Diff for /imach/src/imach.c between versions 1.11 and 1.122

version 1.11, 2001/05/17 16:07:14 version 1.122, 2006/03/20 09:45:41
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 1.122  2006/03/20 09:45:41  brouard
   individuals from different ages are interviewed on their health status    (Module): Weights can have a decimal point as for
   or degree of  disability. At least a second wave of interviews    English (a comma might work with a correct LC_NUMERIC environment,
   ("longitudinal") should  measure each new individual health status.    otherwise the weight is truncated).
   Health expectancies are computed from the transistions observed between    Modification of warning when the covariates values are not 0 or
   waves and are computed for each degree of severity of disability (number    1.
   of life states). More degrees you consider, more time is necessary to    Version 0.98g
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.121  2006/03/16 17:45:01  lievre
   the probabibility to be observed in state j at the second wave conditional    * imach.c (Module): Comments concerning covariates added
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    * imach.c (Module): refinements in the computation of lli if
   is a covariate. If you want to have a more complex model than "constant and    status=-2 in order to have more reliable computation if stepm is
   age", you should modify the program where the markup    not 1 month. Version 0.98f
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
   The advantage that this computer programme claims, comes from that if the    status=-2 in order to have more reliable computation if stepm is
   delay between waves is not identical for each individual, or if some    not 1 month. Version 0.98f
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.119  2006/03/15 17:42:26  brouard
   hPijx is the probability to be    (Module): Bug if status = -2, the loglikelihood was
   observed in state i at age x+h conditional to the observed state i at age    computed as likelihood omitting the logarithm. Version O.98e
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.118  2006/03/14 18:20:07  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    (Module): varevsij Comments added explaining the second
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    table of variances if popbased=1 .
   and the contribution of each individual to the likelihood is simply hPijx.    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Version 0.98d
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.117  2006/03/14 17:16:22  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): varevsij Comments added explaining the second
            Institut national d'études démographiques, Paris.    table of variances if popbased=1 .
   This software have been partly granted by Euro-REVES, a concerted action    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   from the European Union.    (Module): Function pstamp added
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Version 0.98d
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.116  2006/03/06 10:29:27  brouard
   **********************************************************************/    (Module): Variance-covariance wrong links and
      varian-covariance of ej. is needed (Saito).
 #include <math.h>  
 #include <stdio.h>    Revision 1.115  2006/02/27 12:17:45  brouard
 #include <stdlib.h>    (Module): One freematrix added in mlikeli! 0.98c
 #include <unistd.h>  
     Revision 1.114  2006/02/26 12:57:58  brouard
 #define MAXLINE 256    (Module): Some improvements in processing parameter
 #define FILENAMELENGTH 80    filename with strsep.
 /*#define DEBUG*/  
 #define windows    Revision 1.113  2006/02/24 14:20:24  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Memory leaks checks with valgrind and:
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.111  2006/01/25 20:38:18  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): Lots of cleaning and bugs added (Gompertz)
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Comments can be added in data file. Missing date values
 #define MAXN 20000    can be a simple dot '.'.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.110  2006/01/25 00:51:50  brouard
 #define AGEBASE 40    (Module): Lots of cleaning and bugs added (Gompertz)
   
     Revision 1.109  2006/01/24 19:37:15  brouard
 int nvar;    (Module): Comments (lines starting with a #) are allowed in data.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.108  2006/01/19 18:05:42  lievre
 int nlstate=2; /* Number of live states */    Gnuplot problem appeared...
 int ndeath=1; /* Number of dead states */    To be fixed
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
     Revision 1.107  2006/01/19 16:20:37  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Test existence of gnuplot in imach path
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.106  2006/01/19 13:24:36  brouard
 int mle, weightopt;    Some cleaning and links added in html output
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.105  2006/01/05 20:23:19  lievre
 double jmean; /* Mean space between 2 waves */    *** empty log message ***
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.104  2005/09/30 16:11:43  lievre
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    (Module): sump fixed, loop imx fixed, and simplifications.
 FILE *ficgp, *fichtm;    (Module): If the status is missing at the last wave but we know
 FILE *ficreseij;    that the person is alive, then we can code his/her status as -2
   char filerese[FILENAMELENGTH];    (instead of missing=-1 in earlier versions) and his/her
  FILE  *ficresvij;    contributions to the likelihood is 1 - Prob of dying from last
   char fileresv[FILENAMELENGTH];    health status (= 1-p13= p11+p12 in the easiest case of somebody in
  FILE  *ficresvpl;    the healthy state at last known wave). Version is 0.98
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.103  2005/09/30 15:54:49  lievre
 #define NR_END 1    (Module): sump fixed, loop imx fixed, and simplifications.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 #define NRANSI  
 #define ITMAX 200    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 #define TOL 2.0e-4  
     Revision 1.100  2004/07/12 18:29:06  brouard
 #define CGOLD 0.3819660    Add version for Mac OS X. Just define UNIX in Makefile
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.98  2004/05/16 15:05:56  brouard
 #define TINY 1.0e-20    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 static double maxarg1,maxarg2;    state at each age, but using a Gompertz model: log u =a + b*age .
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    This is the basic analysis of mortality and should be done before any
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    other analysis, in order to test if the mortality estimated from the
      cross-longitudinal survey is different from the mortality estimated
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    from other sources like vital statistic data.
 #define rint(a) floor(a+0.5)  
     The same imach parameter file can be used but the option for mle should be -3.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Agnès, who wrote this part of the code, tried to keep most of the
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    former routines in order to include the new code within the former code.
   
 int imx;    The output is very simple: only an estimate of the intercept and of
 int stepm;    the slope with 95% confident intervals.
 /* Stepm, step in month: minimum step interpolation*/  
     Current limitations:
 int m,nb;    A) Even if you enter covariates, i.e. with the
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    B) There is no computation of Life Expectancy nor Life Table.
 double **pmmij;  
     Revision 1.97  2004/02/20 13:25:42  lievre
 double *weight;    Version 0.96d. Population forecasting command line is (temporarily)
 int **s; /* Status */    suppressed.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    rewritten within the same printf. Workaround: many printfs.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.95  2003/07/08 07:54:34  brouard
 /**************** split *************************/    * imach.c (Repository):
 static  int split( char *path, char *dirc, char *name )    (Repository): Using imachwizard code to output a more meaningful covariance
 {    matrix (cov(a12,c31) instead of numbers.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.93  2003/06/25 16:33:55  brouard
    s = strrchr( path, '\\' );           /* find last / */    (Module): On windows (cygwin) function asctime_r doesn't
    if ( s == NULL ) {                   /* no directory, so use current */    exist so I changed back to asctime which exists.
 #if     defined(__bsd__)                /* get current working directory */    (Module): Version 0.96b
       extern char       *getwd( );  
     Revision 1.92  2003/06/25 16:30:45  brouard
       if ( getwd( dirc ) == NULL ) {    (Module): On windows (cygwin) function asctime_r doesn't
 #else    exist so I changed back to asctime which exists.
       extern char       *getcwd( );  
     Revision 1.91  2003/06/25 15:30:29  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    * imach.c (Repository): Duplicated warning errors corrected.
 #endif    (Repository): Elapsed time after each iteration is now output. It
          return( GLOCK_ERROR_GETCWD );    helps to forecast when convergence will be reached. Elapsed time
       }    is stamped in powell.  We created a new html file for the graphs
       strcpy( name, path );             /* we've got it */    concerning matrix of covariance. It has extension -cov.htm.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.90  2003/06/24 12:34:15  brouard
       l2 = strlen( s );                 /* length of filename */    (Module): Some bugs corrected for windows. Also, when
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    mle=-1 a template is output in file "or"mypar.txt with the design
       strcpy( name, s );                /* save file name */    of the covariance matrix to be input.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.89  2003/06/24 12:30:52  brouard
    }    (Module): Some bugs corrected for windows. Also, when
    l1 = strlen( dirc );                 /* length of directory */    mle=-1 a template is output in file "or"mypar.txt with the design
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    of the covariance matrix to be input.
    return( 0 );                         /* we're done */  
 }    Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
 /******************************************/    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 void replace(char *s, char*t)  
 {    Revision 1.86  2003/06/17 20:04:08  brouard
   int i;    (Module): Change position of html and gnuplot routines and added
   int lg=20;    routine fileappend.
   i=0;  
   lg=strlen(t);    Revision 1.85  2003/06/17 13:12:43  brouard
   for(i=0; i<= lg; i++) {    * imach.c (Repository): Check when date of death was earlier that
     (s[i] = t[i]);    current date of interview. It may happen when the death was just
     if (t[i]== '\\') s[i]='/';    prior to the death. In this case, dh was negative and likelihood
   }    was wrong (infinity). We still send an "Error" but patch by
 }    assuming that the date of death was just one stepm after the
     interview.
 int nbocc(char *s, char occ)    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   int i,j=0;    memory allocation. But we also truncated to 8 characters (left
   int lg=20;    truncation)
   i=0;    (Repository): No more line truncation errors.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.84  2003/06/13 21:44:43  brouard
   if  (s[i] == occ ) j++;    * imach.c (Repository): Replace "freqsummary" at a correct
   }    place. It differs from routine "prevalence" which may be called
   return j;    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.83  2003/06/10 13:39:11  lievre
   int i,lg,j,p=0;    *** empty log message ***
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.82  2003/06/05 15:57:20  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Add log in  imach.c and  fullversion number is now printed.
   }  
   */
   lg=strlen(t);  /*
   for(j=0; j<p; j++) {     Interpolated Markov Chain
     (u[j] = t[j]);  
   }    Short summary of the programme:
      u[p]='\0';    
     This program computes Healthy Life Expectancies from
    for(j=0; j<= lg; j++) {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     if (j>=(p+1))(v[j-p-1] = t[j]);    first survey ("cross") where individuals from different ages are
   }    interviewed on their health status or degree of disability (in the
 }    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 /********************** nrerror ********************/    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 void nrerror(char error_text[])    model. More health states you consider, more time is necessary to reach the
 {    Maximum Likelihood of the parameters involved in the model.  The
   fprintf(stderr,"ERREUR ...\n");    simplest model is the multinomial logistic model where pij is the
   fprintf(stderr,"%s\n",error_text);    probability to be observed in state j at the second wave
   exit(1);    conditional to be observed in state i at the first wave. Therefore
 }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /*********************** vector *******************/    'age' is age and 'sex' is a covariate. If you want to have a more
 double *vector(int nl, int nh)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   double *v;    you to do it.  More covariates you add, slower the
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    convergence.
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    The advantage of this computer programme, compared to a simple
 }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 /************************ free vector ******************/    intermediate interview, the information is lost, but taken into
 void free_vector(double*v, int nl, int nh)    account using an interpolation or extrapolation.  
 {  
   free((FREE_ARG)(v+nl-NR_END));    hPijx is the probability to be 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 unobserved intermediate
 /************************ivector *******************************/    states. This elementary transition (by month, quarter,
 int *ivector(long nl,long nh)    semester or year) is modelled as a multinomial logistic.  The hPx
 {    matrix is simply the matrix product of nh*stepm elementary matrices
   int *v;    and the contribution of each individual to the likelihood is simply
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    hPijx.
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /******************free ivector **************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 void free_ivector(int *v, long nl, long nh)             Institut national d'études démographiques, Paris.
 {    This software have been partly granted by Euro-REVES, a concerted action
   free((FREE_ARG)(v+nl-NR_END));    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 /******************* imatrix *******************************/    can be accessed at http://euroreves.ined.fr/imach .
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    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
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    
   int **m;    **********************************************************************/
    /*
   /* allocate pointers to rows */    main
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    read parameterfile
   if (!m) nrerror("allocation failure 1 in matrix()");    read datafile
   m += NR_END;    concatwav
   m -= nrl;    freqsummary
      if (mle >= 1)
        mlikeli
   /* allocate rows and set pointers to them */    print results files
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    if mle==1 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       computes hessian
   m[nrl] += NR_END;    read end of parameter file: agemin, agemax, bage, fage, estepm
   m[nrl] -= ncl;        begin-prev-date,...
      open gnuplot file
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    open html file
      period (stable) prevalence
   /* return pointer to array of pointers to rows */     for age prevalim()
   return m;    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /****************** free_imatrix *************************/    health expectancies
 void free_imatrix(m,nrl,nrh,ncl,nch)    Variance-covariance of DFLE
       int **m;    prevalence()
       long nch,ncl,nrh,nrl;     movingaverage()
      /* free an int matrix allocated by imatrix() */    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    total life expectancies
   free((FREE_ARG) (m+nrl-NR_END));    Variance of period (stable) prevalence
 }   end
   */
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;   
   double **m;  #include <math.h>
   #include <stdio.h>
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <stdlib.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <string.h>
   m += NR_END;  #include <unistd.h>
   m -= nrl;  
   #include <limits.h>
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <sys/types.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <sys/stat.h>
   m[nrl] += NR_END;  #include <errno.h>
   m[nrl] -= ncl;  extern int errno;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* #include <sys/time.h> */
   return m;  #include <time.h>
 }  #include "timeval.h"
   
 /*************************free matrix ************************/  /* #include <libintl.h> */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /* #define _(String) gettext (String) */
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define MAXLINE 256
   free((FREE_ARG)(m+nrl-NR_END));  
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /******************* ma3x *******************************/  #define FILENAMELENGTH 132
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   double ***m;  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define NINTERVMAX 8
   m -= nrl;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define NCOVMAX 8 /* Maximum number of covariates */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define MAXN 20000
   m[nrl] += NR_END;  #define YEARM 12. /* Number of months per year */
   m[nrl] -= ncl;  #define AGESUP 130
   #define AGEBASE 40
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define DIRSEPARATOR '/'
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define CHARSEPARATOR "/"
   m[nrl][ncl] += NR_END;  #define ODIRSEPARATOR '\\'
   m[nrl][ncl] -= nll;  #else
   for (j=ncl+1; j<=nch; j++)  #define DIRSEPARATOR '\\'
     m[nrl][j]=m[nrl][j-1]+nlay;  #define CHARSEPARATOR "\\"
    #define ODIRSEPARATOR '/'
   for (i=nrl+1; i<=nrh; i++) {  #endif
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  /* $Id$ */
       m[i][j]=m[i][j-1]+nlay;  /* $State$ */
   }  
   return m;  char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
 }  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
 /*************************free ma3x ************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int npar=NPARMAX;
   free((FREE_ARG)(m+nrl-NR_END));  int nlstate=2; /* Number of live states */
 }  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 /***************** f1dim *************************/  int popbased=0;
 extern int ncom;  
 extern double *pcom,*xicom;  int *wav; /* Number of waves for this individuual 0 is possible */
 extern double (*nrfunc)(double []);  int maxwav; /* Maxim number of waves */
    int jmin, jmax; /* min, max spacing between 2 waves */
 double f1dim(double x)  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   int j;                     to the likelihood and the sum of weights (done by funcone)*/
   double f;  int mle, weightopt;
   double *xt;  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 */
   xt=vector(1,ncom);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   f=(*nrfunc)(xt);  double jmean; /* Mean space between 2 waves */
   free_vector(xt,1,ncom);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   return f;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 }  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 /*****************brent *************************/  int globpr; /* Global variable for printing or not */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double fretone; /* Only one call to likelihood */
 {  long ipmx; /* Number of contributions */
   int iter;  double sw; /* Sum of weights */
   double a,b,d,etemp;  char filerespow[FILENAMELENGTH];
   double fu,fv,fw,fx;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double ftemp;  FILE *ficresilk;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   double e=0.0;  FILE *ficresprobmorprev;
    FILE *fichtm, *fichtmcov; /* Html File */
   a=(ax < cx ? ax : cx);  FILE *ficreseij;
   b=(ax > cx ? ax : cx);  char filerese[FILENAMELENGTH];
   x=w=v=bx;  FILE *ficresstdeij;
   fw=fv=fx=(*f)(x);  char fileresstde[FILENAMELENGTH];
   for (iter=1;iter<=ITMAX;iter++) {  FILE *ficrescveij;
     xm=0.5*(a+b);  char filerescve[FILENAMELENGTH];
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  FILE  *ficresvij;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  char fileresv[FILENAMELENGTH];
     printf(".");fflush(stdout);  FILE  *ficresvpl;
 #ifdef DEBUG  char fileresvpl[FILENAMELENGTH];
     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);  char title[MAXLINE];
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 #endif  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       *xmin=x;  char command[FILENAMELENGTH];
       return fx;  int  outcmd=0;
     }  
     ftemp=fu;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  char filelog[FILENAMELENGTH]; /* Log file */
       q=(x-v)*(fx-fw);  char filerest[FILENAMELENGTH];
       p=(x-v)*q-(x-w)*r;  char fileregp[FILENAMELENGTH];
       q=2.0*(q-r);  char popfile[FILENAMELENGTH];
       if (q > 0.0) p = -p;  
       q=fabs(q);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       etemp=e;  
       e=d;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  struct timezone tzp;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  extern int gettimeofday();
       else {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
         d=p/q;  long time_value;
         u=x+d;  extern long time();
         if (u-a < tol2 || b-u < tol2)  char strcurr[80], strfor[80];
           d=SIGN(tol1,xm-x);  
       }  char *endptr;
     } else {  long lval;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double dval;
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define NR_END 1
     fu=(*f)(u);  #define FREE_ARG char*
     if (fu <= fx) {  #define FTOL 1.0e-10
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  #define NRANSI 
         SHFT(fv,fw,fx,fu)  #define ITMAX 200 
         } else {  
           if (u < x) a=u; else b=u;  #define TOL 2.0e-4 
           if (fu <= fw || w == x) {  
             v=w;  #define CGOLD 0.3819660 
             w=u;  #define ZEPS 1.0e-10 
             fv=fw;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  #define GOLD 1.618034 
             v=u;  #define GLIMIT 100.0 
             fv=fu;  #define TINY 1.0e-20 
           }  
         }  static double maxarg1,maxarg2;
   }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   nrerror("Too many iterations in brent");  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   *xmin=x;    
   return fx;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
 /****************** mnbrak ***********************/  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
             double (*func)(double))  int agegomp= AGEGOMP;
 {  
   double ulim,u,r,q, dum;  int imx; 
   double fu;  int stepm=1;
    /* Stepm, step in month: minimum step interpolation*/
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  int estepm;
   if (*fb > *fa) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  int m,nb;
       }  long *num;
   *cx=(*bx)+GOLD*(*bx-*ax);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   *fc=(*func)(*cx);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   while (*fb > *fc) {  double **pmmij, ***probs;
     r=(*bx-*ax)*(*fb-*fc);  double *ageexmed,*agecens;
     q=(*bx-*cx)*(*fb-*fa);  double dateintmean=0;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  double *weight;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int **s; /* Status */
     if ((*bx-u)*(u-*cx) > 0.0) {  double *agedc, **covar, idx;
       fu=(*func)(u);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double *lsurv, *lpop, *tpop;
       fu=(*func)(u);  
       if (fu < *fc) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  double ftolhess; /* Tolerance for computing hessian */
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  /**************** split *************************/
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       u=ulim;  {
       fu=(*func)(u);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     } else {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       u=(*cx)+GOLD*(*cx-*bx);    */ 
       fu=(*func)(u);    char  *ss;                            /* pointer */
     }    int   l1, l2;                         /* length counters */
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)    l1 = strlen(path );                   /* length of path */
       }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
 /*************** linmin ************************/      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 int ncom;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 double *pcom,*xicom;      /* get current working directory */
 double (*nrfunc)(double []);      /*    extern  char* getcwd ( char *buf , int len);*/
        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        return( GLOCK_ERROR_GETCWD );
 {      }
   double brent(double ax, double bx, double cx,      /* got dirc from getcwd*/
                double (*f)(double), double tol, double *xmin);      printf(" DIRC = %s \n",dirc);
   double f1dim(double x);    } else {                              /* strip direcotry from path */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      ss++;                               /* after this, the filename */
               double *fc, double (*func)(double));      l2 = strlen( ss );                  /* length of filename */
   int j;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   double xx,xmin,bx,ax;      strcpy( name, ss );         /* save file name */
   double fx,fb,fa;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
        dirc[l1-l2] = 0;                    /* add zero */
   ncom=n;      printf(" DIRC2 = %s \n",dirc);
   pcom=vector(1,n);    }
   xicom=vector(1,n);    /* We add a separator at the end of dirc if not exists */
   nrfunc=func;    l1 = strlen( dirc );                  /* length of directory */
   for (j=1;j<=n;j++) {    if( dirc[l1-1] != DIRSEPARATOR ){
     pcom[j]=p[j];      dirc[l1] =  DIRSEPARATOR;
     xicom[j]=xi[j];      dirc[l1+1] = 0; 
   }      printf(" DIRC3 = %s \n",dirc);
   ax=0.0;    }
   xx=1.0;    ss = strrchr( name, '.' );            /* find last / */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    if (ss >0){
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      ss++;
 #ifdef DEBUG      strcpy(ext,ss);                     /* save extension */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      l1= strlen( name);
 #endif      l2= strlen(ss)+1;
   for (j=1;j<=n;j++) {      strncpy( finame, name, l1-l2);
     xi[j] *= xmin;      finame[l1-l2]= 0;
     p[j] += xi[j];    }
   }  
   free_vector(xicom,1,n);    return( 0 );                          /* we're done */
   free_vector(pcom,1,n);  }
 }  
   
 /*************** powell ************************/  /******************************************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  void replace_back_to_slash(char *s, char*t)
 {  {
   void linmin(double p[], double xi[], int n, double *fret,    int i;
               double (*func)(double []));    int lg=0;
   int i,ibig,j;    i=0;
   double del,t,*pt,*ptt,*xit;    lg=strlen(t);
   double fp,fptt;    for(i=0; i<= lg; i++) {
   double *xits;      (s[i] = t[i]);
   pt=vector(1,n);      if (t[i]== '\\') s[i]='/';
   ptt=vector(1,n);    }
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  int nbocc(char *s, char occ)
   for (j=1;j<=n;j++) pt[j]=p[j];  {
   for (*iter=1;;++(*iter)) {    int i,j=0;
     fp=(*fret);    int lg=20;
     ibig=0;    i=0;
     del=0.0;    lg=strlen(s);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    for(i=0; i<= lg; i++) {
     for (i=1;i<=n;i++)    if  (s[i] == occ ) j++;
       printf(" %d %.12f",i, p[i]);    }
     printf("\n");    return j;
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  void cutv(char *u,char *v, char*t, char occ)
 #ifdef DEBUG  {
       printf("fret=%lf \n",*fret);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 #endif       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       printf("%d",i);fflush(stdout);       gives u="abcedf" and v="ghi2j" */
       linmin(p,xit,n,fret,func);    int i,lg,j,p=0;
       if (fabs(fptt-(*fret)) > del) {    i=0;
         del=fabs(fptt-(*fret));    for(j=0; j<=strlen(t)-1; j++) {
         ibig=i;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       }    }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));    lg=strlen(t);
       for (j=1;j<=n;j++) {    for(j=0; j<p; j++) {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      (u[j] = t[j]);
         printf(" x(%d)=%.12e",j,xit[j]);    }
       }       u[p]='\0';
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);     for(j=0; j<= lg; j++) {
       printf("\n");      if (j>=(p+1))(v[j-p-1] = t[j]);
 #endif    }
     }  }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /********************** nrerror ********************/
       int k[2],l;  
       k[0]=1;  void nrerror(char error_text[])
       k[1]=-1;  {
       printf("Max: %.12e",(*func)(p));    fprintf(stderr,"ERREUR ...\n");
       for (j=1;j<=n;j++)    fprintf(stderr,"%s\n",error_text);
         printf(" %.12e",p[j]);    exit(EXIT_FAILURE);
       printf("\n");  }
       for(l=0;l<=1;l++) {  /*********************** vector *******************/
         for (j=1;j<=n;j++) {  double *vector(int nl, int nh)
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  {
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double *v;
         }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if (!v) nrerror("allocation failure in vector");
       }    return v-nl+NR_END;
 #endif  }
   
   /************************ free vector ******************/
       free_vector(xit,1,n);  void free_vector(double*v, int nl, int nh)
       free_vector(xits,1,n);  {
       free_vector(ptt,1,n);    free((FREE_ARG)(v+nl-NR_END));
       free_vector(pt,1,n);  }
       return;  
     }  /************************ivector *******************************/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int *ivector(long nl,long nh)
     for (j=1;j<=n;j++) {  {
       ptt[j]=2.0*p[j]-pt[j];    int *v;
       xit[j]=p[j]-pt[j];    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       pt[j]=p[j];    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
     fptt=(*func)(ptt);  }
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /******************free ivector **************************/
       if (t < 0.0) {  void free_ivector(int *v, long nl, long nh)
         linmin(p,xit,n,fret,func);  {
         for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
           xi[j][ibig]=xi[j][n];  }
           xi[j][n]=xit[j];  
         }  /************************lvector *******************************/
 #ifdef DEBUG  long *lvector(long nl,long nh)
         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++)    long *v;
           printf(" %.12e",xit[j]);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         printf("\n");    if (!v) nrerror("allocation failure in ivector");
 #endif    return v-nl+NR_END;
       }  }
     }  
   }  /******************free lvector **************************/
 }  void free_lvector(long *v, long nl, long nh)
   {
 /**** Prevalence limit ****************/    free((FREE_ARG)(v+nl-NR_END));
   }
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  /******************* imatrix *******************************/
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int **imatrix(long nrl, long nrh, long ncl, long nch) 
      matrix by transitions matrix until convergence is reached */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
   int i, ii,j,k;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double min, max, maxmin, maxmax,sumnew=0.;    int **m; 
   double **matprod2();    
   double **out, cov[NCOVMAX], **pmij();    /* allocate pointers to rows */ 
   double **newm;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    m -= nrl; 
     for (j=1;j<=nlstate+ndeath;j++){    
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    
     }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
    cov[1]=1.;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
      m[nrl] += NR_END; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl] -= ncl; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    
     newm=savm;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     /* Covariates have to be included here again */    
      cov[2]=agefin;    /* return pointer to array of pointers to rows */ 
      return m; 
       for (k=1; k<=cptcovn;k++) {  } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  /****************** free_imatrix *************************/
       }  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (k=1; k<=cptcovage;k++)        int **m;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        long nch,ncl,nrh,nrl; 
       for (k=1; k<=cptcovprod;k++)       /* free an int matrix allocated by imatrix() */ 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    free((FREE_ARG) (m+nrl-NR_END)); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  } 
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
     savm=oldm;  {
     oldm=newm;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     maxmax=0.;    double **m;
     for(j=1;j<=nlstate;j++){  
       min=1.;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       max=0.;    if (!m) nrerror("allocation failure 1 in matrix()");
       for(i=1; i<=nlstate; i++) {    m += NR_END;
         sumnew=0;    m -= nrl;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         max=FMAX(max,prlim[i][j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         min=FMIN(min,prlim[i][j]);    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     if(maxmax < ftolpl){    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       return prlim;     */
     }  }
   }  
 }  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 /*************** transition probabilities **********/  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   double s1, s2;  
   /*double t34;*/  /******************* ma3x *******************************/
   int i,j,j1, nc, ii, jj;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
     for(i=1; i<= nlstate; i++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for(j=1; j<i;j++){    double ***m;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!m) nrerror("allocation failure 1 in matrix()");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    m += NR_END;
       }    m -= nrl;
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(j=i+1; j<=nlstate+ndeath;j++){    m[nrl] += NR_END;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m[nrl] -= ncl;
         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);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
       ps[i][j]=s2;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   }    m[nrl][ncl] += NR_END;
   for(i=1; i<= nlstate; i++){    m[nrl][ncl] -= nll;
      s1=0;    for (j=ncl+1; j<=nch; j++) 
     for(j=1; j<i; j++)      m[nrl][j]=m[nrl][j-1]+nlay;
       s1+=exp(ps[i][j]);    
     for(j=i+1; j<=nlstate+ndeath; j++)    for (i=nrl+1; i<=nrh; i++) {
       s1+=exp(ps[i][j]);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     ps[i][i]=1./(s1+1.);      for (j=ncl+1; j<=nch; j++) 
     for(j=1; j<i; j++)        m[i][j]=m[i][j-1]+nlay;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     for(j=i+1; j<=nlstate+ndeath; j++)    return m; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   } /* end i */    */
   }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*************************free ma3x ************************/
       ps[ii][jj]=0;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       ps[ii][ii]=1;  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /*************** function subdirf ***********/
    }  char *subdirf(char fileres[])
     printf("\n ");  {
     }    /* Caution optionfilefiname is hidden */
     printf("\n ");printf("%lf ",cov[2]);*/    strcpy(tmpout,optionfilefiname);
 /*    strcat(tmpout,"/"); /* Add to the right */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    strcat(tmpout,fileres);
   goto end;*/    return tmpout;
     return ps;  }
 }  
   /*************** function subdirf2 ***********/
 /**************** Product of 2 matrices ******************/  char *subdirf2(char fileres[], char *preop)
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    
 {    /* Caution optionfilefiname is hidden */
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcpy(tmpout,optionfilefiname);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,"/");
   /* in, b, out are matrice of pointers which should have been initialized    strcat(tmpout,preop);
      before: only the contents of out is modified. The function returns    strcat(tmpout,fileres);
      a pointer to pointers identical to out */    return tmpout;
   long i, j, k;  }
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /*************** function subdirf3 ***********/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  char *subdirf3(char fileres[], char *preop, char *preop2)
         out[i][k] +=in[i][j]*b[j][k];  {
     
   return out;    /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
 /************* Higher Matrix Product ***************/    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    return tmpout;
 {  }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  /***************** f1dim *************************/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  extern int ncom; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  extern double *pcom,*xicom;
      (typically every 2 years instead of every month which is too big).  extern double (*nrfunc)(double []); 
      Model is determined by parameters x and covariates have to be   
      included manually here.  double f1dim(double x) 
   { 
      */    int j; 
     double f;
   int i, j, d, h, k;    double *xt; 
   double **out, cov[NCOVMAX];   
   double **newm;    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   /* Hstepm could be zero and should return the unit matrix */    f=(*nrfunc)(xt); 
   for (i=1;i<=nlstate+ndeath;i++)    free_vector(xt,1,ncom); 
     for (j=1;j<=nlstate+ndeath;j++){    return f; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  /*****************brent *************************/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(h=1; h <=nhstepm; h++){  { 
     for(d=1; d <=hstepm; d++){    int iter; 
       newm=savm;    double a,b,d,etemp;
       /* Covariates have to be included here again */    double fu,fv,fw,fx;
       cov[1]=1.;    double ftemp;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double e=0.0; 
 for (k=1; k<=cptcovage;k++)   
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    a=(ax < cx ? ax : cx); 
    for (k=1; k<=cptcovprod;k++)    b=(ax > cx ? ax : cx); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      xm=0.5*(a+b); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      printf(".");fflush(stdout);
       savm=oldm;      fprintf(ficlog,".");fflush(ficlog);
       oldm=newm;  #ifdef DEBUG
     }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(i=1; i<=nlstate+ndeath; i++)      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       for(j=1;j<=nlstate+ndeath;j++) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         po[i][j][h]=newm[i][j];  #endif
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
          */        *xmin=x; 
       }        return fx; 
   } /* end h */      } 
   return po;      ftemp=fu;
 }      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
 /*************** log-likelihood *************/        p=(x-v)*q-(x-w)*r; 
 double func( double *x)        q=2.0*(q-r); 
 {        if (q > 0.0) p = -p; 
   int i, ii, j, k, mi, d, kk;        q=fabs(q); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        etemp=e; 
   double **out;        e=d; 
   double sw; /* Sum of weights */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double lli; /* Individual log likelihood */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   long ipmx;        else { 
   /*extern weight */          d=p/q; 
   /* We are differentiating ll according to initial status */          u=x+d; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          if (u-a < tol2 || b-u < tol2) 
   /*for(i=1;i<imx;i++)            d=SIGN(tol1,xm-x); 
     printf(" %d\n",s[4][i]);        } 
   */      } else { 
   cov[1]=1.;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      fu=(*f)(u); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      if (fu <= fx) { 
     for(mi=1; mi<= wav[i]-1; mi++){        if (u >= x) a=x; else b=x; 
       for (ii=1;ii<=nlstate+ndeath;ii++)        SHFT(v,w,x,u) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          SHFT(fv,fw,fx,fu) 
       for(d=0; d<dh[mi][i]; d++){          } else { 
         newm=savm;            if (u < x) a=u; else b=u; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            if (fu <= fw || w == x) { 
         for (kk=1; kk<=cptcovage;kk++) {              v=w; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              w=u; 
         }              fv=fw; 
                      fw=fu; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            } else if (fu <= fv || v == x || v == w) { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));              v=u; 
         savm=oldm;              fv=fu; 
         oldm=newm;            } 
                  } 
            } 
       } /* end mult */    nrerror("Too many iterations in brent"); 
          *xmin=x; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    return fx; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  } 
       ipmx +=1;  
       sw += weight[i];  /****************** mnbrak ***********************/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   } /* end of individual */              double (*func)(double)) 
   { 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double ulim,u,r,q, dum;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    double fu; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */   
   return -l;    *fa=(*func)(*ax); 
 }    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /*********** Maximum Likelihood Estimation ***************/        SHFT(dum,*fb,*fa,dum) 
         } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    *cx=(*bx)+GOLD*(*bx-*ax); 
 {    *fc=(*func)(*cx); 
   int i,j, iter;    while (*fb > *fc) { 
   double **xi,*delti;      r=(*bx-*ax)*(*fb-*fc); 
   double fret;      q=(*bx-*cx)*(*fb-*fa); 
   xi=matrix(1,npar,1,npar);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for (i=1;i<=npar;i++)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for (j=1;j<=npar;j++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       xi[i][j]=(i==j ? 1.0 : 0.0);      if ((*bx-u)*(u-*cx) > 0.0) { 
   printf("Powell\n");        fu=(*func)(u); 
   powell(p,xi,npar,ftol,&iter,&fret,func);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        if (fu < *fc) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 /**** Computes Hessian and covariance matrix ***/        u=ulim; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        fu=(*func)(u); 
 {      } else { 
   double  **a,**y,*x,pd;        u=(*cx)+GOLD*(*cx-*bx); 
   double **hess;        fu=(*func)(u); 
   int i, j,jk;      } 
   int *indx;      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
   double hessii(double p[], double delta, int theta, double delti[]);        } 
   double hessij(double p[], double delti[], int i, int j);  } 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*************** linmin ************************/
   
   int ncom; 
   hess=matrix(1,npar,1,npar);  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   printf("\nCalculation of the hessian matrix. Wait...\n");   
   for (i=1;i<=npar;i++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("%d",i);fflush(stdout);  { 
     hess[i][i]=hessii(p,ftolhess,i,delti);    double brent(double ax, double bx, double cx, 
     /*printf(" %f ",p[i]);*/                 double (*f)(double), double tol, double *xmin); 
   }    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   for (i=1;i<=npar;i++) {                double *fc, double (*func)(double)); 
     for (j=1;j<=npar;j++)  {    int j; 
       if (j>i) {    double xx,xmin,bx,ax; 
         printf(".%d%d",i,j);fflush(stdout);    double fx,fb,fa;
         hess[i][j]=hessij(p,delti,i,j);   
         hess[j][i]=hess[i][j];    ncom=n; 
       }    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
   }    nrfunc=func; 
   printf("\n");    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      xicom[j]=xi[j]; 
      } 
   a=matrix(1,npar,1,npar);    ax=0.0; 
   y=matrix(1,npar,1,npar);    xx=1.0; 
   x=vector(1,npar);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   indx=ivector(1,npar);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   ludcmp(a,npar,indx,&pd);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   for (j=1;j<=npar;j++) {    for (j=1;j<=n;j++) { 
     for (i=1;i<=npar;i++) x[i]=0;      xi[j] *= xmin; 
     x[j]=1;      p[j] += xi[j]; 
     lubksb(a,npar,indx,x);    } 
     for (i=1;i<=npar;i++){    free_vector(xicom,1,n); 
       matcov[i][j]=x[i];    free_vector(pcom,1,n); 
     }  } 
   }  
   char *asc_diff_time(long time_sec, char ascdiff[])
   printf("\n#Hessian matrix#\n");  {
   for (i=1;i<=npar;i++) {    long sec_left, days, hours, minutes;
     for (j=1;j<=npar;j++) {    days = (time_sec) / (60*60*24);
       printf("%.3e ",hess[i][j]);    sec_left = (time_sec) % (60*60*24);
     }    hours = (sec_left) / (60*60) ;
     printf("\n");    sec_left = (sec_left) %(60*60);
   }    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   /* Recompute Inverse */    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   for (i=1;i<=npar;i++)    return ascdiff;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /*************** powell ************************/
   /*  printf("\n#Hessian matrix recomputed#\n");  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   for (j=1;j<=npar;j++) {  { 
     for (i=1;i<=npar;i++) x[i]=0;    void linmin(double p[], double xi[], int n, double *fret, 
     x[j]=1;                double (*func)(double [])); 
     lubksb(a,npar,indx,x);    int i,ibig,j; 
     for (i=1;i<=npar;i++){    double del,t,*pt,*ptt,*xit;
       y[i][j]=x[i];    double fp,fptt;
       printf("%.3e ",y[i][j]);    double *xits;
     }    int niterf, itmp;
     printf("\n");  
   }    pt=vector(1,n); 
   */    ptt=vector(1,n); 
     xit=vector(1,n); 
   free_matrix(a,1,npar,1,npar);    xits=vector(1,n); 
   free_matrix(y,1,npar,1,npar);    *fret=(*func)(p); 
   free_vector(x,1,npar);    for (j=1;j<=n;j++) pt[j]=p[j]; 
   free_ivector(indx,1,npar);    for (*iter=1;;++(*iter)) { 
   free_matrix(hess,1,npar,1,npar);      fp=(*fret); 
       ibig=0; 
       del=0.0; 
 }      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
 /*************** hessian matrix ****************/      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 double hessii( double x[], double delta, int theta, double delti[])      /*    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);
   int i;      */
   int l=1, lmax=20;     for (i=1;i<=n;i++) {
   double k1,k2;        printf(" %d %.12f",i, p[i]);
   double p2[NPARMAX+1];        fprintf(ficlog," %d %.12lf",i, p[i]);
   double res;        fprintf(ficrespow," %.12lf", p[i]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      }
   double fx;      printf("\n");
   int k=0,kmax=10;      fprintf(ficlog,"\n");
   double l1;      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   fx=func(x);        tm = *localtime(&curr_time.tv_sec);
   for (i=1;i<=npar;i++) p2[i]=x[i];        strcpy(strcurr,asctime(&tm));
   for(l=0 ; l <=lmax; l++){  /*       asctime_r(&tm,strcurr); */
     l1=pow(10,l);        forecast_time=curr_time; 
     delts=delt;        itmp = strlen(strcurr);
     for(k=1 ; k <kmax; k=k+1){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       delt = delta*(l1*k);          strcurr[itmp-1]='\0';
       p2[theta]=x[theta] +delt;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       k1=func(p2)-fx;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       p2[theta]=x[theta]-delt;        for(niterf=10;niterf<=30;niterf+=10){
       k2=func(p2)-fx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       /*res= (k1-2.0*fx+k2)/delt/delt; */          tmf = *localtime(&forecast_time.tv_sec);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /*      asctime_r(&tmf,strfor); */
                strcpy(strfor,asctime(&tmf));
 #ifdef DEBUG          itmp = strlen(strfor);
       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);          if(strfor[itmp-1]=='\n')
 #endif          strfor[itmp-1]='\0';
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          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);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          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);
         k=kmax;        }
       }      }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for (i=1;i<=n;i++) { 
         k=kmax; l=lmax*10.;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       }        fptt=(*fret); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  #ifdef DEBUG
         delts=delt;        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
     }  #endif
   }        printf("%d",i);fflush(stdout);
   delti[theta]=delts;        fprintf(ficlog,"%d",i);fflush(ficlog);
   return res;        linmin(p,xit,n,fret,func); 
          if (fabs(fptt-(*fret)) > del) { 
 }          del=fabs(fptt-(*fret)); 
           ibig=i; 
 double hessij( double x[], double delti[], int thetai,int thetaj)        } 
 {  #ifdef DEBUG
   int i;        printf("%d %.12e",i,(*fret));
   int l=1, l1, lmax=20;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double k1,k2,k3,k4,res,fx;        for (j=1;j<=n;j++) {
   double p2[NPARMAX+1];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int k;          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   fx=func(x);        }
   for (k=1; k<=2; k++) {        for(j=1;j<=n;j++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];          printf(" p=%.12e",p[j]);
     p2[thetai]=x[thetai]+delti[thetai]/k;          fprintf(ficlog," p=%.12e",p[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        }
     k1=func(p2)-fx;        printf("\n");
          fprintf(ficlog,"\n");
     p2[thetai]=x[thetai]+delti[thetai]/k;  #endif
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } 
     k2=func(p2)-fx;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
    #ifdef DEBUG
     p2[thetai]=x[thetai]-delti[thetai]/k;        int k[2],l;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        k[0]=1;
     k3=func(p2)-fx;        k[1]=-1;
          printf("Max: %.12e",(*func)(p));
     p2[thetai]=x[thetai]-delti[thetai]/k;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for (j=1;j<=n;j++) {
     k4=func(p2)-fx;          printf(" %.12e",p[j]);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          fprintf(ficlog," %.12e",p[j]);
 #ifdef DEBUG        }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("\n");
 #endif        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
   return res;          for (j=1;j<=n;j++) {
 }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 /************** Inverse of matrix **************/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 void ludcmp(double **a, int n, int *indx, double *d)          }
 {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i,imax,j,k;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double big,dum,sum,temp;        }
   double *vv;  #endif
    
   vv=vector(1,n);  
   *d=1.0;        free_vector(xit,1,n); 
   for (i=1;i<=n;i++) {        free_vector(xits,1,n); 
     big=0.0;        free_vector(ptt,1,n); 
     for (j=1;j<=n;j++)        free_vector(pt,1,n); 
       if ((temp=fabs(a[i][j])) > big) big=temp;        return; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      } 
     vv[i]=1.0/big;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   }      for (j=1;j<=n;j++) { 
   for (j=1;j<=n;j++) {        ptt[j]=2.0*p[j]-pt[j]; 
     for (i=1;i<j;i++) {        xit[j]=p[j]-pt[j]; 
       sum=a[i][j];        pt[j]=p[j]; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      } 
       a[i][j]=sum;      fptt=(*func)(ptt); 
     }      if (fptt < fp) { 
     big=0.0;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for (i=j;i<=n;i++) {        if (t < 0.0) { 
       sum=a[i][j];          linmin(p,xit,n,fret,func); 
       for (k=1;k<j;k++)          for (j=1;j<=n;j++) { 
         sum -= a[i][k]*a[k][j];            xi[j][ibig]=xi[j][n]; 
       a[i][j]=sum;            xi[j][n]=xit[j]; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {          }
         big=dum;  #ifdef DEBUG
         imax=i;          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);
     }          for(j=1;j<=n;j++){
     if (j != imax) {            printf(" %.12e",xit[j]);
       for (k=1;k<=n;k++) {            fprintf(ficlog," %.12e",xit[j]);
         dum=a[imax][k];          }
         a[imax][k]=a[j][k];          printf("\n");
         a[j][k]=dum;          fprintf(ficlog,"\n");
       }  #endif
       *d = -(*d);        }
       vv[imax]=vv[j];      } 
     }    } 
     indx[j]=imax;  } 
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  /**** Prevalence limit (stable or period prevalence)  ****************/
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     }  {
   }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   free_vector(vv,1,n);  /* Doesn't work */       matrix by transitions matrix until convergence is reached */
 ;  
 }    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
 void lubksb(double **a, int n, int *indx, double b[])    double **matprod2();
 {    double **out, cov[NCOVMAX], **pmij();
   int i,ii=0,ip,j;    double **newm;
   double sum;    double agefin, delaymax=50 ; /* Max number of years to converge */
    
   for (i=1;i<=n;i++) {    for (ii=1;ii<=nlstate+ndeath;ii++)
     ip=indx[i];      for (j=1;j<=nlstate+ndeath;j++){
     sum=b[ip];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[ip]=b[i];      }
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];     cov[1]=1.;
     else if (sum) ii=i;   
     b[i]=sum;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for (i=n;i>=1;i--) {      newm=savm;
     sum=b[i];      /* Covariates have to be included here again */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];       cov[2]=agefin;
     b[i]=sum/a[i][i];    
   }        for (k=1; k<=cptcovn;k++) {
 }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
 /************ Frequencies ********************/        }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 {  /* Some frequencies */        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]]];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double *pp;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double pos;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   FILE *ficresp;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   char fileresp[FILENAMELENGTH];  
       savm=oldm;
   pp=vector(1,nlstate);      oldm=newm;
       maxmax=0.;
   strcpy(fileresp,"p");      for(j=1;j<=nlstate;j++){
   strcat(fileresp,fileres);        min=1.;
   if((ficresp=fopen(fileresp,"w"))==NULL) {        max=0.;
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(i=1; i<=nlstate; i++) {
     exit(0);          sumnew=0;
   }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          prlim[i][j]= newm[i][j]/(1-sumnew);
   j1=0;          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   for(k1=1; k1<=j;k1++){      }
    for(i1=1; i1<=ncodemax[k1];i1++){      if(maxmax < ftolpl){
        j1++;        return prlim;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      }
          scanf("%d", i);*/    }
         for (i=-1; i<=nlstate+ndeath; i++)    }
          for (jk=-1; jk<=nlstate+ndeath; jk++)    
            for(m=agemin; m <= agemax+3; m++)  /*************** transition probabilities ***************/ 
              freq[i][jk][m]=0;  
          double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
        for (i=1; i<=imx; i++) {  {
          bool=1;    double s1, s2;
          if  (cptcovn>0) {    /*double t34;*/
            for (z1=1; z1<=cptcoveff; z1++)    int i,j,j1, nc, ii, jj;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
                bool=0;      for(i=1; i<= nlstate; i++){
          }        for(j=1; j<i;j++){
           if (bool==1) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
            for(m=firstpass; m<=lastpass-1; m++){            /*s2 += param[i][j][nc]*cov[nc];*/
              if(agev[m][i]==0) agev[m][i]=agemax+1;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
              if(agev[m][i]==1) agev[m][i]=agemax+2;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          }
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          ps[i][j]=s2;
            }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
          }        }
        }        for(j=i+1; j<=nlstate+ndeath;j++){
         if  (cptcovn>0) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
          fprintf(ficresp, "\n#********** Variable ");            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
        fprintf(ficresp, "**********\n#");          }
         }          ps[i][j]=s2;
        for(i=1; i<=nlstate;i++)        }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
        fprintf(ficresp, "\n");      /*ps[3][2]=1;*/
              
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for(i=1; i<= nlstate; i++){
     if(i==(int)agemax+3)        s1=0;
       printf("Total");        for(j=1; j<i; j++)
     else          s1+=exp(ps[i][j]);
       printf("Age %d", i);        for(j=i+1; j<=nlstate+ndeath; j++)
     for(jk=1; jk <=nlstate ; jk++){          s1+=exp(ps[i][j]);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        ps[i][i]=1./(s1+1.);
         pp[jk] += freq[jk][m][i];        for(j=1; j<i; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     for(jk=1; jk <=nlstate ; jk++){        for(j=i+1; j<=nlstate+ndeath; j++)
       for(m=-1, pos=0; m <=0 ; m++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
         pos += freq[jk][m][i];        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       if(pp[jk]>=1.e-10)      } /* end i */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      
       else      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for(jj=1; jj<= nlstate+ndeath; jj++){
     }          ps[ii][jj]=0;
     for(jk=1; jk <=nlstate ; jk++){          ps[ii][ii]=1;
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)        }
         pp[jk] += freq[jk][m][i];      }
     }      
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     for(jk=1; jk <=nlstate ; jk++){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       if(pos>=1.e-5)  /*         printf("ddd %lf ",ps[ii][jj]); */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*       } */
       else  /*       printf("\n "); */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*        } */
       if( i <= (int) agemax){  /*        printf("\n ");printf("%lf ",cov[2]); */
         if(pos>=1.e-5)         /*
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       else        goto end;*/
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      return ps;
       }  }
     }  
     for(jk=-1; jk <=nlstate+ndeath; jk++)  /**************** Product of 2 matrices ******************/
       for(m=-1; m <=nlstate+ndeath; m++)  
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     if(i <= (int) agemax)  {
       fprintf(ficresp,"\n");    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     printf("\n");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     }    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
  }       a pointer to pointers identical to out */
      long i, j, k;
   fclose(ficresp);    for(i=nrl; i<= nrh; i++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for(k=ncolol; k<=ncoloh; k++)
   free_vector(pp,1,nlstate);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
 }  /* End of Freq */  
     return out;
 /************* Waves Concatenation ***************/  }
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  /************* Higher Matrix Product ***************/
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    /* Computes the transition matrix starting at age 'age' over 
      and mw[mi+1][i]. dh depends on stepm.       'nhstepm*hstepm*stepm' months (i.e. until
      */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
   int i, mi, m;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;       (typically every 2 years instead of every month which is too big 
      double sum=0., jmean=0.;*/       for the memory).
        Model is determined by parameters x and covariates have to be 
   int j, k=0,jk, ju, jl;       included manually here. 
   double sum=0.;  
   jmin=1e+5;       */
   jmax=-1;  
   jmean=0.;    int i, j, d, h, k;
   for(i=1; i<=imx; i++){    double **out, cov[NCOVMAX];
     mi=0;    double **newm;
     m=firstpass;  
     while(s[m][i] <= nlstate){    /* Hstepm could be zero and should return the unit matrix */
       if(s[m][i]>=1)    for (i=1;i<=nlstate+ndeath;i++)
         mw[++mi][i]=m;      for (j=1;j<=nlstate+ndeath;j++){
       if(m >=lastpass)        oldm[i][j]=(i==j ? 1.0 : 0.0);
         break;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       else      }
         m++;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }/* end while */    for(h=1; h <=nhstepm; h++){
     if (s[m][i] > nlstate){      for(d=1; d <=hstepm; d++){
       mi++;     /* Death is another wave */        newm=savm;
       /* if(mi==0)  never been interviewed correctly before death */        /* Covariates have to be included here again */
          /* Only death is a correct wave */        cov[1]=1.;
       mw[mi][i]=m;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
     wav[i]=mi;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     if(mi==0)        for (k=1; k<=cptcovprod;k++)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }  
   
   for(i=1; i<=imx; i++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for(mi=1; mi<wav[i];mi++){        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       if (stepm <=0)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         dh[mi][i]=1;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       else{        savm=oldm;
         if (s[mw[mi+1][i]][i] > nlstate) {        oldm=newm;
           if (agedc[i] < 2*AGESUP) {      }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for(i=1; i<=nlstate+ndeath; i++)
           if(j==0) j=1;  /* Survives at least one month after exam */        for(j=1;j<=nlstate+ndeath;j++) {
           k=k+1;          po[i][j][h]=newm[i][j];
           if (j >= jmax) jmax=j;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
           if (j <= jmin) jmin=j;           */
           sum=sum+j;        }
           if (j<0) printf("j=%d num=%d ",j,i);    } /* end h */
           }    return po;
         }  }
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  
           k=k+1;  /*************** log-likelihood *************/
           if (j >= jmax) jmax=j;  double func( double *x)
           else if (j <= jmin)jmin=j;  {
           sum=sum+j;    int i, ii, j, k, mi, d, kk;
         }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         jk= j/stepm;    double **out;
         jl= j -jk*stepm;    double sw; /* Sum of weights */
         ju= j -(jk+1)*stepm;    double lli; /* Individual log likelihood */
         if(jl <= -ju)    int s1, s2;
           dh[mi][i]=jk;    double bbh, survp;
         else    long ipmx;
           dh[mi][i]=jk+1;    /*extern weight */
         if(dh[mi][i]==0)    /* We are differentiating ll according to initial status */
           dh[mi][i]=1; /* At least one step */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
     }      printf(" %d\n",s[4][i]);
   }    */
   jmean=sum/k;    cov[1]=1.;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
 }    for(k=1; k<=nlstate; k++) ll[k]=0.;
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)    if(mle==1){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int Ndum[20],ij=1, k, j, i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int cptcode=0;        for(mi=1; mi<= wav[i]-1; mi++){
   cptcoveff=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   for (k=0; k<19; k++) Ndum[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (k=1; k<=7; k++) ncodemax[k]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(d=0; d<dh[mi][i]; d++){
     for (i=1; i<=imx; i++) {            newm=savm;
       ij=(int)(covar[Tvar[j]][i]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       Ndum[ij]++;            for (kk=1; kk<=cptcovage;kk++) {
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (ij > cptcode) cptcode=ij;            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=0; i<=cptcode; i++) {            savm=oldm;
       if(Ndum[i]!=0) ncodemax[j]++;            oldm=newm;
     }          } /* end mult */
     ij=1;        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
     for (i=1; i<=ncodemax[j]; i++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       for (k=0; k<=19; k++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
         if (Ndum[k] != 0) {           * the nearest (and in case of equal distance, to the lowest) interval but now
           nbcode[Tvar[j]][ij]=k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           ij++;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         }           * probability in order to take into account the bias as a fraction of the way
         if (ij > ncodemax[j]) break;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       }             * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
   }             * For stepm > 1 the results are less biased than in previous versions. 
            */
  for (k=0; k<19; k++) Ndum[k]=0;          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
  for (i=1; i<=ncovmodel; i++) {          bbh=(double)bh[mi][i]/(double)stepm; 
       ij=Tvar[i];          /* bias bh is positive if real duration
       Ndum[ij]++;           * is higher than the multiple of stepm and negative otherwise.
     }           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
  ij=1;          if( s2 > nlstate){ 
  for (i=1; i<=10; i++) {            /* i.e. if s2 is a death state and if the date of death is known 
    if((Ndum[i]!=0) && (i<=ncov)){               then the contribution to the likelihood is the probability to 
      Tvaraff[ij]=i;               die between last step unit time and current  step unit time, 
      ij++;               which is also equal to probability to die before dh 
    }               minus probability to die before dh-stepm . 
  }               In version up to 0.92 likelihood was computed
            as if date of death was unknown. Death was treated as any other
     cptcoveff=ij-1;          health state: the date of the interview describes the actual state
 }          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
 /*********** Health Expectancies ****************/          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          the contribution of an exact death to the likelihood. This new
 {          contribution is smaller and very dependent of the step unit
   /* Health expectancies */          stepm. It is no more the probability to die between last interview
   int i, j, nhstepm, hstepm, h;          and month of death but the probability to survive from last
   double age, agelim,hf;          interview up to one month before death multiplied by the
   double ***p3mat;          probability to die within a month. Thanks to Chris
            Jackson for correcting this bug.  Former versions increased
   fprintf(ficreseij,"# Health expectancies\n");          mortality artificially. The bad side is that we add another loop
   fprintf(ficreseij,"# Age");          which slows down the processing. The difference can be up to 10%
   for(i=1; i<=nlstate;i++)          lower mortality.
     for(j=1; j<=nlstate;j++)            */
       fprintf(ficreseij," %1d-%1d",i,j);            lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficreseij,"\n");  
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */          } else if  (s2==-2) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   agelim=AGESUP;            /*survp += out[s1][j]; */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            lli= log(survp);
     /* nhstepm age range expressed in number of stepm */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          
     /* Typically if 20 years = 20*12/6=40 stepm */          else if  (s2==-4) { 
     if (stepm >= YEARM) hstepm=1;            for (j=3,survp=0. ; j<=nlstate; j++)  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            lli= log(survp); 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          } 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(i=1; i<=nlstate;i++)            lli= log(survp); 
       for(j=1; j<=nlstate;j++)          } 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          
           eij[i][j][(int)age] +=p3mat[i][j][h];          else{
         }            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 */
     hf=1;          } 
     if (stepm >= YEARM) hf=stepm/YEARM;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     fprintf(ficreseij,"%.0f",age );          /*if(lli ==000.0)*/
     for(i=1; i<=nlstate;i++)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       for(j=1; j<=nlstate;j++){          ipmx +=1;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     fprintf(ficreseij,"\n");        } /* end of wave */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end of individual */
   }    }  else if(mle==2){
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************ Variance ******************/        for(mi=1; mi<= wav[i]-1; mi++){
 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 (ii=1;ii<=nlstate+ndeath;ii++)
 {            for (j=1;j<=nlstate+ndeath;j++){
   /* Variance of health expectancies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **newm;            }
   double **dnewm,**doldm;          for(d=0; d<=dh[mi][i]; d++){
   int i, j, nhstepm, hstepm, h;            newm=savm;
   int k, cptcode;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    double *xp;            for (kk=1; kk<=cptcovage;kk++) {
   double **gp, **gm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double ***gradg, ***trgradg;            }
   double ***p3mat;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double age,agelim;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int theta;            savm=oldm;
             oldm=newm;
    fprintf(ficresvij,"# Covariances of life expectancies\n");          } /* end mult */
   fprintf(ficresvij,"# Age");        
   for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
     for(j=1; j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficresvij,"\n");          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           ipmx +=1;
   xp=vector(1,npar);          sw += weight[i];
   dnewm=matrix(1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   doldm=matrix(1,nlstate,1,nlstate);        } /* end of wave */
        } /* end of individual */
   hstepm=1*YEARM; /* Every year of age */    }  else if(mle==3){  /* exponential inter-extrapolation */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   agelim = AGESUP;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for(mi=1; mi<= wav[i]-1; mi++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (stepm >= YEARM) hstepm=1;            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            }
     gp=matrix(0,nhstepm,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     gm=matrix(0,nhstepm,1,nlstate);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(theta=1; theta <=npar; theta++){            for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            savm=oldm;
       for(j=1; j<= nlstate; j++){            oldm=newm;
         for(h=0; h<=nhstepm; h++){          } /* end mult */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          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 */
       for(i=1; i<=npar; i++) /* Computes gradient */          ipmx +=1;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          sw += weight[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of wave */
       for(j=1; j<= nlstate; j++){      } /* end of individual */
         for(h=0; h<=nhstepm; h++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<= nlstate; j++)            for (j=1;j<=nlstate+ndeath;j++){
         for(h=0; h<=nhstepm; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
     } /* End theta */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(h=0; h<=nhstepm; h++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)            }
         for(theta=1; theta <=npar; theta++)          
           trgradg[h][j][theta]=gradg[h][theta][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1;i<=nlstate;i++)            savm=oldm;
       for(j=1;j<=nlstate;j++)            oldm=newm;
         vareij[i][j][(int)age] =0.;          } /* end mult */
     for(h=0;h<=nhstepm;h++){        
       for(k=0;k<=nhstepm;k++){          s1=s[mw[mi][i]][i];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          s2=s[mw[mi+1][i]][i];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          if( s2 > nlstate){ 
         for(i=1;i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
           for(j=1;j<=nlstate;j++)          }else{
             vareij[i][j][(int)age] += doldm[i][j];            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
     }          ipmx +=1;
     h=1;          sw += weight[i];
     if (stepm >= YEARM) h=stepm/YEARM;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     fprintf(ficresvij,"%.0f ",age );  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(i=1; i<=nlstate;i++)        } /* end of wave */
       for(j=1; j<=nlstate;j++){      } /* end of individual */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficresvij,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_matrix(gp,0,nhstepm,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
     free_matrix(gm,0,nhstepm,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* End age */            }
            for(d=0; d<dh[mi][i]; d++){
   free_vector(xp,1,npar);            newm=savm;
   free_matrix(doldm,1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_matrix(dnewm,1,nlstate,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
           
 /************ Variance of prevlim ******************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 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)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   /* Variance of prevalence limit */            oldm=newm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          } /* end mult */
   double **newm;        
   double **dnewm,**doldm;          s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm;          s2=s[mw[mi+1][i]][i];
   int k, cptcode;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double *xp;          ipmx +=1;
   double *gp, *gm;          sw += weight[i];
   double **gradg, **trgradg;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim;          /*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]);*/
   int theta;        } /* end of wave */
          } /* end of individual */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    } /* End of if */
   fprintf(ficresvpl,"# Age");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for(i=1; i<=nlstate;i++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       fprintf(ficresvpl," %1d-%1d",i,i);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficresvpl,"\n");    return -l;
   }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  /*************** log-likelihood *************/
   doldm=matrix(1,nlstate,1,nlstate);  double funcone( double *x)
    {
   hstepm=1*YEARM; /* Every year of age */    /* Same as likeli but slower because of a lot of printf and if */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int i, ii, j, k, mi, d, kk;
   agelim = AGESUP;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double **out;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double lli; /* Individual log likelihood */
     if (stepm >= YEARM) hstepm=1;    double llt;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int s1, s2;
     gradg=matrix(1,npar,1,nlstate);    double bbh, survp;
     gp=vector(1,nlstate);    /*extern weight */
     gm=vector(1,nlstate);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(theta=1; theta <=npar; theta++){    /*for(i=1;i<imx;i++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */      printf(" %d\n",s[4][i]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    */
       }    cov[1]=1.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         gp[i] = prlim[i][i];  
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<=npar; i++) /* Computes gradient */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(mi=1; mi<= wav[i]-1; mi++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1;i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
         gm[i] = prlim[i][i];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)          }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for(d=0; d<dh[mi][i]; d++){
     } /* End theta */          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     trgradg =matrix(1,nlstate,1,npar);          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         trgradg[j][theta]=gradg[theta][j];                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
     for(i=1;i<=nlstate;i++)          oldm=newm;
       varpl[i][(int)age] =0.;        } /* end mult */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)        s2=s[mw[mi+1][i]][i];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
     fprintf(ficresvpl,"%.0f ",age );         * is higher than the multiple of stepm and negative otherwise.
     for(i=1; i<=nlstate;i++)         */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     fprintf(ficresvpl,"\n");          lli=log(out[s1][s2] - savm[s1][s2]);
     free_vector(gp,1,nlstate);        } else if  (s2==-2) {
     free_vector(gm,1,nlstate);          for (j=1,survp=0. ; j<=nlstate; j++) 
     free_matrix(gradg,1,npar,1,nlstate);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_matrix(trgradg,1,nlstate,1,npar);          lli= log(survp);
   } /* End age */        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   free_vector(xp,1,npar);        } else if(mle==2){
   free_matrix(doldm,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 */
   free_matrix(dnewm,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 */
 }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
 /***********************************************/        } /* End of if */
 /**************** Main Program *****************/        ipmx +=1;
 /***********************************************/        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*int main(int argc, char *argv[])*/  /*       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]); */
 int main()        if(globpr){
 {          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double agedeb, agefin,hf;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double agemin=1.e20, agemax=-1.e20;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
   double fret;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double **xi,tmp,delta;          }
           fprintf(ficresilk," %10.6f\n", -llt);
   double dum; /* Dummy variable */        }
   double ***p3mat;      } /* end of wave */
   int *indx;    } /* end of individual */
   char line[MAXLINE], linepar[MAXLINE];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   char title[MAXLINE];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    if(globpr==0){ /* First time we count the contributions and weights */
   char filerest[FILENAMELENGTH];      gipmx=ipmx;
   char fileregp[FILENAMELENGTH];      gsw=sw;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    }
   int firstobs=1, lastobs=10;    return -l;
   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;  /*************** function likelione ***********/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    {
   int hstepm, nhstepm;    /* This routine should help understanding what is done with 
   double bage, fage, age, agelim, agebase;       the selection of individuals/waves and
   double ftolpl=FTOL;       to check the exact contribution to the likelihood.
   double **prlim;       Plotting could be done.
   double *severity;     */
   double ***param; /* Matrix of parameters */    int k;
   double  *p;  
   double **matcov; /* Matrix of covariance */    if(*globpri !=0){ /* Just counts and sums, no printings */
   double ***delti3; /* Scale */      strcpy(fileresilk,"ilk"); 
   double *delti; /* Scale */      strcat(fileresilk,fileres);
   double ***eij, ***vareij;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double **varpl; /* Variances of prevalence limits by age */        printf("Problem with resultfile: %s\n", fileresilk);
   double *epj, vepp;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";      }
   char *alph[]={"a","a","b","c","d","e"}, str[4];      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 ");
   char z[1]="c", occ;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 #include <sys/time.h>      for(k=1; k<=nlstate; k++) 
 #include <time.h>        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   /* long total_usecs;    }
   struct timeval start_time, end_time;  
      *fretone=(*funcone)(p);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    if(*globpri !=0){
       fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   printf("\nIMACH, Version 0.64b");      fflush(fichtm); 
   printf("\nEnter the parameter file name: ");    } 
     return;
 #ifdef windows  }
   scanf("%s",pathtot);  
   getcwd(pathcd, size);  
   /*cygwin_split_path(pathtot,path,optionfile);  /*********** Maximum Likelihood Estimation ***************/
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
 split(pathtot, path,optionfile);    int i,j, iter;
   chdir(path);    double **xi;
   replace(pathc,path);    double fret;
 #endif    double fretone; /* Only one call to likelihood */
 #ifdef unix    /*  char filerespow[FILENAMELENGTH];*/
   scanf("%s",optionfile);    xi=matrix(1,npar,1,npar);
 #endif    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
 /*-------- arguments in the command line --------*/        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(fileres,"r");    strcpy(filerespow,"pow"); 
   strcat(fileres, optionfile);    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
   /*---------arguments file --------*/      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     goto end;    for (i=1;i<=nlstate;i++)
   }      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   strcpy(filereso,"o");    fprintf(ficrespow,"\n");
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    powell(p,xi,npar,ftol,&iter,&fret,func);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
   /* Reads comments: lines beginning with '#' */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     ungetc(c,ficpar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fgets(line, MAXLINE, ficpar);  
     puts(line);  }
     fputs(line,ficparo);  
   }  /**** Computes Hessian and covariance matrix ***/
   ungetc(c,ficpar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
   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);    double  **a,**y,*x,pd;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    double **hess;
   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);    int i, j,jk;
     int *indx;
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
   ncovmodel=2+cptcovn;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double gompertz(double p[]);
      hess=matrix(1,npar,1,npar);
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */    printf("\nCalculation of the hessian matrix. Wait...\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     ungetc(c,ficpar);    for (i=1;i<=npar;i++){
     fgets(line, MAXLINE, ficpar);      printf("%d",i);fflush(stdout);
     puts(line);      fprintf(ficlog,"%d",i);fflush(ficlog);
     fputs(line,ficparo);     
   }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   ungetc(c,ficpar);      
        /*  printf(" %f ",p[i]);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     for(i=1; i <=nlstate; i++)    }
     for(j=1; j <=nlstate+ndeath-1; j++){    
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (i=1;i<=npar;i++) {
       fprintf(ficparo,"%1d%1d",i1,j1);      for (j=1;j<=npar;j++)  {
       printf("%1d%1d",i,j);        if (j>i) { 
       for(k=1; k<=ncovmodel;k++){          printf(".%d%d",i,j);fflush(stdout);
         fscanf(ficpar," %lf",&param[i][j][k]);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         printf(" %lf",param[i][j][k]);          hess[i][j]=hessij(p,delti,i,j,func,npar);
         fprintf(ficparo," %lf",param[i][j][k]);          
       }          hess[j][i]=hess[i][j];    
       fscanf(ficpar,"\n");          /*printf(" %lf ",hess[i][j]);*/
       printf("\n");        }
       fprintf(ficparo,"\n");      }
     }    }
      printf("\n");
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fprintf(ficlog,"\n");
   p=param[1][1];  
      printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    a=matrix(1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);    y=matrix(1,npar,1,npar);
     puts(line);    x=vector(1,npar);
     fputs(line,ficparo);    indx=ivector(1,npar);
   }    for (i=1;i<=npar;i++)
   ungetc(c,ficpar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for (j=1;j<=npar;j++) {
   for(i=1; i <=nlstate; i++){      for (i=1;i<=npar;i++) x[i]=0;
     for(j=1; j <=nlstate+ndeath-1; j++){      x[j]=1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      lubksb(a,npar,indx,x);
       printf("%1d%1d",i,j);      for (i=1;i<=npar;i++){ 
       fprintf(ficparo,"%1d%1d",i1,j1);        matcov[i][j]=x[i];
       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]);    printf("\n#Hessian matrix#\n");
       }    fprintf(ficlog,"\n#Hessian matrix#\n");
       fscanf(ficpar,"\n");    for (i=1;i<=npar;i++) { 
       printf("\n");      for (j=1;j<=npar;j++) { 
       fprintf(ficparo,"\n");        printf("%.3e ",hess[i][j]);
     }        fprintf(ficlog,"%.3e ",hess[i][j]);
   }      }
   delti=delti3[1][1];      printf("\n");
        fprintf(ficlog,"\n");
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /* Recompute Inverse */
     fgets(line, MAXLINE, ficpar);    for (i=1;i<=npar;i++)
     puts(line);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fputs(line,ficparo);    ludcmp(a,npar,indx,&pd);
   }  
   ungetc(c,ficpar);    /*  printf("\n#Hessian matrix recomputed#\n");
    
   matcov=matrix(1,npar,1,npar);    for (j=1;j<=npar;j++) {
   for(i=1; i <=npar; i++){      for (i=1;i<=npar;i++) x[i]=0;
     fscanf(ficpar,"%s",&str);      x[j]=1;
     printf("%s",str);      lubksb(a,npar,indx,x);
     fprintf(ficparo,"%s",str);      for (i=1;i<=npar;i++){ 
     for(j=1; j <=i; j++){        y[i][j]=x[i];
       fscanf(ficpar," %le",&matcov[i][j]);        printf("%.3e ",y[i][j]);
       printf(" %.5le",matcov[i][j]);        fprintf(ficlog,"%.3e ",y[i][j]);
       fprintf(ficparo," %.5le",matcov[i][j]);      }
     }      printf("\n");
     fscanf(ficpar,"\n");      fprintf(ficlog,"\n");
     printf("\n");    }
     fprintf(ficparo,"\n");    */
   }  
   for(i=1; i <=npar; i++)    free_matrix(a,1,npar,1,npar);
     for(j=i+1;j<=npar;j++)    free_matrix(y,1,npar,1,npar);
       matcov[i][j]=matcov[j][i];    free_vector(x,1,npar);
        free_ivector(indx,1,npar);
   printf("\n");    free_matrix(hess,1,npar,1,npar);
   
   
     /*-------- data file ----------*/  }
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;  /*************** hessian matrix ****************/
     }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     fprintf(ficres,"#%s\n",version);  {
        int i;
     if((fic=fopen(datafile,"r"))==NULL)    {    int l=1, lmax=20;
       printf("Problem with datafile: %s\n", datafile);goto end;    double k1,k2;
     }    double p2[NPARMAX+1];
     double res;
     n= lastobs;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     severity = vector(1,maxwav);    double fx;
     outcome=imatrix(1,maxwav+1,1,n);    int k=0,kmax=10;
     num=ivector(1,n);    double l1;
     moisnais=vector(1,n);  
     annais=vector(1,n);    fx=func(x);
     moisdc=vector(1,n);    for (i=1;i<=npar;i++) p2[i]=x[i];
     andc=vector(1,n);    for(l=0 ; l <=lmax; l++){
     agedc=vector(1,n);      l1=pow(10,l);
     cod=ivector(1,n);      delts=delt;
     weight=vector(1,n);      for(k=1 ; k <kmax; k=k+1){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        delt = delta*(l1*k);
     mint=matrix(1,maxwav,1,n);        p2[theta]=x[theta] +delt;
     anint=matrix(1,maxwav,1,n);        k1=func(p2)-fx;
     s=imatrix(1,maxwav+1,1,n);        p2[theta]=x[theta]-delt;
     adl=imatrix(1,maxwav+1,1,n);            k2=func(p2)-fx;
     tab=ivector(1,NCOVMAX);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     ncodemax=ivector(1,8);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
     i=1;  #ifdef DEBUG
     while (fgets(line, MAXLINE, fic) != NULL)    {        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);
       if ((i >= firstobs) && (i <=lastobs)) {        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 (j=maxwav;j>=1;j--){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           strcpy(line,stra);          k=kmax;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
                }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          delts=delt;
         }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     delti[theta]=delts;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    return res; 
         for (j=ncov;j>=1;j--){    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  }
         }  
         num[i]=atol(stra);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
         /*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]));*/    int i;
     int l=1, l1, lmax=20;
         i=i+1;    double k1,k2,k3,k4,res,fx;
       }    double p2[NPARMAX+1];
     }    int k;
   
     /*scanf("%d",i);*/    fx=func(x);
   imx=i-1; /* Number of individuals */    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   /* Calculation of the number of parameter from char model*/      p2[thetai]=x[thetai]+delti[thetai]/k;
   Tvar=ivector(1,15);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   Tprod=ivector(1,15);      k1=func(p2)-fx;
   Tvaraff=ivector(1,15);    
   Tvard=imatrix(1,15,1,2);      p2[thetai]=x[thetai]+delti[thetai]/k;
   Tage=ivector(1,15);            p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k2=func(p2)-fx;
   if (strlen(model) >1){    
     j=0, j1=0, k1=1, k2=1;      p2[thetai]=x[thetai]-delti[thetai]/k;
     j=nbocc(model,'+');      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     j1=nbocc(model,'*');      k3=func(p2)-fx;
     cptcovn=j+1;    
     cptcovprod=j1;      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k4=func(p2)-fx;
     strcpy(modelsav,model);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  #ifdef DEBUG
       printf("Error. Non available option model=%s ",model);      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);
       goto end;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }  #endif
        }
     for(i=(j+1); i>=1;i--){    return res;
       cutv(stra,strb,modelsav,'+');  }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  /************** Inverse of matrix **************/
       /*scanf("%d",i);*/  void ludcmp(double **a, int n, int *indx, double *d) 
       if (strchr(strb,'*')) {  { 
         cutv(strd,strc,strb,'*');    int i,imax,j,k; 
         if (strcmp(strc,"age")==0) {    double big,dum,sum,temp; 
           cptcovprod--;    double *vv; 
           cutv(strb,stre,strd,'V');   
           Tvar[i]=atoi(stre);    vv=vector(1,n); 
           cptcovage++;    *d=1.0; 
             Tage[cptcovage]=i;    for (i=1;i<=n;i++) { 
             /*printf("stre=%s ", stre);*/      big=0.0; 
         }      for (j=1;j<=n;j++) 
         else if (strcmp(strd,"age")==0) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
           cptcovprod--;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           cutv(strb,stre,strc,'V');      vv[i]=1.0/big; 
           Tvar[i]=atoi(stre);    } 
           cptcovage++;    for (j=1;j<=n;j++) { 
           Tage[cptcovage]=i;      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
         else {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           cutv(strb,stre,strc,'V');        a[i][j]=sum; 
           Tvar[i]=ncov+k1;      } 
           cutv(strb,strc,strd,'V');      big=0.0; 
           Tprod[k1]=i;      for (i=j;i<=n;i++) { 
           Tvard[k1][1]=atoi(strc);        sum=a[i][j]; 
           Tvard[k1][2]=atoi(stre);        for (k=1;k<j;k++) 
           Tvar[cptcovn+k2]=Tvard[k1][1];          sum -= a[i][k]*a[k][j]; 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        a[i][j]=sum; 
           for (k=1; k<=lastobs;k++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          big=dum; 
           k1++;          imax=i; 
           k2=k2+2;        } 
         }      } 
       }      if (j != imax) { 
       else {        for (k=1;k<=n;k++) { 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          dum=a[imax][k]; 
        /*  scanf("%d",i);*/          a[imax][k]=a[j][k]; 
       cutv(strd,strc,strb,'V');          a[j][k]=dum; 
       Tvar[i]=atoi(strc);        } 
       }        *d = -(*d); 
       strcpy(modelsav,stra);          vv[imax]=vv[j]; 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      } 
         scanf("%d",i);*/      indx[j]=imax; 
     }      if (a[j][j] == 0.0) a[j][j]=TINY; 
 }      if (j != n) { 
          dum=1.0/(a[j][j]); 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   printf("cptcovprod=%d ", cptcovprod);      } 
   scanf("%d ",i);*/    } 
     fclose(fic);    free_vector(vv,1,n);  /* Doesn't work */
   ;
     /*  if(mle==1){*/  } 
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;  void lubksb(double **a, int n, int *indx, double b[]) 
     }  { 
     /*-calculation of age at interview from date of interview and age at death -*/    int i,ii=0,ip,j; 
     agev=matrix(1,maxwav,1,imx);    double sum; 
       
     for (i=1; i<=imx; i++)  {    for (i=1;i<=n;i++) { 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      ip=indx[i]; 
       for(m=1; (m<= maxwav); m++){      sum=b[ip]; 
         if(s[m][i] >0){      b[ip]=b[i]; 
           if (s[m][i] == nlstate+1) {      if (ii) 
             if(agedc[i]>0)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
               if(moisdc[i]!=99 && andc[i]!=9999)      else if (sum) ii=i; 
               agev[m][i]=agedc[i];      b[i]=sum; 
             else {    } 
               if (andc[i]!=9999){    for (i=n;i>=1;i--) { 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      sum=b[i]; 
               agev[m][i]=-1;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
               }      b[i]=sum/a[i][i]; 
             }    } 
           }  } 
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  void pstamp(FILE *fichier)
             if(mint[m][i]==99 || anint[m][i]==9999)  {
               agev[m][i]=1;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
             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);*/  /************ Frequencies ********************/
             }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
             else if(agev[m][i] >agemax){  {  /* Some frequencies */
               agemax=agev[m][i];    
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
             }    int first;
             /*agev[m][i]=anint[m][i]-annais[i];*/    double ***freq; /* Frequencies */
             /*   agev[m][i] = age[i]+2*m;*/    double *pp, **prop;
           }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           else { /* =9 */    char fileresp[FILENAMELENGTH];
             agev[m][i]=1;    
             s[m][i]=-1;    pp=vector(1,nlstate);
           }    prop=matrix(1,nlstate,iagemin,iagemax+3);
         }    strcpy(fileresp,"p");
         else /*= 0 Unknown */    strcat(fileresp,fileres);
           agev[m][i]=1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
       }      printf("Problem with prevalence resultfile: %s\n", fileresp);
          fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     }      exit(0);
     for (i=1; i<=imx; i++)  {    }
       for(m=1; (m<= maxwav); m++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         if (s[m][i] > (nlstate+ndeath)) {    j1=0;
           printf("Error: Wrong value in nlstate or ndeath\n");      
           goto end;    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }  
     }    first=1;
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     free_vector(severity,1,maxwav);        j1++;
     free_imatrix(outcome,1,maxwav+1,1,n);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     free_vector(moisnais,1,n);          scanf("%d", i);*/
     free_vector(annais,1,n);        for (i=-5; i<=nlstate+ndeath; i++)  
     free_matrix(mint,1,maxwav,1,n);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     free_matrix(anint,1,maxwav,1,n);            for(m=iagemin; m <= iagemax+3; m++)
     free_vector(moisdc,1,n);              freq[i][jk][m]=0;
     free_vector(andc,1,n);  
       for (i=1; i<=nlstate; i++)  
            for(m=iagemin; m <= iagemax+3; m++)
     wav=ivector(1,imx);          prop[i][m]=0;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        dateintsum=0;
            k2cpt=0;
     /* Concatenates waves */        for (i=1; i<=imx; i++) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
       Tcode=ivector(1,100);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                bool=0;
       ncodemax[1]=1;          }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          if (bool==1){
                  for(m=firstpass; m<=lastpass; m++){
    codtab=imatrix(1,100,1,10);              k2=anint[m][i]+(mint[m][i]/12.);
    h=0;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
    m=pow(2,cptcoveff);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
    for(k=1;k<=cptcoveff; k++){                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      for(i=1; i <=(m/pow(2,k));i++){                if (m<lastpass) {
        for(j=1; j <= ncodemax[k]; j++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
            h++;                }
            if (h>m) h=1;codtab[h][k]=j;                
          }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
        }                  dateintsum=dateintsum+k2;
      }                  k2cpt++;
    }                }
                 /*}*/
             }
    /*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);         
      }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      printf("\n");        pstamp(ficresp);
    }        if  (cptcovn>0) {
    scanf("%d",i);*/          fprintf(ficresp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    /* Calculates basic frequencies. Computes observed prevalence at single age          fprintf(ficresp, "**********\n#");
        and prints on file fileres'p'. */        }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresp, "\n");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=iagemin; i <= iagemax+3; i++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(i==iagemax+3){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            fprintf(ficlog,"Total");
              }else{
     /* For Powell, parameters are in a vector p[] starting at p[1]            if(first==1){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              first=0;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              printf("See log file for details...\n");
             }
     if(mle==1){            fprintf(ficlog,"Age %d", i);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          }
     }          for(jk=1; jk <=nlstate ; jk++){
                for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     /*--------- results files --------------*/              pp[jk] += freq[jk][m][i]; 
     fprintf(ficres,"\ntitle=%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=1; jk <=nlstate ; jk++){
    jk=1;            for(m=-1, pos=0; m <=0 ; m++)
    fprintf(ficres,"# Parameters\n");              pos += freq[jk][m][i];
    printf("# Parameters\n");            if(pp[jk]>=1.e-10){
    for(i=1,jk=1; i <=nlstate; i++){              if(first==1){
      for(k=1; k <=(nlstate+ndeath); k++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        if (k != i)              }
          {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
            printf("%d%d ",i,k);            }else{
            fprintf(ficres,"%1d%1d ",i,k);              if(first==1)
            for(j=1; j <=ncovmodel; j++){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              printf("%f ",p[jk]);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              fprintf(ficres,"%f ",p[jk]);            }
              jk++;          }
            }  
            printf("\n");          for(jk=1; jk <=nlstate ; jk++){
            fprintf(ficres,"\n");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
          }              pp[jk] += freq[jk][m][i];
      }          }       
    }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
  if(mle==1){            pos += pp[jk];
     /* Computing hessian and covariance matrix */            posprop += prop[jk][i];
     ftolhess=ftol; /* Usually correct */          }
     hesscov(matcov, p, npar, delti, ftolhess, func);          for(jk=1; jk <=nlstate ; jk++){
  }            if(pos>=1.e-5){
     fprintf(ficres,"# Scales\n");              if(first==1)
     printf("# Scales\n");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      for(i=1,jk=1; i <=nlstate; i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(j=1; j <=nlstate+ndeath; j++){            }else{
         if (j!=i) {              if(first==1)
           fprintf(ficres,"%1d%1d",i,j);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           printf("%1d%1d",i,j);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           for(k=1; k<=ncovmodel;k++){            }
             printf(" %.5e",delti[jk]);            if( i <= iagemax){
             fprintf(ficres," %.5e",delti[jk]);              if(pos>=1.e-5){
             jk++;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           }                /*probs[i][jk][j1]= pp[jk]/pos;*/
           printf("\n");                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           fprintf(ficres,"\n");              }
         }              else
       }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       }            }
              }
     k=1;          
     fprintf(ficres,"# Covariance\n");          for(jk=-1; jk <=nlstate+ndeath; jk++)
     printf("# Covariance\n");            for(m=-1; m <=nlstate+ndeath; m++)
     for(i=1;i<=npar;i++){              if(freq[jk][m][i] !=0 ) {
       /*  if (k>nlstate) k=1;              if(first==1)
       i1=(i-1)/(ncovmodel*nlstate)+1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       printf("%s%d%d",alph[k],i1,tab[i]);*/              }
       fprintf(ficres,"%3d",i);          if(i <= iagemax)
       printf("%3d",i);            fprintf(ficresp,"\n");
       for(j=1; j<=i;j++){          if(first==1)
         fprintf(ficres," %.5e",matcov[i][j]);            printf("Others in log...\n");
         printf(" %.5e",matcov[i][j]);          fprintf(ficlog,"\n");
       }        }
       fprintf(ficres,"\n");      }
       printf("\n");    }
       k++;    dateintmean=dateintsum/k2cpt; 
     }   
        fclose(ficresp);
     while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       ungetc(c,ficpar);    free_vector(pp,1,nlstate);
       fgets(line, MAXLINE, ficpar);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       puts(line);    /* End of Freq */
       fputs(line,ficparo);  }
     }  
     ungetc(c,ficpar);  /************ Prevalence ********************/
    void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  {  
        /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     if (fage <= 2) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
       bage = agemin;       We still use firstpass and lastpass as another selection.
       fage = agemax;    */
     }   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    double ***freq; /* Frequencies */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    double *pp, **prop;
     double pos,posprop; 
        double  y2; /* in fractional years */
 /*------------ gnuplot -------------*/    int iagemin, iagemax;
 chdir(pathcd);  
   if((ficgp=fopen("graph.plt","w"))==NULL) {    iagemin= (int) agemin;
     printf("Problem with file graph.gp");goto end;    iagemax= (int) agemax;
   }    /*pp=vector(1,nlstate);*/
 #ifdef windows    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   fprintf(ficgp,"cd \"%s\" \n",pathc);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 #endif    j1=0;
 m=pow(2,cptcoveff);    
      j=cptcoveff;
  /* 1eme*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for (cpt=1; cpt<= nlstate ; cpt ++) {    
    for (k1=1; k1<= m ; k1 ++) {    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
 #ifdef windows        j1++;
     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        for (i=1; i<=nlstate; i++)  
 #ifdef unix          for(m=iagemin; m <= iagemax+3; m++)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);            prop[i][m]=0.0;
 #endif       
         for (i=1; i<=imx; i++) { /* Each individual */
 for (i=1; i<= nlstate ; i ++) {          bool=1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if  (cptcovn>0) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for (z1=1; z1<=cptcoveff; z1++) 
 }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                bool=0;
     for (i=1; i<= nlstate ; i ++) {          } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if (bool==1) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
      for (i=1; i<= nlstate ; i ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
 }                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                  /*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]]);*/
 #ifdef unix                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 fprintf(ficgp,"\nset ter gif small size 400,300");                  prop[s[m][i]][iagemax+3] += weight[i]; 
 #endif                } 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
    }            } /* end selection of waves */
   }          }
   /*2 eme*/        }
         for(i=iagemin; i <= iagemax+3; i++){  
   for (k1=1; k1<= m ; k1 ++) {          
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                posprop += prop[jk][i]; 
     for (i=1; i<= nlstate+1 ; i ++) {          } 
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          for(jk=1; jk <=nlstate ; jk++){     
       for (j=1; j<= nlstate+1 ; j ++) {            if( i <=  iagemax){ 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if(posprop>=1.e-5){ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");                probs[i][jk][j1]= prop[jk][i]/posprop;
 }                } 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            } 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          }/* end jk */ 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        }/* end i */ 
       for (j=1; j<= nlstate+1 ; j ++) {      } /* end i1 */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    } /* end k1 */
         else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       fprintf(ficgp,"\" t\"\" w l 0,");    /*free_vector(pp,1,nlstate);*/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       for (j=1; j<= nlstate+1 ; j ++) {  }  /* End of prevalence */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /************* Waves Concatenation ***************/
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  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 fprintf(ficgp,"\" t\"\" w l 0,");  {
     }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);       Death is a valid wave (if date is known).
   }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   /*3eme*/       and mw[mi+1][i]. dh depends on stepm.
        */
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {    int i, mi, m;
       k=2+nlstate*(cpt-1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);       double sum=0., jmean=0.;*/
       for (i=1; i< nlstate ; i ++) {    int first;
         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);    int j, k=0,jk, ju, jl;
       }    double sum=0.;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    first=0;
     }    jmin=1e+5;
   }    jmax=-1;
      jmean=0.;
   /* CV preval stat */    for(i=1; i<=imx; i++){
   for (k1=1; k1<= m ; k1 ++) {      mi=0;
     for (cpt=1; cpt<nlstate ; cpt ++) {      m=firstpass;
       k=3;      while(s[m][i] <= nlstate){
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       for (i=1; i< nlstate ; i ++)          mw[++mi][i]=m;
         fprintf(ficgp,"+$%d",k+i+1);        if(m >=lastpass)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          break;
              else
       l=3+(nlstate+ndeath)*cpt;          m++;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      }/* end while */
       for (i=1; i< nlstate ; i ++) {      if (s[m][i] > nlstate){
         l=3+(nlstate+ndeath)*cpt;        mi++;     /* Death is another wave */
         fprintf(ficgp,"+$%d",l+i+1);        /* if(mi==0)  never been interviewed correctly before death */
       }           /* Only death is a correct wave */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          mw[mi][i]=m;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      }
     }  
   }      wav[i]=mi;
       if(mi==0){
   /* proba elementaires */        nbwarn++;
    for(i=1,jk=1; i <=nlstate; i++){        if(first==0){
     for(k=1; k <=(nlstate+ndeath); k++){          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       if (k != i) {          first=1;
         for(j=1; j <=ncovmodel; j++){        }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        if(first==1){
           /*fprintf(ficgp,"%s",alph[1]);*/          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        }
           jk++;      } /* end mi==0 */
           fprintf(ficgp,"\n");    } /* End individuals */
         }  
       }    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
     }        if (stepm <=0)
           dh[mi][i]=1;
   for(jk=1; jk <=m; jk++) {        else{
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
    i=1;            if (agedc[i] < 2*AGESUP) {
    for(k2=1; k2<=nlstate; k2++) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
      k3=i;              if(j==0) j=1;  /* Survives at least one month after exam */
      for(k=1; k<=(nlstate+ndeath); k++) {              else if(j<0){
        if (k != k2){                nberr++;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                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]);
 ij=1;                j=1; /* Temporary Dangerous patch */
         for(j=3; j <=ncovmodel; j++) {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                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);
             ij++;              }
           }              k=k+1;
           else              if (j >= jmax){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                jmax=j;
         }                ijmax=i;
           fprintf(ficgp,")/(1");              }
                      if (j <= jmin){
         for(k1=1; k1 <=nlstate; k1++){                  jmin=j;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                ijmin=i;
 ij=1;              }
           for(j=3; j <=ncovmodel; j++){              sum=sum+j;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             ij++;            }
           }          }
           else          else{
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            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]); */
           fprintf(ficgp,")");  
         }            k=k+1;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            if (j >= jmax) {
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              jmax=j;
         i=i+ncovmodel;              ijmax=i;
        }            }
      }            else if (j <= jmin){
    }              jmin=j;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              ijmin=i;
   }            }
                /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   fclose(ficgp);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                if(j<0){
 chdir(path);              nberr++;
     free_matrix(agev,1,maxwav,1,imx);              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]);
     free_ivector(wav,1,imx);              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]);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            sum=sum+j;
              }
     free_imatrix(s,1,maxwav+1,1,n);          jk= j/stepm;
              jl= j -jk*stepm;
              ju= j -(jk+1)*stepm;
     free_ivector(num,1,n);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     free_vector(agedc,1,n);            if(jl==0){
     free_vector(weight,1,n);              dh[mi][i]=jk;
     /*free_matrix(covar,1,NCOVMAX,1,n);*/              bh[mi][i]=0;
     fclose(ficparo);            }else{ /* We want a negative bias in order to only have interpolation ie
     fclose(ficres);                    * at the price of an extra matrix product in likelihood */
     /*  }*/              dh[mi][i]=jk+1;
                  bh[mi][i]=ju;
    /*________fin mle=1_________*/            }
              }else{
             if(jl <= -ju){
                dh[mi][i]=jk;
     /* No more information from the sample is required now */              bh[mi][i]=jl;       /* bias is positive if real duration
   /* Reads comments: lines beginning with '#' */                                   * is higher than the multiple of stepm and negative otherwise.
   while((c=getc(ficpar))=='#' && c!= EOF){                                   */
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);            else{
     puts(line);              dh[mi][i]=jk+1;
     fputs(line,ficparo);              bh[mi][i]=ju;
   }            }
   ungetc(c,ficpar);            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              bh[mi][i]=ju; /* At least one step */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              /*  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);*/
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            }
 /*--------- index.htm --------*/          } /* end if mle */
         }
   strcpy(optionfilehtm,optionfile);      } /* end wave */
   strcat(optionfilehtm,".htm");    }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    jmean=sum/k;
     printf("Problem with %s \n",optionfilehtm);goto end;    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);
   }    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
    }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  /*********** Tricode ****************************/
 Total number of observations=%d <br>  void tricode(int *Tvar, int **nbcode, int imx)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  {
 <hr  size=\"2\" color=\"#EC5E5E\">    
 <li>Outputs files<br><br>\n    int Ndum[20],ij=1, k, j, i, maxncov=19;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    int cptcode=0;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    cptcoveff=0; 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>   
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    for (k=0; k<maxncov; k++) Ndum[k]=0;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for (k=1; k<=7; k++) ncodemax[k]=0;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%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);                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
  fprintf(fichtm," <li>Graphs</li><p>");        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  m=cptcoveff;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                                         Tvar[j]. If V=sex and male is 0 and 
                                          female is 1, then  cptcode=1.*/
  j1=0;      }
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      for (i=0; i<=cptcode; i++) {
        j1++;        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 */
        if (cptcovn > 0) {      }
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
          for (cpt=1; cpt<=cptcoveff;cpt++)      ij=1; 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      for (i=1; i<=ncodemax[j]; i++) {
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        for (k=0; k<= maxncov; k++) {
        }          if (Ndum[k] != 0) {
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            nbcode[Tvar[j]][ij]=k; 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
        for(cpt=1; cpt<nlstate;cpt++){            
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            ij++;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          }
        }          if (ij > ncodemax[j]) break; 
     for(cpt=1; cpt<=nlstate;cpt++) {        }  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      } 
 interval) in state (%d): v%s%d%d.gif <br>    }  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }   for (k=0; k< maxncov; k++) Ndum[k]=0;
      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>   for (i=1; i<=ncovmodel-2; i++) { 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     /* 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];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     Ndum[ij]++;
 health expectancies in states (1) and (2): e%s%d.gif<br>   }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  
 fprintf(fichtm,"\n</body>");   ij=1;
    }   for (i=1; i<= maxncov; i++) {
  }     if((Ndum[i]!=0) && (i<=ncovcol)){
 fclose(fichtm);       Tvaraff[ij]=i; /*For printing */
        ij++;
   /*--------------- Prevalence limit --------------*/     }
     }
   strcpy(filerespl,"pl");   
   strcat(filerespl,fileres);   cptcoveff=ij-1; /*Number of simple covariates*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }  /*********** Health Expectancies ****************/
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  {
   fprintf(ficrespl,"\n");    /* Health expectancies, no variances */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   prlim=matrix(1,nlstate,1,nlstate);    double age, agelim, hf;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***p3mat;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double eip;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficreseij);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   k=0;    fprintf(ficreseij,"# Age");
   agebase=agemin;    for(i=1; i<=nlstate;i++){
   agelim=agemax;      for(j=1; j<=nlstate;j++){
   ftolpl=1.e-10;        fprintf(ficreseij," e%1d%1d ",i,j);
   i1=cptcoveff;      }
   if (cptcovn < 1){i1=1;}      fprintf(ficreseij," e%1d. ",i);
     }
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficreseij,"\n");
     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]);*/    if(estepm < stepm){
         fprintf(ficrespl,"\n#******");      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(j=1;j<=cptcoveff;j++)    }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    else  hstepm=estepm;   
         fprintf(ficrespl,"******\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
             * This is mainly to measure the difference between two models: for example
         for (age=agebase; age<=agelim; age++){     * if stepm=24 months pijx are given only every 2 years and by summing them
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           fprintf(ficrespl,"%.0f",age );     * progression in between and thus overestimating or underestimating according
           for(i=1; i<=nlstate;i++)     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficrespl," %.5f", prlim[i][i]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           fprintf(ficrespl,"\n");     * to compare the new estimate of Life expectancy with the same linear 
         }     * hypothesis. A more precise result, taking into account a more precise
       }     * curvature will be obtained if estepm is as small as stepm. */
     }  
   fclose(ficrespl);    /* For example we decided to compute the life expectancy with the smallest unit */
   /*------------- h Pij x at various ages ------------*/    /* 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 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);       nstepm is the number of stepm from age to agelin. 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       Look at hpijx to understand the reason of that which relies in memory size
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       and note for a fixed period like estepm months */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   printf("Computing pij: result on file '%s' \n", filerespij);       survival function given by stepm (the optimization length). Unfortunately it
         means that if the survival funtion is printed only each two years of age and if
   stepsize=(int) (stepm+YEARM-1)/YEARM;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if (stepm<=24) stepsize=2;       results. So we changed our mind and took the option of the best precision.
     */
   agelim=AGESUP;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    agelim=AGESUP;
      /* nhstepm age range expressed in number of stepm */
   k=0;    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   for(cptcov=1;cptcov<=i1;cptcov++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* if (stepm >= YEARM) hstepm=1;*/
       k=k+1;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fprintf(ficrespij,"\n#****** ");    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         fprintf(ficrespij,"******\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           oldm=oldms;savm=savms;      
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf("%d|",(int)age);fflush(stdout);
           fprintf(ficrespij,"# Age");      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           for(i=1; i<=nlstate;i++)      
             for(j=1; j<=nlstate+ndeath;j++)      /* Computing expectancies */
               fprintf(ficrespij," %1d-%1d",i,j);      for(i=1; i<=nlstate;i++)
           fprintf(ficrespij,"\n");        for(j=1; j<=nlstate;j++)
           for (h=0; h<=nhstepm; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             for(i=1; i<=nlstate;i++)            
               for(j=1; j<=nlstate+ndeath;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]);*/
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");          }
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficreseij,"%3.0f",age );
           fprintf(ficrespij,"\n");      for(i=1; i<=nlstate;i++){
         }        eip=0;
     }        for(j=1; j<=nlstate;j++){
   }          eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   fclose(ficrespij);        }
         fprintf(ficreseij,"%9.4f", eip );
   /*---------- Health expectancies and variances ------------*/      }
       fprintf(ficreseij,"\n");
   strcpy(filerest,"t");      
   strcat(filerest,fileres);    }
   if((ficrest=fopen(filerest,"w"))==NULL) {    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    printf("\n");
   }    fprintf(ficlog,"\n");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    
   }
   
   strcpy(filerese,"e");  void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {  {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    /* Covariances of health expectancies eij and of total life expectancies according
   }     to initial status i, ei. .
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
  strcpy(fileresv,"v");    double age, agelim, hf;
   strcat(fileresv,fileres);    double ***p3matp, ***p3matm, ***varhe;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    double **dnewm,**doldm;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double *xp, *xm;
   }    double **gp, **gm;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double ***gradg, ***trgradg;
     int theta;
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    double eip, vip;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       fprintf(ficrest,"\n#****** ");    xp=vector(1,npar);
       for(j=1;j<=cptcoveff;j++)    xm=vector(1,npar);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       fprintf(ficrest,"******\n");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
       fprintf(ficreseij,"\n#****** ");    pstamp(ficresstdeij);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(ficresstdeij,"# Age");
       fprintf(ficreseij,"******\n");    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       for(j=1;j<=cptcoveff;j++)      fprintf(ficresstdeij," e%1d. ",i);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    }
       fprintf(ficresvij,"******\n");    fprintf(ficresstdeij,"\n");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    pstamp(ficrescveij);
       oldm=oldms;savm=savms;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      fprintf(ficrescveij,"# Age");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for(i=1; i<=nlstate;i++)
       oldm=oldms;savm=savms;      for(j=1; j<=nlstate;j++){
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        cptj= (j-1)*nlstate+i;
              for(i2=1; i2<=nlstate;i2++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          for(j2=1; j2<=nlstate;j2++){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            cptj2= (j2-1)*nlstate+i2;
       fprintf(ficrest,"\n");            if(cptj2 <= cptj)
                      fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       hf=1;          }
       if (stepm >= YEARM) hf=stepm/YEARM;      }
       epj=vector(1,nlstate+1);    fprintf(ficrescveij,"\n");
       for(age=bage; age <=fage ;age++){    
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if(estepm < stepm){
         fprintf(ficrest," %.0f",age);      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    else  hstepm=estepm;   
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    /* We compute the life expectancy from trapezoids spaced every estepm months
           }     * This is mainly to measure the difference between two models: for example
           epj[nlstate+1] +=epj[j];     * 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 
         for(i=1, vepp=0.;i <=nlstate;i++)     * progression in between and thus overestimating or underestimating according
           for(j=1;j <=nlstate;j++)     * to the curvature of the survival function. If, for the same date, we 
             vepp += vareij[i][j][(int)age];     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));     * to compare the new estimate of Life expectancy with the same linear 
         for(j=1;j <=nlstate;j++){     * hypothesis. A more precise result, taking into account a more precise
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));     * curvature will be obtained if estepm is as small as stepm. */
         }  
         fprintf(ficrest,"\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. 
     }       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
               Look at hpijx to understand the reason of that which relies in memory size
  fclose(ficreseij);       and note for a fixed period like estepm months */
  fclose(ficresvij);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fclose(ficrest);       survival function given by stepm (the optimization length). Unfortunately it
   fclose(ficpar);       means that if the survival funtion is printed only each two years of age and if
   free_vector(epj,1,nlstate+1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /*  scanf("%d ",i); */       results. So we changed our mind and took the option of the best precision.
     */
   /*------- Variance limit prevalence------*/      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
 strcpy(fileresvpl,"vpl");    /* If stepm=6 months */
   strcat(fileresvpl,fileres);    /* nhstepm age range expressed in number of stepm */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    agelim=AGESUP;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     exit(0);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }    /* if (stepm >= YEARM) hstepm=1;*/
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
  k=0;    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  for(cptcov=1;cptcov<=i1;cptcov++){    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
      k=k+1;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      fprintf(ficresvpl,"\n#****** ");    gp=matrix(0,nhstepm,1,nlstate*nlstate);
      for(j=1;j<=cptcoveff;j++)    gm=matrix(0,nhstepm,1,nlstate*nlstate);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");    for (age=bage; age<=fage; age ++){ 
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
      oldm=oldms;savm=savms;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   
    }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  }  
       /* Computing  Variances of health expectancies */
   fclose(ficresvpl);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
   /*---------- End : free ----------------*/      for(theta=1; theta <=npar; theta++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1; j<= nlstate; j++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(i=1; i<=nlstate; i++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            for(h=0; h<=nhstepm-1; h++){
                gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   free_matrix(matcov,1,npar,1,npar);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   free_vector(delti,1,npar);            }
            }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        }
        
   printf("End of Imach\n");        for(ij=1; ij<= nlstate*nlstate; ij++)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          for(h=0; h<=nhstepm-1; h++){
              gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          }
   /*printf("Total time was %d uSec.\n", total_usecs);*/      }/* End theta */
   /*------ End -----------*/      
       
  end:      for(h=0; h<=nhstepm-1; h++)
 #ifdef windows        for(j=1; j<=nlstate*nlstate;j++)
  chdir(pathcd);          for(theta=1; theta <=npar; theta++)
 #endif            trgradg[h][j][theta]=gradg[h][theta][j];
  /*system("wgnuplot graph.plt");*/      
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/       for(ij=1;ij<=nlstate*nlstate;ij++)
  system("..\\gp37mgw\\wgnuplot graph.plt");        for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
 #ifdef windows  
   while (z[0] != 'q') {       printf("%d|",(int)age);fflush(stdout);
     chdir(pathcd);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       for(h=0;h<=nhstepm-1;h++){
     scanf("%s",z);        for(k=0;k<=nhstepm-1;k++){
     if (z[0] == 'c') system("./imach");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     else if (z[0] == 'e') {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       chdir(path);          for(ij=1;ij<=nlstate*nlstate;ij++)
       system(optionfilehtm);            for(ji=1;ji<=nlstate*nlstate;ji++)
     }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     else if (z[0] == 'q') exit(0);        }
   }      }
 #endif      /* Computing expectancies */
 }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     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);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* 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(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     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 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         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++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       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);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     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)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   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);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* 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;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       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);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   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[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     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;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     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);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     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 \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    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");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           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 "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           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]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             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,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       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 for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
           cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.11  
changed lines
  Added in v.1.122


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