod--;    /*free_vector(pp,1,nlstate);*/
           cutv(strb,stre,strd,'V');    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           Tvar[i]=atoi(stre);  }  /* End of prevalence */
           cptcovage++;  
             Tage[cptcovage]=i;  /************* Waves Concatenation ***************/
             /*printf("stre=%s ", stre);*/  
         }  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)
         else if (strcmp(strd,"age")==0) {  {
           cptcovprod--;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           cutv(strb,stre,strc,'V');       Death is a valid wave (if date is known).
           Tvar[i]=atoi(stre);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           cptcovage++;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           Tage[cptcovage]=i;       and mw[mi+1][i]. dh depends on stepm.
         }       */
         else {  
           cutv(strb,stre,strc,'V');    int i, mi, m;
           Tvar[i]=ncov+k1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           cutv(strb,strc,strd,'V');       double sum=0., jmean=0.;*/
           Tprod[k1]=i;    int first;
           Tvard[k1][1]=atoi(strc);    int j, k=0,jk, ju, jl;
           Tvard[k1][2]=atoi(stre);    double sum=0.;
           Tvar[cptcovn+k2]=Tvard[k1][1];    first=0;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    jmin=1e+5;
           for (k=1; k<=lastobs;k++)    jmax=-1;
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    jmean=0.;
           k1++;    for(i=1; i<=imx; i++){
           k2=k2+2;      mi=0;
         }      m=firstpass;
       }      while(s[m][i] <= nlstate){
       else {        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          mw[++mi][i]=m;
        /*  scanf("%d",i);*/        if(m >=lastpass)
       cutv(strd,strc,strb,'V');          break;
       Tvar[i]=atoi(strc);        else
       }          m++;
       strcpy(modelsav,stra);        }/* end while */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      if (s[m][i] > nlstate){
         scanf("%d",i);*/        mi++;     /* Death is another wave */
     }        /* if(mi==0)  never been interviewed correctly before death */
 }           /* Only death is a correct wave */
          mw[mi][i]=m;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      }
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/      wav[i]=mi;
     fclose(fic);      if(mi==0){
         nbwarn++;
     /*  if(mle==1){*/        if(first==0){
     if (weightopt != 1) { /* Maximisation without weights*/          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       for(i=1;i<=n;i++) weight[i]=1.0;          first=1;
     }        }
     /*-calculation of age at interview from date of interview and age at death -*/        if(first==1){
     agev=matrix(1,maxwav,1,imx);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
    for (i=1; i<=imx; i++)      } /* end mi==0 */
      for(m=2; (m<= maxwav); m++)    } /* End individuals */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;    for(i=1; i<=imx; i++){
          s[m][i]=-1;      for(mi=1; mi<wav[i];mi++){
        }        if (stepm <=0)
              dh[mi][i]=1;
     for (i=1; i<=imx; i++)  {        else{
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for(m=1; (m<= maxwav); m++){            if (agedc[i] < 2*AGESUP) {
         if(s[m][i] >0){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           if (s[m][i] == nlstate+1) {              if(j==0) j=1;  /* Survives at least one month after exam */
             if(agedc[i]>0)              else if(j<0){
               if(moisdc[i]!=99 && andc[i]!=9999)                nberr++;
               agev[m][i]=agedc[i];                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             else {                j=1; /* Temporary Dangerous patch */
               if (andc[i]!=9999){                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);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               agev[m][i]=-1;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }              }
             }              k=k+1;
           }              if (j >= jmax){
           else if(s[m][i] !=9){ /* Should no more exist */                jmax=j;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                ijmax=i;
             if(mint[m][i]==99 || anint[m][i]==9999)              }
               agev[m][i]=1;              if (j <= jmin){
             else if(agev[m][i] <agemin){                jmin=j;
               agemin=agev[m][i];                ijmin=i;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              }
             }              sum=sum+j;
             else if(agev[m][i] >agemax){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               agemax=agev[m][i];              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,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];*/          else{
             /*   agev[m][i] = age[i]+2*m;*/            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]); */
           else { /* =9 */  
             agev[m][i]=1;            k=k+1;
             s[m][i]=-1;            if (j >= jmax) {
           }              jmax=j;
         }              ijmax=i;
         else /*= 0 Unknown */            }
           agev[m][i]=1;            else if (j <= jmin){
       }              jmin=j;
                  ijmin=i;
     }            }
     for (i=1; i<=imx; i++)  {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(m=1; (m<= maxwav); m++){            /*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 (s[m][i] > (nlstate+ndeath)) {            if(j<0){
           printf("Error: Wrong value in nlstate or ndeath\n");                nberr++;
           goto end;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       }            }
     }            sum=sum+j;
           }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          jk= j/stepm;
           jl= j -jk*stepm;
     free_vector(severity,1,maxwav);          ju= j -(jk+1)*stepm;
     free_imatrix(outcome,1,maxwav+1,1,n);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     free_vector(moisnais,1,n);            if(jl==0){
     free_vector(annais,1,n);              dh[mi][i]=jk;
     /* free_matrix(mint,1,maxwav,1,n);              bh[mi][i]=0;
        free_matrix(anint,1,maxwav,1,n);*/            }else{ /* We want a negative bias in order to only have interpolation ie
     free_vector(moisdc,1,n);                    * at the price of an extra matrix product in likelihood */
     free_vector(andc,1,n);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
                }
     wav=ivector(1,imx);          }else{
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            if(jl <= -ju){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
     /* Concatenates waves */                                   * is higher than the multiple of stepm and negative otherwise.
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                                   */
             }
             else{
       Tcode=ivector(1,100);              dh[mi][i]=jk+1;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              bh[mi][i]=ju;
       ncodemax[1]=1;            }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            if(dh[mi][i]==0){
                    dh[mi][i]=1; /* At least one step */
    codtab=imatrix(1,100,1,10);              bh[mi][i]=ju; /* At least one step */
    h=0;              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
    m=pow(2,cptcoveff);            }
            } /* end if mle */
    for(k=1;k<=cptcoveff; k++){        }
      for(i=1; i <=(m/pow(2,k));i++){      } /* end wave */
        for(j=1; j <= ncodemax[k]; j++){    }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    jmean=sum/k;
            h++;    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
            if (h>m) h=1;codtab[h][k]=j;    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
          }   }
        }  
      }  /*********** Tricode ****************************/
    }  void tricode(int *Tvar, int **nbcode, int imx)
      {
    /* Calculates basic frequencies. Computes observed prevalence at single age    
        and prints on file fileres'p'. */    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
        cptcoveff=0; 
       
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (k=0; k<maxncov; k++) Ndum[k]=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (k=1; k<=7; k++) ncodemax[k]=0;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                       modality*/ 
     /* For Powell, parameters are in a vector p[] starting at p[1]        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        Ndum[ij]++; /*store the modality */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     if(mle==1){                                         Tvar[j]. If V=sex and male is 0 and 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                                         female is 1, then  cptcode=1.*/
     }      }
      
     /*--------- results files --------------*/      for (i=0; i<=cptcode; i++) {
     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);        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 */
        }
   
    jk=1;      ij=1; 
    fprintf(ficres,"# Parameters\n");      for (i=1; i<=ncodemax[j]; i++) {
    printf("# Parameters\n");        for (k=0; k<= maxncov; k++) {
    for(i=1,jk=1; i <=nlstate; i++){          if (Ndum[k] != 0) {
      for(k=1; k <=(nlstate+ndeath); k++){            nbcode[Tvar[j]][ij]=k; 
        if (k != i)            /* 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; */
          {            
            printf("%d%d ",i,k);            ij++;
            fprintf(ficres,"%1d%1d ",i,k);          }
            for(j=1; j <=ncovmodel; j++){          if (ij > ncodemax[j]) break; 
              printf("%f ",p[jk]);        }  
              fprintf(ficres,"%f ",p[jk]);      } 
              jk++;    }  
            }  
            printf("\n");   for (k=0; k< maxncov; k++) Ndum[k]=0;
            fprintf(ficres,"\n");  
          }   for (i=1; i<=ncovmodel-2; i++) { 
      }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    }     ij=Tvar[i];
  if(mle==1){     Ndum[ij]++;
     /* Computing hessian and covariance matrix */   }
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);   ij=1;
  }   for (i=1; i<= maxncov; i++) {
     fprintf(ficres,"# Scales\n");     if((Ndum[i]!=0) && (i<=ncovcol)){
     printf("# Scales\n");       Tvaraff[ij]=i; /*For printing */
      for(i=1,jk=1; i <=nlstate; i++){       ij++;
       for(j=1; j <=nlstate+ndeath; j++){     }
         if (j!=i) {   }
           fprintf(ficres,"%1d%1d",i,j);   
           printf("%1d%1d",i,j);   cptcoveff=ij-1; /*Number of simple covariates*/
           for(k=1; k<=ncovmodel;k++){  }
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);  /*********** Health Expectancies ****************/
             jk++;  
           }  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[] )
           printf("\n");  
           fprintf(ficres,"\n");  {
         }    /* Health expectancies */
       }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
      }    double age, agelim, hf;
        double ***p3mat,***varhe;
     k=1;    double **dnewm,**doldm;
     fprintf(ficres,"# Covariance\n");    double *xp;
     printf("# Covariance\n");    double **gp, **gm;
     for(i=1;i<=npar;i++){    double ***gradg, ***trgradg;
       /*  if (k>nlstate) k=1;    int theta;
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    xp=vector(1,npar);
       fprintf(ficres,"%3d",i);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       printf("%3d",i);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       for(j=1; j<=i;j++){    
         fprintf(ficres," %.5e",matcov[i][j]);    fprintf(ficreseij,"# Local time at start: %s", strstart);
         printf(" %.5e",matcov[i][j]);    fprintf(ficreseij,"# Health expectancies\n");
       }    fprintf(ficreseij,"# Age");
       fprintf(ficres,"\n");    for(i=1; i<=nlstate;i++)
       printf("\n");      for(j=1; j<=nlstate;j++)
       k++;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     }    fprintf(ficreseij,"\n");
      
     while((c=getc(ficpar))=='#' && c!= EOF){    if(estepm < stepm){
       ungetc(c,ficpar);      printf ("Problem %d lower than %d\n",estepm, stepm);
       fgets(line, MAXLINE, ficpar);    }
       puts(line);    else  hstepm=estepm;   
       fputs(line,ficparo);    /* We compute the life expectancy from trapezoids spaced every estepm months
     }     * This is mainly to measure the difference between two models: for example
     ungetc(c,ficpar);     * 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 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);     * progression in between and thus overestimating or underestimating according
         * to the curvature of the survival function. If, for the same date, we 
     if (fage <= 2) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       bage = agemin;     * to compare the new estimate of Life expectancy with the same linear 
       fage = agemax;     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
   
     fprintf(ficres,"# agemin agemax for life expectancy.\n");    /* 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. 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       nhstepm is the number of hstepm from age to agelim 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
     while((c=getc(ficpar))=='#' && c!= EOF){       and note for a fixed period like estepm months */
     ungetc(c,ficpar);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fgets(line, MAXLINE, ficpar);       survival function given by stepm (the optimization length). Unfortunately it
     puts(line);       means that if the survival funtion is printed only each two years of age and if
     fputs(line,ficparo);       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.
   ungetc(c,ficpar);    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);  
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    agelim=AGESUP;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
            /* nhstepm age range expressed in number of stepm */
   while((c=getc(ficpar))=='#' && c!= EOF){      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     ungetc(c,ficpar);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fgets(line, MAXLINE, ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
     puts(line);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fputs(line,ficparo);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   ungetc(c,ficpar);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
        gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
    dateprev2=anprev2+mprev2/12.+jprev2/365.;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   fscanf(ficpar,"pop_based=%d\n",&popbased);   
    fprintf(ficparo,"pop_based=%d\n",popbased);    
    fprintf(ficres,"pop_based=%d\n",popbased);        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Computing  Variances of health expectancies */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);       for(theta=1; theta <=npar; theta++){
     puts(line);        for(i=1; i<=npar; i++){ 
     fputs(line,ficparo);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
   ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);        cptj=0;
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);            cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
  /*------------ gnuplot -------------*/              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 chdir(pathcd);            }
   if((ficgp=fopen("graph.plt","w"))==NULL) {          }
     printf("Problem with file graph.gp");goto end;        }
   }       
 #ifdef windows       
   fprintf(ficgp,"cd \"%s\" \n",pathc);        for(i=1; i<=npar; i++) 
 #endif          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 m=pow(2,cptcoveff);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
  /* 1eme*/        cptj=0;
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for(j=1; j<= nlstate; j++){
    for (k1=1; k1<= m ; k1 ++) {          for(i=1;i<=nlstate;i++){
             cptj=cptj+1;
 #ifdef windows            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     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);  
 #endif              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 #ifdef unix            }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          }
 #endif        }
         for(j=1; j<= nlstate*nlstate; j++)
 for (i=1; i<= nlstate ; i ++) {          for(h=0; h<=nhstepm-1; h++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   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 ++) {  /* End theta */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       for(h=0; h<=nhstepm-1; h++)
      for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate*nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(theta=1; theta <=npar; theta++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            trgradg[h][j][theta]=gradg[h][theta][j];
 }         
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix       for(i=1;i<=nlstate*nlstate;i++)
 fprintf(ficgp,"\nset ter gif small size 400,300");        for(j=1;j<=nlstate*nlstate;j++)
 #endif          varhe[i][j][(int)age] =0.;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   /*2 eme*/       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
   for (k1=1; k1<= m ; k1 ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
              for(i=1;i<=nlstate*nlstate;i++)
     for (i=1; i<= nlstate+1 ; i ++) {            for(j=1;j<=nlstate*nlstate;j++)
       k=2*i;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {      }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /* Computing expectancies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<=nlstate;i++)
 }          for(j=1; j<=nlstate;j++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            
       for (j=1; j<= nlstate+1 ; j ++) {  /* if((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]);*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficreseij,"%3.0f",age );
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      cptj=0;
       for (j=1; j<= nlstate+1 ; j ++) {      for(i=1; i<=nlstate;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          cptj++;
 }            fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        }
       else fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficreseij,"\n");
     }     
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   /*3eme*/      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   for (k1=1; k1<= m ; k1 ++) {    }
     for (cpt=1; cpt<= nlstate ; cpt ++) {    printf("\n");
       k=2+nlstate*(cpt-1);    fprintf(ficlog,"\n");
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {    free_vector(xp,1,npar);
         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);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     }  }
   }  
    /************ Variance ******************/
   /* CV preval stat */  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[])
   for (k1=1; k1<= m ; k1 ++) {  {
     for (cpt=1; cpt<nlstate ; cpt ++) {    /* Variance of health expectancies */
       k=3;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    /* double **newm;*/
       for (i=1; i< nlstate ; i ++)    double **dnewm,**doldm;
         fprintf(ficgp,"+$%d",k+i+1);    double **dnewmp,**doldmp;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    int i, j, nhstepm, hstepm, h, nstepm ;
          int k, cptcode;
       l=3+(nlstate+ndeath)*cpt;    double *xp;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double **gp, **gm;  /* for var eij */
       for (i=1; i< nlstate ; i ++) {    double ***gradg, ***trgradg; /*for var eij */
         l=3+(nlstate+ndeath)*cpt;    double **gradgp, **trgradgp; /* for var p point j */
         fprintf(ficgp,"+$%d",l+i+1);    double *gpp, *gmp; /* for var p point j */
       }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      double ***p3mat;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double age,agelim, hf;
     }    double ***mobaverage;
   }      int theta;
     char digit[4];
   /* proba elementaires */    char digitp[25];
    for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){    char fileresprobmorprev[FILENAMELENGTH];
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){    if(popbased==1){
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      if(mobilav!=0)
           /*fprintf(ficgp,"%s",alph[1]);*/        strcpy(digitp,"-populbased-mobilav-");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      else strcpy(digitp,"-populbased-nomobil-");
           jk++;    }
           fprintf(ficgp,"\n");    else 
         }      strcpy(digitp,"-stablbased-");
       }  
     }    if (mobilav!=0) {
     }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   for(jk=1; jk <=m; jk++) {        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
    i=1;      }
    for(k2=1; k2<=nlstate; k2++) {    }
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {    strcpy(fileresprobmorprev,"prmorprev"); 
        if (k != k2){    sprintf(digit,"%-d",ij);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 ij=1;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         for(j=3; j <=ncovmodel; j++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    strcat(fileresprobmorprev,fileres);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             ij++;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           else    }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         }   
           fprintf(ficgp,")/(1");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
            fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
         for(k1=1; k1 <=nlstate; k1++){      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 ij=1;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           for(j=3; j <=ncovmodel; j++){      fprintf(ficresprobmorprev," p.%-d SE",j);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(i=1; i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
             ij++;    }  
           }    fprintf(ficresprobmorprev,"\n");
           else    fprintf(ficgp,"\n# Routine varevsij");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* 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");
           fprintf(ficgp,")");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         }  /*   } */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");   fprintf(ficresvij, "#Local time at start: %s", strstart);
         i=i+ncovmodel;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
        }    fprintf(ficresvij,"# Age");
      }    for(i=1; i<=nlstate;i++)
    }      for(j=1; j<=nlstate;j++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   }    fprintf(ficresvij,"\n");
      
   fclose(ficgp);    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
 chdir(path);    doldm=matrix(1,nlstate,1,nlstate);
        dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     free_ivector(wav,1,imx);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     free_ivector(num,1,n);    gpp=vector(nlstate+1,nlstate+ndeath);
     free_vector(agedc,1,n);    gmp=vector(nlstate+1,nlstate+ndeath);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fclose(ficparo);    
     fclose(ficres);    if(estepm < stepm){
     /*  }*/      printf ("Problem %d lower than %d\n",estepm, stepm);
        }
    /*________fin mle=1_________*/    else  hstepm=estepm;   
        /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         nhstepm is the number of hstepm from age to agelim 
     /* No more information from the sample is required now */       nstepm is the number of stepm from age to agelin. 
   /* Reads comments: lines beginning with '#' */       Look at hpijx to understand the reason of that which relies in memory size
   while((c=getc(ficpar))=='#' && c!= EOF){       and note for a fixed period like k years */
     ungetc(c,ficpar);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fgets(line, MAXLINE, ficpar);       survival function given by stepm (the optimization length). Unfortunately it
     puts(line);       means that if the survival funtion is printed every two years of age and if
     fputs(line,ficparo);       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.
   ungetc(c,ficpar);    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    agelim = AGESUP;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 /*--------- index.htm --------*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(optionfilehtm,optionfile);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   strcat(optionfilehtm,".htm");      gp=matrix(0,nhstepm,1,nlstate);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      gm=matrix(0,nhstepm,1,nlstate);
     printf("Problem with %s \n",optionfilehtm);goto end;  
   }  
       for(theta=1; theta <=npar; theta++){
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 Total number of observations=%d <br>        }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 <hr  size=\"2\" color=\"#EC5E5E\">        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        if (popbased==1) {
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          if(mobilav ==0){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            for(i=1; i<=nlstate;i++)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>              prlim[i][i]=probs[(int)age][i][ij];
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          }else{ /* mobilav */ 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>            for(i=1; i<=nlstate;i++)
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              prlim[i][i]=mobaverage[(int)age][i][ij];
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          }
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>        }
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
  fprintf(fichtm," <li>Graphs</li><p>");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
  m=cptcoveff;          }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        }
         /* This for computing probability of death (h=1 means
  j1=0;           computed over hstepm matrices product = hstepm*stepm months) 
  for(k1=1; k1<=m;k1++){           as a weighted average of prlim.
    for(i1=1; i1<=ncodemax[k1];i1++){        */
        j1++;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
        if (cptcovn > 0) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
          for (cpt=1; cpt<=cptcoveff;cpt++)        }    
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        /* end probability of death */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        for(cpt=1; cpt<nlstate;cpt++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>   
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        if (popbased==1) {
        }          if(mobilav ==0){
     for(cpt=1; cpt<=nlstate;cpt++) {            for(i=1; i<=nlstate;i++)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              prlim[i][i]=probs[(int)age][i][ij];
 interval) in state (%d): v%s%d%d.gif <br>          }else{ /* mobilav */ 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              for(i=1; i<=nlstate;i++)
      }              prlim[i][i]=mobaverage[(int)age][i][ij];
      for(cpt=1; cpt<=nlstate;cpt++) {          }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }        for(j=1; j<= nlstate; j++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          for(h=0; h<=nhstepm; h++){
 health expectancies in states (1) and (2): e%s%d.gif<br>            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 fprintf(fichtm,"\n</body>");          }
    }        }
  }        /* This for computing probability of death (h=1 means
 fclose(fichtm);           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   /*--------------- Prevalence limit --------------*/        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcpy(filerespl,"pl");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   strcat(filerespl,fileres);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        }    
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        /* end probability of death */
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        for(j=1; j<= nlstate; j++) /* vareij */
   fprintf(ficrespl,"#Prevalence limit\n");          for(h=0; h<=nhstepm; h++){
   fprintf(ficrespl,"#Age ");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          }
   fprintf(ficrespl,"\n");  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   prlim=matrix(1,nlstate,1,nlstate);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   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 */      } /* End theta */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   k=0;  
   agebase=agemin;      for(h=0; h<=nhstepm; h++) /* veij */
   agelim=agemax;        for(j=1; j<=nlstate;j++)
   ftolpl=1.e-10;          for(theta=1; theta <=npar; theta++)
   i1=cptcoveff;            trgradg[h][j][theta]=gradg[h][theta][j];
   if (cptcovn < 1){i1=1;}  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   for(cptcov=1;cptcov<=i1;cptcov++){        for(theta=1; theta <=npar; theta++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          trgradgp[j][theta]=gradgp[theta][j];
         k=k+1;    
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         for(j=1;j<=cptcoveff;j++)      for(i=1;i<=nlstate;i++)
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1;j<=nlstate;j++)
         fprintf(ficrespl,"******\n");          vareij[i][j][(int)age] =0.;
          
         for (age=agebase; age<=agelim; age++){      for(h=0;h<=nhstepm;h++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(k=0;k<=nhstepm;k++){
           fprintf(ficrespl,"%.0f",age );          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           for(i=1; i<=nlstate;i++)          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           fprintf(ficrespl," %.5f", prlim[i][i]);          for(i=1;i<=nlstate;i++)
           fprintf(ficrespl,"\n");            for(j=1;j<=nlstate;j++)
         }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
   fclose(ficrespl);    
       /* pptj */
   /*------------- h Pij x at various ages ------------*/      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
   printf("Computing pij: result on file '%s' \n", filerespij);      /*  x centered again */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   stepsize=(int) (stepm+YEARM-1)/YEARM;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   /*if (stepm<=24) stepsize=2;*/   
       if (popbased==1) {
   agelim=AGESUP;        if(mobilav ==0){
   hstepm=stepsize*YEARM; /* Every year of age */          for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
   k=0;          for(i=1; i<=nlstate;i++)
   for(cptcov=1;cptcov<=i1;cptcov++){            prlim[i][i]=mobaverage[(int)age][i][ij];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;      }
         fprintf(ficrespij,"\n#****** ");               
         for(j=1;j<=cptcoveff;j++)      /* This for computing probability of death (h=1 means
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fprintf(ficrespij,"******\n");         as a weighted average of prlim.
              */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }    
           oldm=oldms;savm=savms;      /* end probability of death */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           for(i=1; i<=nlstate;i++)      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
               fprintf(ficrespij," %1d-%1d",i,j);        for(i=1; i<=nlstate;i++){
           fprintf(ficrespij,"\n");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           for (h=0; h<=nhstepm; h++){        }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      } 
             for(i=1; i<=nlstate;i++)      fprintf(ficresprobmorprev,"\n");
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      fprintf(ficresvij,"%.0f ",age );
             fprintf(ficrespij,"\n");      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           fprintf(ficrespij,"\n");        }
         }      fprintf(ficresvij,"\n");
     }      free_matrix(gp,0,nhstepm,1,nlstate);
   }      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficrespij);    } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
   /*---------- Forecasting ------------------*/    free_vector(gmp,nlstate+1,nlstate+ndeath);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   strcpy(fileresf,"f");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   strcat(fileresf,fileres);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   free_matrix(mint,1,maxwav,1,n);    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);
   free_matrix(anint,1,maxwav,1,n);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   free_matrix(agev,1,maxwav,1,imx);  */
   /* Mobile average */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
     free_vector(xp,1,npar);
   if (mobilav==1) {    free_matrix(doldm,1,nlstate,1,nlstate);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(dnewm,1,nlstate,1,npar);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for (i=1; i<=nlstate;i++)    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           mobaverage[(int)agedeb][i][cptcod]=0.;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        fclose(ficresprobmorprev);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    fflush(ficgp);
       for (i=1; i<=nlstate;i++){    fflush(fichtm); 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  }  /* end varevsij */
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  /************ 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[])
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  {
         }    /* Variance of prevalence limit */
       }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     }      double **newm;
   }    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int k, cptcode;
   if (stepm<=12) stepsize=1;    double *xp;
     double *gp, *gm;
   agelim=AGESUP;    double **gradg, **trgradg;
   /*hstepm=stepsize*YEARM; *//* Every year of age */    double age,agelim;
   hstepm=1;    int theta;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
   yp1=modf(dateintmean,&yp);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   anprojmean=yp;    fprintf(ficresvpl,"# Age");
   yp2=modf((yp1*12),&yp);    for(i=1; i<=nlstate;i++)
   mprojmean=yp;        fprintf(ficresvpl," %1d-%1d",i,i);
   yp1=modf((yp2*30.5),&yp);    fprintf(ficresvpl,"\n");
   jprojmean=yp;  
   fprintf(ficresf,"Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   if (popforecast==1) {    doldm=matrix(1,nlstate,1,nlstate);
     if((ficpop=fopen(popfile,"r"))==NULL)    {    
       printf("Problem with population file : %s\n",popfile);goto end;    hstepm=1*YEARM; /* Every year of age */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     popage=ivector(0,AGESUP);    agelim = AGESUP;
     popeffectif=vector(0,AGESUP);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     popcount=vector(0,AGESUP);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
     i=1;        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)      gradg=matrix(1,npar,1,nlstate);
       {      gp=vector(1,nlstate);
         i=i+1;      gm=vector(1,nlstate);
       }  
     imx=i;      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   for(cptcov=1;cptcov<=i1;cptcov++){        for(i=1;i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          gp[i] = prlim[i][i];
       k=k+1;      
       fprintf(ficresf,"\n#******");        for(i=1; i<=npar; i++) /* Computes gradient */
       for(j=1;j<=cptcoveff;j++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }        for(i=1;i<=nlstate;i++)
       fprintf(ficresf,"******\n");          gm[i] = prlim[i][i];
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for(i=1;i<=nlstate;i++)
       if (popforecast==1)  fprintf(ficresf," [Population]");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        } /* End theta */
       for (cpt=0; cpt<=1;cpt++) {  
         fprintf(ficresf,"\n");      trgradg =matrix(1,nlstate,1,npar);
   fprintf(ficresf,"\nForecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
       for (agedeb=(fage-(1/12.)); agedeb>=(bage-(1/12.)); agedeb--){ /* If stepm=6 months */      for(j=1; j<=nlstate;j++)
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(theta=1; theta <=npar; theta++)
         nhstepm = nhstepm/hstepm;          trgradg[j][theta]=gradg[theta][j];
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/  
       for(i=1;i<=nlstate;i++)
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        varpl[i][(int)age] =0.;
         oldm=oldms;savm=savms;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
                      for(i=1;i<=nlstate;i++)
         for (h=0; h<=nhstepm; h++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           if (h==(int) (calagedate+12*cpt)) {  
             fprintf(ficresf,"h=%d ", h);      fprintf(ficresvpl,"%.0f ",age );
             fprintf(ficresf,"\n %f %f ",agedeb,agedeb+h*hstepm/YEARM*stepm);      for(i=1; i<=nlstate;i++)
           }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           for(j=1; j<=nlstate+ndeath;j++) {      fprintf(ficresvpl,"\n");
             kk1=0.;kk2=0;      free_vector(gp,1,nlstate);
             for(i=1; i<=nlstate;i++) {              free_vector(gm,1,nlstate);
               if (mobilav==1)      free_matrix(gradg,1,npar,1,nlstate);
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];      free_matrix(trgradg,1,nlstate,1,npar);
               else {    } /* End age */
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 /*  fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h],probs[(int)(agedeb)+1][i][cptcod]);*/    free_vector(xp,1,npar);
               }    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];  
             }  }
            
             if (h==(int)(calagedate+12*cpt)){  /************ Variance of one-step probabilities  ******************/
               fprintf(ficresf," %.3f", kk1);  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[])
                {
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    int i, j=0,  i1, k1, l1, t, tj;
             }    int k2, l2, j1,  z1;
           }    int k=0,l, cptcode;
         }    int first=1, first1;
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       }    double **dnewm,**doldm;
       }    double *xp;
     }    double *gp, *gm;
   }    double **gradg, **trgradg;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **mu;
   if (popforecast==1) {    double age,agelim, cov[NCOVMAX];
     free_ivector(popage,0,AGESUP);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     free_vector(popeffectif,0,AGESUP);    int theta;
     free_vector(popcount,0,AGESUP);    char fileresprob[FILENAMELENGTH];
   }    char fileresprobcov[FILENAMELENGTH];
   free_imatrix(s,1,maxwav+1,1,n);    char fileresprobcor[FILENAMELENGTH];
   free_vector(weight,1,n);  
   fclose(ficresf);    double ***varpij;
   /*---------- Health expectancies and variances ------------*/  
     strcpy(fileresprob,"prob"); 
   strcpy(filerest,"t");    strcat(fileresprob,fileres);
   strcat(filerest,fileres);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if((ficrest=fopen(filerest,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprob);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   strcpy(filerese,"e");      printf("Problem with resultfile: %s\n", fileresprobcov);
   strcat(filerese,fileres);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    strcpy(fileresprobcor,"probcor"); 
   }    strcat(fileresprobcor,fileres);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
  strcpy(fileresv,"v");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   strcat(fileresv,fileres);    }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   k=0;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresprob, "#Local time at start: %s", strstart);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       k=k+1;    fprintf(ficresprob,"# Age");
       fprintf(ficrest,"\n#****** ");    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcov,"# Age");
       fprintf(ficrest,"******\n");    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       fprintf(ficreseij,"\n#****** ");    fprintf(ficresprobcov,"# Age");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       fprintf(ficresvij,"******\n");      }  
    /* fprintf(ficresprob,"\n");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficresprobcov,"\n");
       oldm=oldms;savm=savms;    fprintf(ficresprobcor,"\n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);     */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   xp=vector(1,npar);
       oldm=oldms;savm=savms;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
          mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    first=1;
       fprintf(ficrest,"\n");    fprintf(ficgp,"\n# Routine varprob");
            fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       hf=1;    fprintf(fichtm,"\n");
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       for(age=bage; age <=fage ;age++){    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    file %s<br>\n",optionfilehtmcov);
         if (popbased==1) {    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
           for(i=1; i<=nlstate;i++)  and drawn. It helps understanding how is the covariance between two incidences.\
             prlim[i][i]=probs[(int)age][i][k];   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
         }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
          It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
         fprintf(ficrest," %.0f",age);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  standard deviations wide on each axis. <br>\
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
           }  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
           epj[nlstate+1] +=epj[j];  
         }    cov[1]=1;
         for(i=1, vepp=0.;i <=nlstate;i++)    tj=cptcoveff;
           for(j=1;j <=nlstate;j++)    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
             vepp += vareij[i][j][(int)age];    j1=0;
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    for(t=1; t<=tj;t++){
         for(j=1;j <=nlstate;j++){      for(i1=1; i1<=ncodemax[t];i1++){ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));        j1++;
         }        if  (cptcovn>0) {
         fprintf(ficrest,"\n");          fprintf(ficresprob, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprob, "**********\n#\n");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
  fclose(ficreseij);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  fclose(ficresvij);          fprintf(ficgp, "**********\n#\n");
   fclose(ficrest);          
   fclose(ficpar);          
   free_vector(epj,1,nlstate+1);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   /*  scanf("%d ",i); */          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\">");
   /*------- Variance limit prevalence------*/            
           fprintf(ficresprobcor, "\n#********** Variable ");    
 strcpy(fileresvpl,"vpl");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(fileresvpl,fileres);          fprintf(ficresprobcor, "**********\n#");    
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        
     exit(0);        for (age=bage; age<=fage; age ++){ 
   }          cov[2]=age;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
  k=0;          }
  for(cptcov=1;cptcov<=i1;cptcov++){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (k=1; k<=cptcovprod;k++)
      k=k+1;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      fprintf(ficresvpl,"\n#****** ");          
      for(j=1;j<=cptcoveff;j++)          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      fprintf(ficresvpl,"******\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
                gm=vector(1,(nlstate)*(nlstate+ndeath));
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      
      oldm=oldms;savm=savms;          for(theta=1; theta <=npar; theta++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            for(i=1; i<=npar; i++)
    }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
  }            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   fclose(ficresvpl);            
             k=0;
   /*---------- End : free ----------------*/            for(i=1; i<= (nlstate); i++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                gp[k]=pmmij[i][j];
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              }
              }
              
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);            for(i=1; i<=npar; i++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
              k=0;
   free_matrix(matcov,1,npar,1,npar);            for(i=1; i<=(nlstate); i++){
   free_vector(delti,1,npar);              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                gm[k]=pmmij[i][j];
               }
   printf("End of Imach\n");            }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       
              for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   /* 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);*/              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   /*printf("Total time was %d uSec.\n", total_usecs);*/          }
   /*------ End -----------*/  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
  end:              trgradg[j][theta]=gradg[theta][j];
 #ifdef windows          
  chdir(pathcd);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 #endif          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
            free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
  system("..\\gp37mgw\\wgnuplot graph.plt");          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 #ifdef windows          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   while (z[0] != 'q') {  
     chdir(pathcd);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          
     scanf("%s",z);          k=0;
     if (z[0] == 'c') system("./imach");          for(i=1; i<=(nlstate); i++){
     else if (z[0] == 'e') {            for(j=1; j<=(nlstate+ndeath);j++){
       chdir(path);              k=k+1;
       system(optionfilehtm);              mu[k][(int) age]=pmmij[i][j];
     }            }
     else if (z[0] == 'q') exit(0);          }
   }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
 #endif            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
 }              varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char 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: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (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(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.19  
changed lines
  Added in v.1.114


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