Diff for /imach/src/imach.c between versions 1.23 and 1.122

version 1.23, 2002/02/22 18:08:30 version 1.122, 2006/03/20 09:45:41
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.122  2006/03/20 09:45:41  brouard
      (Module): Weights can have a decimal point as for
   This program computes Healthy Life Expectancies from    English (a comma might work with a correct LC_NUMERIC environment,
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    otherwise the weight is truncated).
   first survey ("cross") where individuals from different ages are    Modification of warning when the covariates values are not 0 or
   interviewed on their health status or degree of disability (in the    1.
   case of a health survey which is our main interest) -2- at least a    Version 0.98g
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.121  2006/03/16 17:45:01  lievre
   computed from the time spent in each health state according to a    * imach.c (Module): Comments concerning covariates added
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Module): refinements in the computation of lli if
   simplest model is the multinomial logistic model where pij is the    status=-2 in order to have more reliable computation if stepm is
   probabibility to be observed in state j at the second wave    not 1 month. Version 0.98f
   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    Revision 1.120  2006/03/16 15:10:38  lievre
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): refinements in the computation of lli if
   complex model than "constant and age", you should modify the program    status=-2 in order to have more reliable computation if stepm is
   where the markup *Covariates have to be included here again* invites    not 1 month. Version 0.98f
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
   The advantage of this computer programme, compared to a simple    computed as likelihood omitting the logarithm. Version O.98e
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.118  2006/03/14 18:20:07  brouard
   intermediate interview, the information is lost, but taken into    (Module): varevsij Comments added explaining the second
   account using an interpolation or extrapolation.      table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   hPijx is the probability to be observed in state i at age x+h    (Module): Function pstamp added
   conditional to the observed state i at age x. The delay 'h' can be    (Module): Version 0.98d
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.117  2006/03/14 17:16:22  brouard
   semester or year) is model as a multinomial logistic.  The hPx    (Module): varevsij Comments added explaining the second
   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    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   hPijx.    (Module): Function pstamp added
     (Module): Version 0.98d
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.116  2006/03/06 10:29:27  brouard
      (Module): Variance-covariance wrong links and
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    varian-covariance of ej. is needed (Saito).
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.115  2006/02/27 12:17:45  brouard
   from the European Union.    (Module): One freematrix added in mlikeli! 0.98c
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.114  2006/02/26 12:57:58  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Some improvements in processing parameter
   **********************************************************************/    filename with strsep.
    
 #include <math.h>    Revision 1.113  2006/02/24 14:20:24  brouard
 #include <stdio.h>    (Module): Memory leaks checks with valgrind and:
 #include <stdlib.h>    datafile was not closed, some imatrix were not freed and on matrix
 #include <unistd.h>    allocation too.
   
 #define MAXLINE 256    Revision 1.112  2006/01/30 09:55:26  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.111  2006/01/25 20:38:18  brouard
 #define windows    (Module): Lots of cleaning and bugs added (Gompertz)
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Comments can be added in data file. Missing date values
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    can be a simple dot '.'.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.110  2006/01/25 00:51:50  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Lots of cleaning and bugs added (Gompertz)
   
 #define NINTERVMAX 8    Revision 1.109  2006/01/24 19:37:15  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): Comments (lines starting with a #) are allowed in data.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.108  2006/01/19 18:05:42  lievre
 #define MAXN 20000    Gnuplot problem appeared...
 #define YEARM 12. /* Number of months per year */    To be fixed
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
   
 int erreur; /* Error number */    Revision 1.106  2006/01/19 13:24:36  brouard
 int nvar;    Some cleaning and links added in html output
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.105  2006/01/05 20:23:19  lievre
 int nlstate=2; /* Number of live states */    *** empty log message ***
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.104  2005/09/30 16:11:43  lievre
 int popbased=0;    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 int *wav; /* Number of waves for this individuual 0 is possible */    that the person is alive, then we can code his/her status as -2
 int maxwav; /* Maxim number of waves */    (instead of missing=-1 in earlier versions) and his/her
 int jmin, jmax; /* min, max spacing between 2 waves */    contributions to the likelihood is 1 - Prob of dying from last
 int mle, weightopt;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    the healthy state at last known wave). Version is 0.98
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.103  2005/09/30 15:54:49  lievre
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): sump fixed, loop imx fixed, and simplifications.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Revision 1.102  2004/09/15 17:31:30  brouard
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    Add the possibility to read data file including tab characters.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.101  2004/09/15 10:38:38  brouard
  FILE  *ficresvij;    Fix on curr_time
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.100  2004/07/12 18:29:06  brouard
   char fileresvpl[FILENAMELENGTH];    Add version for Mac OS X. Just define UNIX in Makefile
   
 #define NR_END 1    Revision 1.99  2004/06/05 08:57:40  brouard
 #define FREE_ARG char*    *** empty log message ***
 #define FTOL 1.0e-10  
     Revision 1.98  2004/05/16 15:05:56  brouard
 #define NRANSI    New version 0.97 . First attempt to estimate force of mortality
 #define ITMAX 200    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
 #define TOL 2.0e-4    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 #define CGOLD 0.3819660    cross-longitudinal survey is different from the mortality estimated
 #define ZEPS 1.0e-10    from other sources like vital statistic data.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     The same imach parameter file can be used but the option for mle should be -3.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Agnès, who wrote this part of the code, tried to keep most of the
 #define TINY 1.0e-20    former routines in order to include the new code within the former code.
   
 static double maxarg1,maxarg2;    The output is very simple: only an estimate of the intercept and of
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    the slope with 95% confident intervals.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Current limitations:
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    A) Even if you enter covariates, i.e. with the
 #define rint(a) floor(a+0.5)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.97  2004/02/20 13:25:42  lievre
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 int imx;  
 int stepm;    Revision 1.96  2003/07/15 15:38:55  brouard
 /* Stepm, step in month: minimum step interpolation*/    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.95  2003/07/08 07:54:34  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    * imach.c (Repository):
 double **pmmij, ***probs, ***mobaverage;    (Repository): Using imachwizard code to output a more meaningful covariance
 double dateintmean=0;    matrix (cov(a12,c31) instead of numbers.
   
 double *weight;    Revision 1.94  2003/06/27 13:00:02  brouard
 int **s; /* Status */    Just cleaning
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    exist so I changed back to asctime which exists.
 double ftolhess; /* Tolerance for computing hessian */    (Module): Version 0.96b
   
 /**************** split *************************/    Revision 1.92  2003/06/25 16:30:45  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
    l1 = strlen( path );                 /* length of path */    (Repository): Elapsed time after each iteration is now output. It
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    helps to forecast when convergence will be reached. Elapsed time
 #ifdef windows    is stamped in powell.  We created a new html file for the graphs
    s = strrchr( path, '\\' );           /* find last / */    concerning matrix of covariance. It has extension -cov.htm.
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.90  2003/06/24 12:34:15  brouard
 #endif    (Module): Some bugs corrected for windows. Also, when
    if ( s == NULL ) {                   /* no directory, so use current */    mle=-1 a template is output in file "or"mypar.txt with the design
 #if     defined(__bsd__)                /* get current working directory */    of the covariance matrix to be input.
       extern char       *getwd( );  
     Revision 1.89  2003/06/24 12:30:52  brouard
       if ( getwd( dirc ) == NULL ) {    (Module): Some bugs corrected for windows. Also, when
 #else    mle=-1 a template is output in file "or"mypar.txt with the design
       extern char       *getcwd( );    of the covariance matrix to be input.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.88  2003/06/23 17:54:56  brouard
 #endif    * 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.
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.87  2003/06/18 12:26:01  brouard
       strcpy( name, path );             /* we've got it */    Version 0.96
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.86  2003/06/17 20:04:08  brouard
       l2 = strlen( s );                 /* length of filename */    (Module): Change position of html and gnuplot routines and added
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    routine fileappend.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.85  2003/06/17 13:12:43  brouard
       dirc[l1-l2] = 0;                  /* add zero */    * imach.c (Repository): Check when date of death was earlier that
    }    current date of interview. It may happen when the death was just
    l1 = strlen( dirc );                 /* length of directory */    prior to the death. In this case, dh was negative and likelihood
 #ifdef windows    was wrong (infinity). We still send an "Error" but patch by
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    assuming that the date of death was just one stepm after the
 #else    interview.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Repository): Because some people have very long ID (first column)
 #endif    we changed int to long in num[] and we added a new lvector for
    s = strrchr( name, '.' );            /* find last / */    memory allocation. But we also truncated to 8 characters (left
    s++;    truncation)
    strcpy(ext,s);                       /* save extension */    (Repository): No more line truncation errors.
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.84  2003/06/13 21:44:43  brouard
    strncpy( finame, name, l1-l2);    * imach.c (Repository): Replace "freqsummary" at a correct
    finame[l1-l2]= 0;    place. It differs from routine "prevalence" which may be called
    return( 0 );                         /* we're done */    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /******************************************/    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 void replace(char *s, char*t)  
 {    Revision 1.82  2003/06/05 15:57:20  brouard
   int i;    Add log in  imach.c and  fullversion number is now printed.
   int lg=20;  
   i=0;  */
   lg=strlen(t);  /*
   for(i=0; i<= lg; i++) {     Interpolated Markov Chain
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Short summary of the programme:
   }    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int nbocc(char *s, char occ)    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   int i,j=0;    case of a health survey which is our main interest) -2- at least a
   int lg=20;    second wave of interviews ("longitudinal") which measure each change
   i=0;    (if any) in individual health status.  Health expectancies are
   lg=strlen(s);    computed from the time spent in each health state according to a
   for(i=0; i<= lg; i++) {    model. More health states you consider, more time is necessary to reach the
   if  (s[i] == occ ) j++;    Maximum Likelihood of the parameters involved in the model.  The
   }    simplest model is the multinomial logistic model where pij is the
   return j;    probability to be observed in state j at the second wave
 }    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
 void cutv(char *u,char *v, char*t, char occ)    'age' is age and 'sex' is a covariate. If you want to have a more
 {    complex model than "constant and age", you should modify the program
   int i,lg,j,p=0;    where the markup *Covariates have to be included here again* invites
   i=0;    you to do it.  More covariates you add, slower the
   for(j=0; j<=strlen(t)-1; j++) {    convergence.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
   lg=strlen(t);    identical for each individual. Also, if a individual missed an
   for(j=0; j<p; j++) {    intermediate interview, the information is lost, but taken into
     (u[j] = t[j]);    account using an interpolation or extrapolation.  
   }  
      u[p]='\0';    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
    for(j=0; j<= lg; j++) {    split into an exact number (nh*stepm) of unobserved intermediate
     if (j>=(p+1))(v[j-p-1] = t[j]);    states. This elementary transition (by month, quarter,
   }    semester or year) is modelled as a multinomial logistic.  The hPx
 }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 /********************** nrerror ********************/    hPijx.
   
 void nrerror(char error_text[])    Also this programme outputs the covariance matrix of the parameters but also
 {    of the life expectancies. It also computes the period (stable) prevalence. 
   fprintf(stderr,"ERREUR ...\n");    
   fprintf(stderr,"%s\n",error_text);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   exit(1);             Institut national d'études démographiques, Paris.
 }    This software have been partly granted by Euro-REVES, a concerted action
 /*********************** vector *******************/    from the European Union.
 double *vector(int nl, int nh)    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   double *v;    can be accessed at http://euroreves.ined.fr/imach .
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   return v-nl+NR_END;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 }    
     **********************************************************************/
 /************************ free vector ******************/  /*
 void free_vector(double*v, int nl, int nh)    main
 {    read parameterfile
   free((FREE_ARG)(v+nl-NR_END));    read datafile
 }    concatwav
     freqsummary
 /************************ivector *******************************/    if (mle >= 1)
 int *ivector(long nl,long nh)      mlikeli
 {    print results files
   int *v;    if mle==1 
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));       computes hessian
   if (!v) nrerror("allocation failure in ivector");    read end of parameter file: agemin, agemax, bage, fage, estepm
   return v-nl+NR_END;        begin-prev-date,...
 }    open gnuplot file
     open html file
 /******************free ivector **************************/    period (stable) prevalence
 void free_ivector(int *v, long nl, long nh)     for age prevalim()
 {    h Pij x
   free((FREE_ARG)(v+nl-NR_END));    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /******************* imatrix *******************************/    Variance-covariance of DFLE
 int **imatrix(long nrl, long nrh, long ncl, long nch)    prevalence()
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */     movingaverage()
 {    varevsij() 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    if popbased==1 varevsij(,popbased)
   int **m;    total life expectancies
      Variance of period (stable) prevalence
   /* allocate pointers to rows */   end
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;  
     
    #include <math.h>
   /* allocate rows and set pointers to them */  #include <stdio.h>
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #include <stdlib.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <string.h>
   m[nrl] += NR_END;  #include <unistd.h>
   m[nrl] -= ncl;  
    #include <limits.h>
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #include <sys/types.h>
    #include <sys/stat.h>
   /* return pointer to array of pointers to rows */  #include <errno.h>
   return m;  extern int errno;
 }  
   /* #include <sys/time.h> */
 /****************** free_imatrix *************************/  #include <time.h>
 void free_imatrix(m,nrl,nrh,ncl,nch)  #include "timeval.h"
       int **m;  
       long nch,ncl,nrh,nrl;  /* #include <libintl.h> */
      /* free an int matrix allocated by imatrix() */  /* #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"*/
 /******************* matrix *******************************/  #define FILENAMELENGTH 132
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+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 */
   return m;  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /*************************free matrix ************************/  #define ODIRSEPARATOR '\\'
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #else
 {  #define DIRSEPARATOR '\\'
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define CHARSEPARATOR "\\"
   free((FREE_ARG)(m+nrl-NR_END));  #define ODIRSEPARATOR '/'
 }  #endif
   
 /******************* ma3x *******************************/  /* $Id$ */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /* $State$ */
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
   double ***m;  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   m += NR_END;  int nvar;
   m -= nrl;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int nlstate=2; /* Number of live states */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int ndeath=1; /* Number of dead states */
   m[nrl] += NR_END;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m[nrl] -= ncl;  int popbased=0;
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int jmin, jmax; /* min, max spacing between 2 waves */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   m[nrl][ncl] += NR_END;  int gipmx, gsw; /* Global variables on the number of contributions 
   m[nrl][ncl] -= nll;                     to the likelihood and the sum of weights (done by funcone)*/
   for (j=ncl+1; j<=nch; j++)  int mle, weightopt;
     m[nrl][j]=m[nrl][j-1]+nlay;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for (i=nrl+1; i<=nrh; i++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     for (j=ncl+1; j<=nch; j++)  double jmean; /* Mean space between 2 waves */
       m[i][j]=m[i][j-1]+nlay;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   return m;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 }  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
 /*************************free ma3x ************************/  double fretone; /* Only one call to likelihood */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  long ipmx; /* Number of contributions */
 {  double sw; /* Sum of weights */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char filerespow[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /***************** f1dim *************************/  FILE *fichtm, *fichtmcov; /* Html File */
 extern int ncom;  FILE *ficreseij;
 extern double *pcom,*xicom;  char filerese[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  FILE *ficresstdeij;
    char fileresstde[FILENAMELENGTH];
 double f1dim(double x)  FILE *ficrescveij;
 {  char filerescve[FILENAMELENGTH];
   int j;  FILE  *ficresvij;
   double f;  char fileresv[FILENAMELENGTH];
   double *xt;  FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
   xt=vector(1,ncom);  char title[MAXLINE];
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   f=(*nrfunc)(xt);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   free_vector(xt,1,ncom);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   return f;  char command[FILENAMELENGTH];
 }  int  outcmd=0;
   
 /*****************brent *************************/  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  char filelog[FILENAMELENGTH]; /* Log file */
   int iter;  char filerest[FILENAMELENGTH];
   double a,b,d,etemp;  char fileregp[FILENAMELENGTH];
   double fu,fv,fw,fx;  char popfile[FILENAMELENGTH];
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double e=0.0;  
    struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   a=(ax < cx ? ax : cx);  struct timezone tzp;
   b=(ax > cx ? ax : cx);  extern int gettimeofday();
   x=w=v=bx;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   fw=fv=fx=(*f)(x);  long time_value;
   for (iter=1;iter<=ITMAX;iter++) {  extern long time();
     xm=0.5*(a+b);  char strcurr[80], strfor[80];
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  char *endptr;
     printf(".");fflush(stdout);  long lval;
 #ifdef DEBUG  double dval;
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define NR_END 1
 #endif  #define FREE_ARG char*
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #define FTOL 1.0e-10
       *xmin=x;  
       return fx;  #define NRANSI 
     }  #define ITMAX 200 
     ftemp=fu;  
     if (fabs(e) > tol1) {  #define TOL 2.0e-4 
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  #define CGOLD 0.3819660 
       p=(x-v)*q-(x-w)*r;  #define ZEPS 1.0e-10 
       q=2.0*(q-r);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       if (q > 0.0) p = -p;  
       q=fabs(q);  #define GOLD 1.618034 
       etemp=e;  #define GLIMIT 100.0 
       e=d;  #define TINY 1.0e-20 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  static double maxarg1,maxarg2;
       else {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
         d=p/q;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
         u=x+d;    
         if (u-a < tol2 || b-u < tol2)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
           d=SIGN(tol1,xm-x);  #define rint(a) floor(a+0.5)
       }  
     } else {  static double sqrarg;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int agegomp= AGEGOMP;
     fu=(*f)(u);  
     if (fu <= fx) {  int imx; 
       if (u >= x) a=x; else b=x;  int stepm=1;
       SHFT(v,w,x,u)  /* Stepm, step in month: minimum step interpolation*/
         SHFT(fv,fw,fx,fu)  
         } else {  int estepm;
           if (u < x) a=u; else b=u;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
           if (fu <= fw || w == x) {  
             v=w;  int m,nb;
             w=u;  long *num;
             fv=fw;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
             fw=fu;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
           } else if (fu <= fv || v == x || v == w) {  double **pmmij, ***probs;
             v=u;  double *ageexmed,*agecens;
             fv=fu;  double dateintmean=0;
           }  
         }  double *weight;
   }  int **s; /* Status */
   nrerror("Too many iterations in brent");  double *agedc, **covar, idx;
   *xmin=x;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   return fx;  double *lsurv, *lpop, *tpop;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /****************** mnbrak ***********************/  double ftolhess; /* Tolerance for computing hessian */
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /**************** split *************************/
             double (*func)(double))  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   double ulim,u,r,q, dum;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double fu;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
      */ 
   *fa=(*func)(*ax);    char  *ss;                            /* pointer */
   *fb=(*func)(*bx);    int   l1, l2;                         /* length counters */
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)    l1 = strlen(path );                   /* length of path */
       SHFT(dum,*fb,*fa,dum)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   *cx=(*bx)+GOLD*(*bx-*ax);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   *fc=(*func)(*cx);      strcpy( name, path );               /* we got the fullname name because no directory */
   while (*fb > *fc) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     r=(*bx-*ax)*(*fb-*fc);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     q=(*bx-*cx)*(*fb-*fa);      /* get current working directory */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      /*    extern  char* getcwd ( char *buf , int len);*/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     ulim=(*bx)+GLIMIT*(*cx-*bx);        return( GLOCK_ERROR_GETCWD );
     if ((*bx-u)*(u-*cx) > 0.0) {      }
       fu=(*func)(u);      /* got dirc from getcwd*/
     } else if ((*cx-u)*(u-ulim) > 0.0) {      printf(" DIRC = %s \n",dirc);
       fu=(*func)(u);    } else {                              /* strip direcotry from path */
       if (fu < *fc) {      ss++;                               /* after this, the filename */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      l2 = strlen( ss );                  /* length of filename */
           SHFT(*fb,*fc,fu,(*func)(u))      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           }      strcpy( name, ss );         /* save file name */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       u=ulim;      dirc[l1-l2] = 0;                    /* add zero */
       fu=(*func)(u);      printf(" DIRC2 = %s \n",dirc);
     } else {    }
       u=(*cx)+GOLD*(*cx-*bx);    /* We add a separator at the end of dirc if not exists */
       fu=(*func)(u);    l1 = strlen( dirc );                  /* length of directory */
     }    if( dirc[l1-1] != DIRSEPARATOR ){
     SHFT(*ax,*bx,*cx,u)      dirc[l1] =  DIRSEPARATOR;
       SHFT(*fa,*fb,*fc,fu)      dirc[l1+1] = 0; 
       }      printf(" DIRC3 = %s \n",dirc);
 }    }
     ss = strrchr( name, '.' );            /* find last / */
 /*************** linmin ************************/    if (ss >0){
       ss++;
 int ncom;      strcpy(ext,ss);                     /* save extension */
 double *pcom,*xicom;      l1= strlen( name);
 double (*nrfunc)(double []);      l2= strlen(ss)+1;
        strncpy( finame, name, l1-l2);
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      finame[l1-l2]= 0;
 {    }
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);    return( 0 );                          /* we're done */
   double f1dim(double x);  }
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  
   int j;  /******************************************/
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  void replace_back_to_slash(char *s, char*t)
    {
   ncom=n;    int i;
   pcom=vector(1,n);    int lg=0;
   xicom=vector(1,n);    i=0;
   nrfunc=func;    lg=strlen(t);
   for (j=1;j<=n;j++) {    for(i=0; i<= lg; i++) {
     pcom[j]=p[j];      (s[i] = t[i]);
     xicom[j]=xi[j];      if (t[i]== '\\') s[i]='/';
   }    }
   ax=0.0;  }
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int nbocc(char *s, char occ)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  {
 #ifdef DEBUG    int i,j=0;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    int lg=20;
 #endif    i=0;
   for (j=1;j<=n;j++) {    lg=strlen(s);
     xi[j] *= xmin;    for(i=0; i<= lg; i++) {
     p[j] += xi[j];    if  (s[i] == occ ) j++;
   }    }
   free_vector(xicom,1,n);    return j;
   free_vector(pcom,1,n);  }
 }  
   void cutv(char *u,char *v, char*t, char occ)
 /*************** powell ************************/  {
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
             double (*func)(double []))       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
 {       gives u="abcedf" and v="ghi2j" */
   void linmin(double p[], double xi[], int n, double *fret,    int i,lg,j,p=0;
               double (*func)(double []));    i=0;
   int i,ibig,j;    for(j=0; j<=strlen(t)-1; j++) {
   double del,t,*pt,*ptt,*xit;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   double fp,fptt;    }
   double *xits;  
   pt=vector(1,n);    lg=strlen(t);
   ptt=vector(1,n);    for(j=0; j<p; j++) {
   xit=vector(1,n);      (u[j] = t[j]);
   xits=vector(1,n);    }
   *fret=(*func)(p);       u[p]='\0';
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {     for(j=0; j<= lg; j++) {
     fp=(*fret);      if (j>=(p+1))(v[j-p-1] = t[j]);
     ibig=0;    }
     del=0.0;  }
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /********************** nrerror ********************/
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  void nrerror(char error_text[])
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    fprintf(stderr,"ERREUR ...\n");
       fptt=(*fret);    fprintf(stderr,"%s\n",error_text);
 #ifdef DEBUG    exit(EXIT_FAILURE);
       printf("fret=%lf \n",*fret);  }
 #endif  /*********************** vector *******************/
       printf("%d",i);fflush(stdout);  double *vector(int nl, int nh)
       linmin(p,xit,n,fret,func);  {
       if (fabs(fptt-(*fret)) > del) {    double *v;
         del=fabs(fptt-(*fret));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         ibig=i;    if (!v) nrerror("allocation failure in vector");
       }    return v-nl+NR_END;
 #ifdef DEBUG  }
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  /************************ free vector ******************/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  void free_vector(double*v, int nl, int nh)
         printf(" x(%d)=%.12e",j,xit[j]);  {
       }    free((FREE_ARG)(v+nl-NR_END));
       for(j=1;j<=n;j++)  }
         printf(" p=%.12e",p[j]);  
       printf("\n");  /************************ivector *******************************/
 #endif  int *ivector(long nl,long nh)
     }  {
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    int *v;
 #ifdef DEBUG    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       int k[2],l;    if (!v) nrerror("allocation failure in ivector");
       k[0]=1;    return v-nl+NR_END;
       k[1]=-1;  }
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  /******************free ivector **************************/
         printf(" %.12e",p[j]);  void free_ivector(int *v, long nl, long nh)
       printf("\n");  {
       for(l=0;l<=1;l++) {    free((FREE_ARG)(v+nl-NR_END));
         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]);  /************************lvector *******************************/
         }  long *lvector(long nl,long nh)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  {
       }    long *v;
 #endif    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
       free_vector(xit,1,n);  }
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  /******************free lvector **************************/
       free_vector(pt,1,n);  void free_lvector(long *v, long nl, long nh)
       return;  {
     }    free((FREE_ARG)(v+nl-NR_END));
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  /******************* imatrix *******************************/
       xit[j]=p[j]-pt[j];  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       pt[j]=p[j];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     }  { 
     fptt=(*func)(ptt);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     if (fptt < fp) {    int **m; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    
       if (t < 0.0) {    /* allocate pointers to rows */ 
         linmin(p,xit,n,fret,func);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         for (j=1;j<=n;j++) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
           xi[j][ibig]=xi[j][n];    m += NR_END; 
           xi[j][n]=xit[j];    m -= nrl; 
         }    
 #ifdef DEBUG    
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    /* allocate rows and set pointers to them */ 
         for(j=1;j<=n;j++)    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
           printf(" %.12e",xit[j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         printf("\n");    m[nrl] += NR_END; 
 #endif    m[nrl] -= ncl; 
       }    
     }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   }    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /**** Prevalence limit ****************/  } 
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        int **m;
      matrix by transitions matrix until convergence is reached */        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   int i, ii,j,k;  { 
   double min, max, maxmin, maxmax,sumnew=0.;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double **matprod2();    free((FREE_ARG) (m+nrl-NR_END)); 
   double **out, cov[NCOVMAX], **pmij();  } 
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   for (ii=1;ii<=nlstate+ndeath;ii++)  {
     for (j=1;j<=nlstate+ndeath;j++){    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double **m;
     }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
    cov[1]=1.;    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m -= nrl;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     /* Covariates have to be included here again */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      cov[2]=agefin;    m[nrl] += NR_END;
      m[nrl] -= ncl;
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    return m;
       }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       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]]];  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   
     savm=oldm;  /******************* ma3x *******************************/
     oldm=newm;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     maxmax=0.;  {
     for(j=1;j<=nlstate;j++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       min=1.;    double ***m;
       max=0.;  
       for(i=1; i<=nlstate; i++) {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         sumnew=0;    if (!m) nrerror("allocation failure 1 in matrix()");
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    m += NR_END;
         prlim[i][j]= newm[i][j]/(1-sumnew);    m -= nrl;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       maxmin=max-min;    m[nrl] += NR_END;
       maxmax=FMAX(maxmax,maxmin);    m[nrl] -= ncl;
     }  
     if(maxmax < ftolpl){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       return prlim;  
     }    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;
     m[nrl][ncl] -= nll;
 /*************** transition probabilities ***************/    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    
 {    for (i=nrl+1; i<=nrh; i++) {
   double s1, s2;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   /*double t34;*/      for (j=ncl+1; j<=nch; j++) 
   int i,j,j1, nc, ii, jj;        m[i][j]=m[i][j-1]+nlay;
     }
     for(i=1; i<= nlstate; i++){    return m; 
     for(j=1; j<i;j++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         /*s2 += param[i][j][nc]*cov[nc];*/    */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /*************************free ma3x ************************/
       ps[i][j]=s2;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for(j=i+1; j<=nlstate+ndeath;j++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free((FREE_ARG)(m+nrl-NR_END));
         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);*/  
       }  /*************** function subdirf ***********/
       ps[i][j]=s2;  char *subdirf(char fileres[])
     }  {
   }    /* Caution optionfilefiname is hidden */
     /*ps[3][2]=1;*/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   for(i=1; i<= nlstate; i++){    strcat(tmpout,fileres);
      s1=0;    return tmpout;
     for(j=1; j<i; j++)  }
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************** function subdirf2 ***********/
       s1+=exp(ps[i][j]);  char *subdirf2(char fileres[], char *preop)
     ps[i][i]=1./(s1+1.);  {
     for(j=1; j<i; j++)    
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /* Caution optionfilefiname is hidden */
     for(j=i+1; j<=nlstate+ndeath; j++)    strcpy(tmpout,optionfilefiname);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    strcat(tmpout,"/");
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    strcat(tmpout,preop);
   } /* end i */    strcat(tmpout,fileres);
     return tmpout;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /*************** function subdirf3 ***********/
       ps[ii][ii]=1;  char *subdirf3(char fileres[], char *preop, char *preop2)
     }  {
   }    
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    strcat(tmpout,"/");
     for(jj=1; jj<= nlstate+ndeath; jj++){    strcat(tmpout,preop);
      printf("%lf ",ps[ii][jj]);    strcat(tmpout,preop2);
    }    strcat(tmpout,fileres);
     printf("\n ");    return tmpout;
     }  }
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*  /***************** f1dim *************************/
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  extern int ncom; 
   goto end;*/  extern double *pcom,*xicom;
     return ps;  extern double (*nrfunc)(double []); 
 }   
   double f1dim(double x) 
 /**************** Product of 2 matrices ******************/  { 
     int j; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double f;
 {    double *xt; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times   
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    xt=vector(1,ncom); 
   /* in, b, out are matrice of pointers which should have been initialized    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
      before: only the contents of out is modified. The function returns    f=(*nrfunc)(xt); 
      a pointer to pointers identical to out */    free_vector(xt,1,ncom); 
   long i, j, k;    return f; 
   for(i=nrl; i<= nrh; i++)  } 
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*****************brent *************************/
         out[i][k] +=in[i][j]*b[j][k];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
   return out;    int iter; 
 }    double a,b,d,etemp;
     double fu,fv,fw,fx;
     double ftemp;
 /************* Higher Matrix Product ***************/    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )   
 {    a=(ax < cx ? ax : cx); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    b=(ax > cx ? ax : cx); 
      duration (i.e. until    x=w=v=bx; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    fw=fv=fx=(*f)(x); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    for (iter=1;iter<=ITMAX;iter++) { 
      (typically every 2 years instead of every month which is too big).      xm=0.5*(a+b); 
      Model is determined by parameters x and covariates have to be      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
      included manually here.      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
      */      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
   int i, j, d, h, k;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double **out, cov[NCOVMAX];      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);
   double **newm;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
   /* Hstepm could be zero and should return the unit matrix */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   for (i=1;i<=nlstate+ndeath;i++)        *xmin=x; 
     for (j=1;j<=nlstate+ndeath;j++){        return fx; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      ftemp=fu;
     }      if (fabs(e) > tol1) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        r=(x-w)*(fx-fv); 
   for(h=1; h <=nhstepm; h++){        q=(x-v)*(fx-fw); 
     for(d=1; d <=hstepm; d++){        p=(x-v)*q-(x-w)*r; 
       newm=savm;        q=2.0*(q-r); 
       /* Covariates have to be included here again */        if (q > 0.0) p = -p; 
       cov[1]=1.;        q=fabs(q); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        etemp=e; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        e=d; 
       for (k=1; k<=cptcovage;k++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (k=1; k<=cptcovprod;k++)        else { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          d=p/q; 
           u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/            d=SIGN(tol1,xm-x); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        } 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      } else { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       savm=oldm;      } 
       oldm=newm;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     }      fu=(*f)(u); 
     for(i=1; i<=nlstate+ndeath; i++)      if (fu <= fx) { 
       for(j=1;j<=nlstate+ndeath;j++) {        if (u >= x) a=x; else b=x; 
         po[i][j][h]=newm[i][j];        SHFT(v,w,x,u) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          SHFT(fv,fw,fx,fu) 
          */          } else { 
       }            if (u < x) a=u; else b=u; 
   } /* end h */            if (fu <= fw || w == x) { 
   return po;              v=w; 
 }              w=u; 
               fv=fw; 
               fw=fu; 
 /*************** log-likelihood *************/            } else if (fu <= fv || v == x || v == w) { 
 double func( double *x)              v=u; 
 {              fv=fu; 
   int i, ii, j, k, mi, d, kk;            } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          } 
   double **out;    } 
   double sw; /* Sum of weights */    nrerror("Too many iterations in brent"); 
   double lli; /* Individual log likelihood */    *xmin=x; 
   long ipmx;    return fx; 
   /*extern weight */  } 
   /* We are differentiating ll according to initial status */  
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  /****************** mnbrak ***********************/
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   */              double (*func)(double)) 
   cov[1]=1.;  { 
     double ulim,u,r,q, dum;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    double fu; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){   
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    *fa=(*func)(*ax); 
     for(mi=1; mi<= wav[i]-1; mi++){    *fb=(*func)(*bx); 
       for (ii=1;ii<=nlstate+ndeath;ii++)    if (*fb > *fa) { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      SHFT(dum,*ax,*bx,dum) 
       for(d=0; d<dh[mi][i]; d++){        SHFT(dum,*fb,*fa,dum) 
         newm=savm;        } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    *cx=(*bx)+GOLD*(*bx-*ax); 
         for (kk=1; kk<=cptcovage;kk++) {    *fc=(*func)(*cx); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    while (*fb > *fc) { 
         }      r=(*bx-*ax)*(*fb-*fc); 
              q=(*bx-*cx)*(*fb-*fa); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         savm=oldm;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         oldm=newm;      if ((*bx-u)*(u-*cx) > 0.0) { 
                fu=(*func)(u); 
              } else if ((*cx-u)*(u-ulim) > 0.0) { 
       } /* end mult */        fu=(*func)(u); 
              if (fu < *fc) { 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
       ipmx +=1;            } 
       sw += weight[i];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        u=ulim; 
     } /* end of wave */        fu=(*func)(u); 
   } /* end of individual */      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        fu=(*func)(u); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      } 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      SHFT(*ax,*bx,*cx,u) 
   return -l;        SHFT(*fa,*fb,*fc,fu) 
 }        } 
   } 
   
 /*********** Maximum Likelihood Estimation ***************/  /*************** linmin ************************/
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  int ncom; 
 {  double *pcom,*xicom;
   int i,j, iter;  double (*nrfunc)(double []); 
   double **xi,*delti;   
   double fret;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   xi=matrix(1,npar,1,npar);  { 
   for (i=1;i<=npar;i++)    double brent(double ax, double bx, double cx, 
     for (j=1;j<=npar;j++)                 double (*f)(double), double tol, double *xmin); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    double f1dim(double x); 
   printf("Powell\n");    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   powell(p,xi,npar,ftol,&iter,&fret,func);                double *fc, double (*func)(double)); 
     int j; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double xx,xmin,bx,ax; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double fx,fb,fa;
    
 }    ncom=n; 
     pcom=vector(1,n); 
 /**** Computes Hessian and covariance matrix ***/    xicom=vector(1,n); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    nrfunc=func; 
 {    for (j=1;j<=n;j++) { 
   double  **a,**y,*x,pd;      pcom[j]=p[j]; 
   double **hess;      xicom[j]=xi[j]; 
   int i, j,jk;    } 
   int *indx;    ax=0.0; 
     xx=1.0; 
   double hessii(double p[], double delta, int theta, double delti[]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double hessij(double p[], double delti[], int i, int j);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  #ifdef DEBUG
   void ludcmp(double **a, int npar, int *indx, double *d) ;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   hess=matrix(1,npar,1,npar);  #endif
     for (j=1;j<=n;j++) { 
   printf("\nCalculation of the hessian matrix. Wait...\n");      xi[j] *= xmin; 
   for (i=1;i<=npar;i++){      p[j] += xi[j]; 
     printf("%d",i);fflush(stdout);    } 
     hess[i][i]=hessii(p,ftolhess,i,delti);    free_vector(xicom,1,n); 
     /*printf(" %f ",p[i]);*/    free_vector(pcom,1,n); 
     /*printf(" %lf ",hess[i][i]);*/  } 
   }  
    char *asc_diff_time(long time_sec, char ascdiff[])
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++)  {    long sec_left, days, hours, minutes;
       if (j>i) {    days = (time_sec) / (60*60*24);
         printf(".%d%d",i,j);fflush(stdout);    sec_left = (time_sec) % (60*60*24);
         hess[i][j]=hessij(p,delti,i,j);    hours = (sec_left) / (60*60) ;
         hess[j][i]=hess[i][j];        sec_left = (sec_left) %(60*60);
         /*printf(" %lf ",hess[i][j]);*/    minutes = (sec_left) /60;
       }    sec_left = (sec_left) % (60);
     }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   }    return ascdiff;
   printf("\n");  }
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /*************** powell ************************/
    void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   a=matrix(1,npar,1,npar);              double (*func)(double [])) 
   y=matrix(1,npar,1,npar);  { 
   x=vector(1,npar);    void linmin(double p[], double xi[], int n, double *fret, 
   indx=ivector(1,npar);                double (*func)(double [])); 
   for (i=1;i<=npar;i++)    int i,ibig,j; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    double del,t,*pt,*ptt,*xit;
   ludcmp(a,npar,indx,&pd);    double fp,fptt;
     double *xits;
   for (j=1;j<=npar;j++) {    int niterf, itmp;
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;    pt=vector(1,n); 
     lubksb(a,npar,indx,x);    ptt=vector(1,n); 
     for (i=1;i<=npar;i++){    xit=vector(1,n); 
       matcov[i][j]=x[i];    xits=vector(1,n); 
     }    *fret=(*func)(p); 
   }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   printf("\n#Hessian matrix#\n");      fp=(*fret); 
   for (i=1;i<=npar;i++) {      ibig=0; 
     for (j=1;j<=npar;j++) {      del=0.0; 
       printf("%.3e ",hess[i][j]);      last_time=curr_time;
     }      (void) gettimeofday(&curr_time,&tzp);
     printf("\n");      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);
   }      /*    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);
   /* Recompute Inverse */      */
   for (i=1;i<=npar;i++)     for (i=1;i<=n;i++) {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        printf(" %d %.12f",i, p[i]);
   ludcmp(a,npar,indx,&pd);        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   /*  printf("\n#Hessian matrix recomputed#\n");      }
       printf("\n");
   for (j=1;j<=npar;j++) {      fprintf(ficlog,"\n");
     for (i=1;i<=npar;i++) x[i]=0;      fprintf(ficrespow,"\n");fflush(ficrespow);
     x[j]=1;      if(*iter <=3){
     lubksb(a,npar,indx,x);        tm = *localtime(&curr_time.tv_sec);
     for (i=1;i<=npar;i++){        strcpy(strcurr,asctime(&tm));
       y[i][j]=x[i];  /*       asctime_r(&tm,strcurr); */
       printf("%.3e ",y[i][j]);        forecast_time=curr_time; 
     }        itmp = strlen(strcurr);
     printf("\n");        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   }          strcurr[itmp-1]='\0';
   */        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   free_matrix(a,1,npar,1,npar);        for(niterf=10;niterf<=30;niterf+=10){
   free_matrix(y,1,npar,1,npar);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   free_vector(x,1,npar);          tmf = *localtime(&forecast_time.tv_sec);
   free_ivector(indx,1,npar);  /*      asctime_r(&tmf,strfor); */
   free_matrix(hess,1,npar,1,npar);          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
 }          strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 /*************** hessian matrix ****************/          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);
 double hessii( double x[], double delta, int theta, double delti[])        }
 {      }
   int i;      for (i=1;i<=n;i++) { 
   int l=1, lmax=20;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double k1,k2;        fptt=(*fret); 
   double p2[NPARMAX+1];  #ifdef DEBUG
   double res;        printf("fret=%lf \n",*fret);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        fprintf(ficlog,"fret=%lf \n",*fret);
   double fx;  #endif
   int k=0,kmax=10;        printf("%d",i);fflush(stdout);
   double l1;        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
   fx=func(x);        if (fabs(fptt-(*fret)) > del) { 
   for (i=1;i<=npar;i++) p2[i]=x[i];          del=fabs(fptt-(*fret)); 
   for(l=0 ; l <=lmax; l++){          ibig=i; 
     l1=pow(10,l);        } 
     delts=delt;  #ifdef DEBUG
     for(k=1 ; k <kmax; k=k+1){        printf("%d %.12e",i,(*fret));
       delt = delta*(l1*k);        fprintf(ficlog,"%d %.12e",i,(*fret));
       p2[theta]=x[theta] +delt;        for (j=1;j<=n;j++) {
       k1=func(p2)-fx;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       p2[theta]=x[theta]-delt;          printf(" x(%d)=%.12e",j,xit[j]);
       k2=func(p2)-fx;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */        }
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        for(j=1;j<=n;j++) {
                printf(" p=%.12e",p[j]);
 #ifdef DEBUG          fprintf(ficlog," p=%.12e",p[j]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        }
 #endif        printf("\n");
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        fprintf(ficlog,"\n");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  #endif
         k=kmax;      } 
       }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  #ifdef DEBUG
         k=kmax; l=lmax*10.;        int k[2],l;
       }        k[0]=1;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        k[1]=-1;
         delts=delt;        printf("Max: %.12e",(*func)(p));
       }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
   delti[theta]=delts;          fprintf(ficlog," %.12e",p[j]);
   return res;        }
          printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 double hessij( double x[], double delti[], int thetai,int thetaj)          for (j=1;j<=n;j++) {
 {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   int i;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int l=1, l1, lmax=20;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double k1,k2,k3,k4,res,fx;          }
   double p2[NPARMAX+1];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int k;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   fx=func(x);  #endif
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;        free_vector(xit,1,n); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        free_vector(xits,1,n); 
     k1=func(p2)-fx;        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
     p2[thetai]=x[thetai]+delti[thetai]/k;        return; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } 
     k2=func(p2)-fx;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
        for (j=1;j<=n;j++) { 
     p2[thetai]=x[thetai]-delti[thetai]/k;        ptt[j]=2.0*p[j]-pt[j]; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        xit[j]=p[j]-pt[j]; 
     k3=func(p2)-fx;        pt[j]=p[j]; 
        } 
     p2[thetai]=x[thetai]-delti[thetai]/k;      fptt=(*func)(ptt); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      if (fptt < fp) { 
     k4=func(p2)-fx;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        if (t < 0.0) { 
 #ifdef DEBUG          linmin(p,xit,n,fret,func); 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          for (j=1;j<=n;j++) { 
 #endif            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
   return res;          }
 }  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 /************** Inverse of matrix **************/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 void ludcmp(double **a, int n, int *indx, double *d)          for(j=1;j<=n;j++){
 {            printf(" %.12e",xit[j]);
   int i,imax,j,k;            fprintf(ficlog," %.12e",xit[j]);
   double big,dum,sum,temp;          }
   double *vv;          printf("\n");
            fprintf(ficlog,"\n");
   vv=vector(1,n);  #endif
   *d=1.0;        }
   for (i=1;i<=n;i++) {      } 
     big=0.0;    } 
     for (j=1;j<=n;j++)  } 
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /**** Prevalence limit (stable or period prevalence)  ****************/
     vv[i]=1.0/big;  
   }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (j=1;j<=n;j++) {  {
     for (i=1;i<j;i++) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       sum=a[i][j];       matrix by transitions matrix until convergence is reached */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
     big=0.0;    double **matprod2();
     for (i=j;i<=n;i++) {    double **out, cov[NCOVMAX], **pmij();
       sum=a[i][j];    double **newm;
       for (k=1;k<j;k++)    double agefin, delaymax=50 ; /* Max number of years to converge */
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;    for (ii=1;ii<=nlstate+ndeath;ii++)
       if ( (dum=vv[i]*fabs(sum)) >= big) {      for (j=1;j<=nlstate+ndeath;j++){
         big=dum;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         imax=i;      }
       }  
     }     cov[1]=1.;
     if (j != imax) {   
       for (k=1;k<=n;k++) {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         dum=a[imax][k];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         a[imax][k]=a[j][k];      newm=savm;
         a[j][k]=dum;      /* Covariates have to be included here again */
       }       cov[2]=agefin;
       *d = -(*d);    
       vv[imax]=vv[j];        for (k=1; k<=cptcovn;k++) {
     }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     indx[j]=imax;          /*      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]]);*/
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       dum=1.0/(a[j][j]);        for (k=1; k<=cptcovprod;k++)
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     }  
   }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   free_vector(vv,1,n);  /* Doesn't work */        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 ;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
 void lubksb(double **a, int n, int *indx, double b[])      savm=oldm;
 {      oldm=newm;
   int i,ii=0,ip,j;      maxmax=0.;
   double sum;      for(j=1;j<=nlstate;j++){
          min=1.;
   for (i=1;i<=n;i++) {        max=0.;
     ip=indx[i];        for(i=1; i<=nlstate; i++) {
     sum=b[ip];          sumnew=0;
     b[ip]=b[i];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     if (ii)          prlim[i][j]= newm[i][j]/(1-sumnew);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          max=FMAX(max,prlim[i][j]);
     else if (sum) ii=i;          min=FMIN(min,prlim[i][j]);
     b[i]=sum;        }
   }        maxmin=max-min;
   for (i=n;i>=1;i--) {        maxmax=FMAX(maxmax,maxmin);
     sum=b[i];      }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      if(maxmax < ftolpl){
     b[i]=sum/a[i][i];        return prlim;
   }      }
 }    }
   }
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)  /*************** transition probabilities ***************/ 
 {  /* Some frequencies */  
    double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  {
   double ***freq; /* Frequencies */    double s1, s2;
   double *pp;    /*double t34;*/
   double pos, k2, dateintsum=0,k2cpt=0;    int i,j,j1, nc, ii, jj;
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
   pp=vector(1,nlstate);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            /*s2 += param[i][j][nc]*cov[nc];*/
   strcpy(fileresp,"p");            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   strcat(fileresp,fileres);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   if((ficresp=fopen(fileresp,"w"))==NULL) {          }
     printf("Problem with prevalence resultfile: %s\n", fileresp);          ps[i][j]=s2;
     exit(0);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   }        }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for(j=i+1; j<=nlstate+ndeath;j++){
   j1=0;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
             s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   j=cptcoveff;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          }
           ps[i][j]=s2;
   for(k1=1; k1<=j;k1++){        }
    for(i1=1; i1<=ncodemax[k1];i1++){      }
        j1++;      /*ps[3][2]=1;*/
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      
          scanf("%d", i);*/      for(i=1; i<= nlstate; i++){
         for (i=-1; i<=nlstate+ndeath; i++)          s1=0;
          for (jk=-1; jk<=nlstate+ndeath; jk++)          for(j=1; j<i; j++)
            for(m=agemin; m <= agemax+3; m++)          s1+=exp(ps[i][j]);
              freq[i][jk][m]=0;        for(j=i+1; j<=nlstate+ndeath; j++)
           s1+=exp(ps[i][j]);
         dateintsum=0;        ps[i][i]=1./(s1+1.);
         k2cpt=0;        for(j=1; j<i; j++)
        for (i=1; i<=imx; i++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
          bool=1;        for(j=i+1; j<=nlstate+ndeath; j++)
          if  (cptcovn>0) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
            for (z1=1; z1<=cptcoveff; z1++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      } /* end i */
                bool=0;      
          }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
          if (bool==1) {        for(jj=1; jj<= nlstate+ndeath; jj++){
            for(m=firstpass; m<=lastpass; m++){          ps[ii][jj]=0;
              k2=anint[m][i]+(mint[m][i]/12.);          ps[ii][ii]=1;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        }
                if(agev[m][i]==0) agev[m][i]=agemax+1;      }
                if(agev[m][i]==1) agev[m][i]=agemax+2;      
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
                  dateintsum=dateintsum+k2;  /*         printf("ddd %lf ",ps[ii][jj]); */
                  k2cpt++;  /*       } */
                }  /*       printf("\n "); */
   /*        } */
              }  /*        printf("\n ");printf("%lf ",cov[2]); */
            }         /*
          }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
        }        goto end;*/
         if  (cptcovn>0) {      return ps;
          fprintf(ficresp, "\n#********** Variable ");  }
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
        fprintf(ficresp, "**********\n#");  /**************** Product of 2 matrices ******************/
         }  
        for(i=1; i<=nlstate;i++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  {
        fprintf(ficresp, "\n");    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
               b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   for(i=(int)agemin; i <= (int)agemax+3; i++){    /* in, b, out are matrice of pointers which should have been initialized 
     if(i==(int)agemax+3)       before: only the contents of out is modified. The function returns
       printf("Total");       a pointer to pointers identical to out */
     else    long i, j, k;
       printf("Age %d", i);    for(i=nrl; i<= nrh; i++)
     for(jk=1; jk <=nlstate ; jk++){      for(k=ncolol; k<=ncoloh; k++)
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         pp[jk] += freq[jk][m][i];          out[i][k] +=in[i][j]*b[j][k];
     }  
     for(jk=1; jk <=nlstate ; jk++){    return out;
       for(m=-1, pos=0; m <=0 ; m++)  }
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)  
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  /************* Higher Matrix Product ***************/
       else  
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     }  {
     /* Computes the transition matrix starting at age 'age' over 
      for(jk=1; jk <=nlstate ; jk++){       'nhstepm*hstepm*stepm' months (i.e. until
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         pp[jk] += freq[jk][m][i];       nhstepm*hstepm matrices. 
      }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
     for(jk=1,pos=0; jk <=nlstate ; jk++)       for the memory).
       pos += pp[jk];       Model is determined by parameters x and covariates have to be 
     for(jk=1; jk <=nlstate ; jk++){       included manually here. 
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);       */
       else  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    int i, j, d, h, k;
       if( i <= (int) agemax){    double **out, cov[NCOVMAX];
         if(pos>=1.e-5){    double **newm;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
           probs[i][jk][j1]= pp[jk]/pos;    /* Hstepm could be zero and should return the unit matrix */
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    for (i=1;i<=nlstate+ndeath;i++)
         }      for (j=1;j<=nlstate+ndeath;j++){
       else        oldm[i][j]=(i==j ? 1.0 : 0.0);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }      }
     }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    for(h=1; h <=nhstepm; h++){
       for(m=-1; m <=nlstate+ndeath; m++)      for(d=1; d <=hstepm; d++){
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        newm=savm;
     if(i <= (int) agemax)        /* Covariates have to be included here again */
       fprintf(ficresp,"\n");        cov[1]=1.;
     printf("\n");        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++)
  }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   dateintmean=dateintsum/k2cpt;        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]]];
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   /* End of Freq */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 /************ Prevalence ********************/        oldm=newm;
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      }
 {  /* Some frequencies */      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          po[i][j][h]=newm[i][j];
   double ***freq; /* Frequencies */          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   double *pp;           */
   double pos, k2;        }
     } /* end h */
   pp=vector(1,nlstate);    return po;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
    
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  /*************** log-likelihood *************/
    double func( double *x)
   j=cptcoveff;  {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
  for(k1=1; k1<=j;k1++){    double **out;
     for(i1=1; i1<=ncodemax[k1];i1++){    double sw; /* Sum of weights */
       j1++;    double lli; /* Individual log likelihood */
      int s1, s2;
       for (i=-1; i<=nlstate+ndeath; i++)      double bbh, survp;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      long ipmx;
           for(m=agemin; m <= agemax+3; m++)    /*extern weight */
             freq[i][jk][m]=0;    /* We are differentiating ll according to initial status */
          /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for (i=1; i<=imx; i++) {    /*for(i=1;i<imx;i++) 
         bool=1;      printf(" %d\n",s[4][i]);
         if  (cptcovn>0) {    */
           for (z1=1; z1<=cptcoveff; z1++)    cov[1]=1.;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
         if (bool==1) {    if(mle==1){
           for(m=firstpass; m<=lastpass; m++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=1;j<=nlstate+ndeath;j++){
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];                savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                  for (kk=1; kk<=cptcovage;kk++) {
         for(i=(int)agemin; i <= (int)agemax+3; i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(jk=1; jk <=nlstate ; jk++){            }
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }            savm=oldm;
           for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
             for(m=-1, pos=0; m <=0 ; m++)          } /* end mult */
             pos += freq[jk][m][i];        
         }          /*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(jk=1; jk <=nlstate ; jk++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
              pp[jk] += freq[jk][m][i];           * the nearest (and in case of equal distance, to the lowest) interval but now
          }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                     * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
          for(jk=1; jk <=nlstate ; jk++){                     * -stepm/2 to stepm/2 .
            if( i <= (int) agemax){           * For stepm=1 the results are the same as for previous versions of Imach.
              if(pos>=1.e-5){           * For stepm > 1 the results are less biased than in previous versions. 
                probs[i][jk][j1]= pp[jk]/pos;           */
              }          s1=s[mw[mi][i]][i];
            }          s2=s[mw[mi+1][i]][i];
          }          bbh=(double)bh[mi][i]/(double)stepm; 
                    /* bias bh is positive if real duration
         }           * is higher than the multiple of stepm and negative otherwise.
     }           */
   }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            if( s2 > nlstate){ 
              /* i.e. if s2 is a death state and if the date of death is known 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);               then the contribution to the likelihood is the probability to 
   free_vector(pp,1,nlstate);               die between last step unit time and current  step unit time, 
                 which is also equal to probability to die before dh 
 }  /* End of Freq */               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
 /************* Waves Concatenation ***************/          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          and not the date of a change in health state. The former idea was
 {          to consider that at each interview the state was recorded
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          (healthy, disable or death) and IMaCh was corrected; but when we
      Death is a valid wave (if date is known).          introduced the exact date of death then we should have modified
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          the contribution of an exact death to the likelihood. This new
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          contribution is smaller and very dependent of the step unit
      and mw[mi+1][i]. dh depends on stepm.          stepm. It is no more the probability to die between last interview
      */          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
   int i, mi, m;          probability to die within a month. Thanks to Chris
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          Jackson for correcting this bug.  Former versions increased
      double sum=0., jmean=0.;*/          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
   int j, k=0,jk, ju, jl;          lower mortality.
   double sum=0.;            */
   jmin=1e+5;            lli=log(out[s1][s2] - savm[s1][s2]);
   jmax=-1;  
   jmean=0.;  
   for(i=1; i<=imx; i++){          } else if  (s2==-2) {
     mi=0;            for (j=1,survp=0. ; j<=nlstate; j++) 
     m=firstpass;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     while(s[m][i] <= nlstate){            /*survp += out[s1][j]; */
       if(s[m][i]>=1)            lli= log(survp);
         mw[++mi][i]=m;          }
       if(m >=lastpass)          
         break;          else if  (s2==-4) { 
       else            for (j=3,survp=0. ; j<=nlstate; j++)  
         m++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }/* end while */            lli= log(survp); 
     if (s[m][i] > nlstate){          } 
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */          else if  (s2==-5) { 
          /* Only death is a correct wave */            for (j=1,survp=0. ; j<=2; j++)  
       mw[mi][i]=m;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }            lli= log(survp); 
           } 
     wav[i]=mi;          
     if(mi==0)          else{
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            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 */
           } 
   for(i=1; i<=imx; i++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for(mi=1; mi<wav[i];mi++){          /*if(lli ==000.0)*/
       if (stepm <=0)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         dh[mi][i]=1;          ipmx +=1;
       else{          sw += weight[i];
         if (s[mw[mi+1][i]][i] > nlstate) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if (agedc[i] < 2*AGESUP) {        } /* end of wave */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      } /* end of individual */
           if(j==0) j=1;  /* Survives at least one month after exam */    }  else if(mle==2){
           k=k+1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if (j >= jmax) jmax=j;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (j <= jmin) jmin=j;        for(mi=1; mi<= wav[i]-1; mi++){
           sum=sum+j;          for (ii=1;ii<=nlstate+ndeath;ii++)
           /* if (j<10) printf("j=%d num=%d ",j,i); */            for (j=1;j<=nlstate+ndeath;j++){
           }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         else{            }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          for(d=0; d<=dh[mi][i]; d++){
           k=k+1;            newm=savm;
           if (j >= jmax) jmax=j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           else if (j <= jmin)jmin=j;            for (kk=1; kk<=cptcovage;kk++) {
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           sum=sum+j;            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         jk= j/stepm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         jl= j -jk*stepm;            savm=oldm;
         ju= j -(jk+1)*stepm;            oldm=newm;
         if(jl <= -ju)          } /* end mult */
           dh[mi][i]=jk;        
         else          s1=s[mw[mi][i]][i];
           dh[mi][i]=jk+1;          s2=s[mw[mi+1][i]][i];
         if(dh[mi][i]==0)          bbh=(double)bh[mi][i]/(double)stepm; 
           dh[mi][i]=1; /* At least one step */          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;
     }          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   jmean=sum/k;        } /* end of wave */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      } /* end of individual */
  }    }  else if(mle==3){  /* exponential inter-extrapolation */
 /*********** Tricode ****************************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void tricode(int *Tvar, int **nbcode, int imx)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   int Ndum[20],ij=1, k, j, i;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int cptcode=0;            for (j=1;j<=nlstate+ndeath;j++){
   cptcoveff=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (k=0; k<19; k++) Ndum[k]=0;            }
   for (k=1; k<=7; k++) ncodemax[k]=0;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for (i=1; i<=imx; i++) {            for (kk=1; kk<=cptcovage;kk++) {
       ij=(int)(covar[Tvar[j]][i]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       Ndum[ij]++;            }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if (ij > cptcode) cptcode=ij;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
             oldm=newm;
     for (i=0; i<=cptcode; i++) {          } /* end mult */
       if(Ndum[i]!=0) ncodemax[j]++;        
     }          s1=s[mw[mi][i]][i];
     ij=1;          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<=ncodemax[j]; i++) {          ipmx +=1;
       for (k=0; k<=19; k++) {          sw += weight[i];
         if (Ndum[k] != 0) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           nbcode[Tvar[j]][ij]=k;        } /* end of wave */
           ij++;      } /* end of individual */
         }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         if (ij > ncodemax[j]) break;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }            for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
  for (k=0; k<19; k++) Ndum[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (i=1; i<=ncovmodel-2; i++) {            }
       ij=Tvar[i];          for(d=0; d<dh[mi][i]; d++){
       Ndum[ij]++;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
  ij=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
  for (i=1; i<=10; i++) {            }
    if((Ndum[i]!=0) && (i<=ncov)){          
      Tvaraff[ij]=i;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      ij++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    }            savm=oldm;
  }            oldm=newm;
            } /* end mult */
     cptcoveff=ij-1;        
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /*********** Health Expectancies ****************/          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          }else{
 {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   /* Health expectancies */          }
   int i, j, nhstepm, hstepm, h;          ipmx +=1;
   double age, agelim,hf;          sw += weight[i];
   double ***p3mat;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   fprintf(ficreseij,"# Health expectancies\n");        } /* end of wave */
   fprintf(ficreseij,"# Age");      } /* end of individual */
   for(i=1; i<=nlstate;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(j=1; j<=nlstate;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficreseij," %1d-%1d",i,j);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficreseij,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   hstepm=1*YEARM; /*  Every j years of age (in month) */            for (j=1;j<=nlstate+ndeath;j++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim=AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for(d=0; d<dh[mi][i]; d++){
     /* nhstepm age range expressed in number of stepm */            newm=savm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /* Typically if 20 years = 20*12/6=40 stepm */            for (kk=1; kk<=cptcovage;kk++) {
     if (stepm >= YEARM) hstepm=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              savm=oldm;
             oldm=newm;
           } /* end mult */
     for(i=1; i<=nlstate;i++)        
       for(j=1; j<=nlstate;j++)          s1=s[mw[mi][i]][i];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          s2=s[mw[mi+1][i]][i];
           eij[i][j][(int)age] +=p3mat[i][j][h];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          ipmx +=1;
              sw += weight[i];
     hf=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     if (stepm >= YEARM) hf=stepm/YEARM;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     fprintf(ficreseij,"%.0f",age );        } /* end of wave */
     for(i=1; i<=nlstate;i++)      } /* end of individual */
       for(j=1; j<=nlstate;j++){    } /* End of if */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     fprintf(ficreseij,"\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    return -l;
   }  }
 }  
   /*************** log-likelihood *************/
 /************ Variance ******************/  double funcone( double *x)
 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)  {
 {    /* Same as likeli but slower because of a lot of printf and if */
   /* Variance of health expectancies */    int i, ii, j, k, mi, d, kk;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double **newm;    double **out;
   double **dnewm,**doldm;    double lli; /* Individual log likelihood */
   int i, j, nhstepm, hstepm, h;    double llt;
   int k, cptcode;    int s1, s2;
   double *xp;    double bbh, survp;
   double **gp, **gm;    /*extern weight */
   double ***gradg, ***trgradg;    /* We are differentiating ll according to initial status */
   double ***p3mat;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double age,agelim;    /*for(i=1;i<imx;i++) 
   int theta;      printf(" %d\n",s[4][i]);
     */
    fprintf(ficresvij,"# Covariances of life expectancies\n");    cov[1]=1.;
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    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];
       for(mi=1; mi<= wav[i]-1; mi++){
   xp=vector(1,npar);        for (ii=1;ii<=nlstate+ndeath;ii++)
   dnewm=matrix(1,nlstate,1,npar);          for (j=1;j<=nlstate+ndeath;j++){
   doldm=matrix(1,nlstate,1,nlstate);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=1*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for(d=0; d<dh[mi][i]; d++){
   agelim = AGESUP;          newm=savm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for (kk=1; kk<=cptcovage;kk++) {
     if (stepm >= YEARM) hstepm=1;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gp=matrix(0,nhstepm,1,nlstate);          savm=oldm;
     gm=matrix(0,nhstepm,1,nlstate);          oldm=newm;
         } /* end mult */
     for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++){ /* Computes gradient */        s1=s[mw[mi][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* bias is positive if real duration
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);         * is higher than the multiple of stepm and negative otherwise.
          */
       if (popbased==1) {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         for(i=1; i<=nlstate;i++)          lli=log(out[s1][s2] - savm[s1][s2]);
           prlim[i][i]=probs[(int)age][i][ij];        } else if  (s2==-2) {
       }          for (j=1,survp=0. ; j<=nlstate; j++) 
                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<= nlstate; j++){          lli= log(survp);
         for(h=0; h<=nhstepm; h++){        }else if (mle==1){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        } else if(mle==2){
         }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       }        } else if(mle==3){  /* exponential inter-extrapolation */
              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 */
       for(i=1; i<=npar; i++) /* Computes gradient */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          lli=log(out[s1][s2]); /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
       if (popbased==1) {        ipmx +=1;
         for(i=1; i<=nlstate;i++)        sw += weight[i];
           prlim[i][i]=probs[(int)age][i][ij];        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
       for(j=1; j<= nlstate; j++){          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         for(h=0; h<=nhstepm; h++){   %11.6f %11.6f %11.6f ", \
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       }            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(j=1; j<= nlstate; j++)          }
         for(h=0; h<=nhstepm; h++){          fprintf(ficresilk," %10.6f\n", -llt);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        }
         }      } /* end of wave */
     } /* End theta */    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(h=0; h<=nhstepm; h++)    if(globpr==0){ /* First time we count the contributions and weights */
       for(j=1; j<=nlstate;j++)      gipmx=ipmx;
         for(theta=1; theta <=npar; theta++)      gsw=sw;
           trgradg[h][j][theta]=gradg[h][theta][j];    }
     return -l;
     for(i=1;i<=nlstate;i++)  }
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;  
     for(h=0;h<=nhstepm;h++){  /*************** function likelione ***********/
       for(k=0;k<=nhstepm;k++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);  {
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    /* This routine should help understanding what is done with 
         for(i=1;i<=nlstate;i++)       the selection of individuals/waves and
           for(j=1;j<=nlstate;j++)       to check the exact contribution to the likelihood.
             vareij[i][j][(int)age] += doldm[i][j];       Plotting could be done.
       }     */
     }    int k;
     h=1;  
     if (stepm >= YEARM) h=stepm/YEARM;    if(*globpri !=0){ /* Just counts and sums, no printings */
     fprintf(ficresvij,"%.0f ",age );      strcpy(fileresilk,"ilk"); 
     for(i=1; i<=nlstate;i++)      strcat(fileresilk,fileres);
       for(j=1; j<=nlstate;j++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        printf("Problem with resultfile: %s\n", fileresilk);
       }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     fprintf(ficresvij,"\n");      }
     free_matrix(gp,0,nhstepm,1,nlstate);      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");
     free_matrix(gm,0,nhstepm,1,nlstate);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for(k=1; k<=nlstate; k++) 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   } /* End age */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    *fretone=(*funcone)(p);
   free_matrix(dnewm,1,nlstate,1,nlstate);    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));
       fflush(fichtm); 
 /************ 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)    return;
 {  }
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /*********** Maximum Likelihood Estimation ***************/
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   int k, cptcode;  {
   double *xp;    int i,j, iter;
   double *gp, *gm;    double **xi;
   double **gradg, **trgradg;    double fret;
   double age,agelim;    double fretone; /* Only one call to likelihood */
   int theta;    /*  char filerespow[FILENAMELENGTH];*/
        xi=matrix(1,npar,1,npar);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (i=1;i<=npar;i++)
   fprintf(ficresvpl,"# Age");      for (j=1;j<=npar;j++)
   for(i=1; i<=nlstate;i++)        xi[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficresvpl," %1d-%1d",i,i);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   fprintf(ficresvpl,"\n");    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
   xp=vector(1,npar);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   dnewm=matrix(1,nlstate,1,npar);      printf("Problem with resultfile: %s\n", filerespow);
   doldm=matrix(1,nlstate,1,nlstate);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      }
   hstepm=1*YEARM; /* Every year of age */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=1;i<=nlstate;i++)
   agelim = AGESUP;      for(j=1;j<=nlstate+ndeath;j++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficrespow,"\n");
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    powell(p,xi,npar,ftol,&iter,&fret,func);
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);    free_matrix(xi,1,npar,1,npar);
     gm=vector(1,nlstate);    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     for(theta=1; theta <=npar; theta++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for(i=1; i<=npar; i++){ /* Computes gradient */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  /**** Computes Hessian and covariance matrix ***/
         gp[i] = prlim[i][i];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      {
       for(i=1; i<=npar; i++) /* Computes gradient */    double  **a,**y,*x,pd;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double **hess;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i, j,jk;
       for(i=1;i<=nlstate;i++)    int *indx;
         gm[i] = prlim[i][i];  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       for(i=1;i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    void lubksb(double **a, int npar, int *indx, double b[]) ;
     } /* End theta */    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
     trgradg =matrix(1,nlstate,1,npar);    hess=matrix(1,npar,1,npar);
   
     for(j=1; j<=nlstate;j++)    printf("\nCalculation of the hessian matrix. Wait...\n");
       for(theta=1; theta <=npar; theta++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
     for(i=1;i<=nlstate;i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
       varpl[i][(int)age] =0.;     
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      
     for(i=1;i<=nlstate;i++)      /*  printf(" %f ",p[i]);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
     fprintf(ficresvpl,"%.0f ",age );    
     for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++) {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for (j=1;j<=npar;j++)  {
     fprintf(ficresvpl,"\n");        if (j>i) { 
     free_vector(gp,1,nlstate);          printf(".%d%d",i,j);fflush(stdout);
     free_vector(gm,1,nlstate);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     free_matrix(gradg,1,npar,1,nlstate);          hess[i][j]=hessij(p,delti,i,j,func,npar);
     free_matrix(trgradg,1,nlstate,1,npar);          
   } /* End age */          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
   free_vector(xp,1,npar);        }
   free_matrix(doldm,1,nlstate,1,npar);      }
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
     printf("\n");
 }    fprintf(ficlog,"\n");
   
 /************ Variance of one-step probabilities  ******************/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 {    
   int i, j;    a=matrix(1,npar,1,npar);
   int k=0, cptcode;    y=matrix(1,npar,1,npar);
   double **dnewm,**doldm;    x=vector(1,npar);
   double *xp;    indx=ivector(1,npar);
   double *gp, *gm;    for (i=1;i<=npar;i++)
   double **gradg, **trgradg;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double age,agelim, cov[NCOVMAX];    ludcmp(a,npar,indx,&pd);
   int theta;  
   char fileresprob[FILENAMELENGTH];    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   strcpy(fileresprob,"prob");      x[j]=1;
   strcat(fileresprob,fileres);      lubksb(a,npar,indx,x);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      for (i=1;i<=npar;i++){ 
     printf("Problem with resultfile: %s\n", fileresprob);        matcov[i][j]=x[i];
   }      }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    }
    
     printf("\n#Hessian matrix#\n");
   xp=vector(1,npar);    fprintf(ficlog,"\n#Hessian matrix#\n");
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=npar;i++) { 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   cov[1]=1;        fprintf(ficlog,"%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){      }
     cov[2]=age;      printf("\n");
     gradg=matrix(1,npar,1,9);      fprintf(ficlog,"\n");
     trgradg=matrix(1,9,1,npar);    }
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    /* Recompute Inverse */
        for (i=1;i<=npar;i++)
     for(theta=1; theta <=npar; theta++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       for(i=1; i<=npar; i++)    ludcmp(a,npar,indx,&pd);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
          /*  printf("\n#Hessian matrix recomputed#\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
        for (j=1;j<=npar;j++) {
       k=0;      for (i=1;i<=npar;i++) x[i]=0;
       for(i=1; i<= (nlstate+ndeath); i++){      x[j]=1;
         for(j=1; j<=(nlstate+ndeath);j++){      lubksb(a,npar,indx,x);
            k=k+1;      for (i=1;i<=npar;i++){ 
           gp[k]=pmmij[i][j];        y[i][j]=x[i];
         }        printf("%.3e ",y[i][j]);
       }        fprintf(ficlog,"%.3e ",y[i][j]);
       }
       for(i=1; i<=npar; i++)      printf("\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      fprintf(ficlog,"\n");
        }
     */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
       k=0;    free_matrix(a,1,npar,1,npar);
       for(i=1; i<=(nlstate+ndeath); i++){    free_matrix(y,1,npar,1,npar);
         for(j=1; j<=(nlstate+ndeath);j++){    free_vector(x,1,npar);
           k=k+1;    free_ivector(indx,1,npar);
           gm[k]=pmmij[i][j];    free_matrix(hess,1,npar,1,npar);
         }  
       }  
        }
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    /*************** hessian matrix ****************/
     }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    int i;
       for(theta=1; theta <=npar; theta++)    int l=1, lmax=20;
       trgradg[j][theta]=gradg[theta][j];    double k1,k2;
      double p2[NPARMAX+1];
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    double res;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
      pmij(pmmij,cov,ncovmodel,x,nlstate);    int k=0,kmax=10;
     double l1;
      k=0;  
      for(i=1; i<=(nlstate+ndeath); i++){    fx=func(x);
        for(j=1; j<=(nlstate+ndeath);j++){    for (i=1;i<=npar;i++) p2[i]=x[i];
          k=k+1;    for(l=0 ; l <=lmax; l++){
          gm[k]=pmmij[i][j];      l1=pow(10,l);
         }      delts=delt;
      }      for(k=1 ; k <kmax; k=k+1){
              delt = delta*(l1*k);
      /*printf("\n%d ",(int)age);        p2[theta]=x[theta] +delt;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        k1=func(p2)-fx;
                p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        /*res= (k1-2.0*fx+k2)/delt/delt; */
      }*/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   fprintf(ficresprob,"\n%d ",(int)age);  #ifdef DEBUG
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        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);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  #endif
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          k=kmax; l=lmax*10.;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
 }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
  free_vector(xp,1,npar);          delts=delt;
 fclose(ficresprob);        }
  exit(0);      }
 }    }
     delti[theta]=delts;
 /***********************************************/    return res; 
 /**************** Main Program *****************/    
 /***********************************************/  }
   
 int main(int argc, char *argv[])  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
     int i;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int l=1, l1, lmax=20;
   double agedeb, agefin,hf;    double k1,k2,k3,k4,res,fx;
   double agemin=1.e20, agemax=-1.e20;    double p2[NPARMAX+1];
     int k;
   double fret;  
   double **xi,tmp,delta;    fx=func(x);
     for (k=1; k<=2; k++) {
   double dum; /* Dummy variable */      for (i=1;i<=npar;i++) p2[i]=x[i];
   double ***p3mat;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int *indx;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   char line[MAXLINE], linepar[MAXLINE];      k1=func(p2)-fx;
   char title[MAXLINE];    
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      p2[thetai]=x[thetai]+delti[thetai]/k;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   char filerest[FILENAMELENGTH];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   char fileregp[FILENAMELENGTH];      k3=func(p2)-fx;
   char popfile[FILENAMELENGTH];    
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      p2[thetai]=x[thetai]-delti[thetai]/k;
   int firstobs=1, lastobs=10;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   int sdeb, sfin; /* Status at beginning and end */      k4=func(p2)-fx;
   int c,  h , cpt,l;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   int ju,jl, mi;  #ifdef DEBUG
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      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);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      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);
   int mobilav=0,popforecast=0;  #endif
   int hstepm, nhstepm;    }
   int *popage;/*boolprev=0 if date and zero if wave*/    return res;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;  }
   
   double bage, fage, age, agelim, agebase;  /************** Inverse of matrix **************/
   double ftolpl=FTOL;  void ludcmp(double **a, int n, int *indx, double *d) 
   double **prlim;  { 
   double *severity;    int i,imax,j,k; 
   double ***param; /* Matrix of parameters */    double big,dum,sum,temp; 
   double  *p;    double *vv; 
   double **matcov; /* Matrix of covariance */   
   double ***delti3; /* Scale */    vv=vector(1,n); 
   double *delti; /* Scale */    *d=1.0; 
   double ***eij, ***vareij;    for (i=1;i<=n;i++) { 
   double **varpl; /* Variances of prevalence limits by age */      big=0.0; 
   double *epj, vepp;      for (j=1;j<=n;j++) 
   double kk1, kk2;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   double *popeffectif,*popcount;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;      vv[i]=1.0/big; 
   double yp,yp1,yp2;    } 
     for (j=1;j<=n;j++) { 
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";      for (i=1;i<j;i++) { 
   char *alph[]={"a","a","b","c","d","e"}, str[4];        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   char z[1]="c", occ;      } 
 #include <sys/time.h>      big=0.0; 
 #include <time.h>      for (i=j;i<=n;i++) { 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        sum=a[i][j]; 
          for (k=1;k<j;k++) 
   /* long total_usecs;          sum -= a[i][k]*a[k][j]; 
   struct timeval start_time, end_time;        a[i][j]=sum; 
          if ( (dum=vv[i]*fabs(sum)) >= big) { 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          big=dum; 
           imax=i; 
         } 
   printf("\n%s",version);      } 
   if(argc <=1){      if (j != imax) { 
     printf("\nEnter the parameter file name: ");        for (k=1;k<=n;k++) { 
     scanf("%s",pathtot);          dum=a[imax][k]; 
   }          a[imax][k]=a[j][k]; 
   else{          a[j][k]=dum; 
     strcpy(pathtot,argv[1]);        } 
   }        *d = -(*d); 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        vv[imax]=vv[j]; 
   /*cygwin_split_path(pathtot,path,optionfile);      } 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      indx[j]=imax; 
   /* cutv(path,optionfile,pathtot,'\\');*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        dum=1.0/(a[j][j]); 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   chdir(path);      } 
   replace(pathc,path);    } 
     free_vector(vv,1,n);  /* Doesn't work */
 /*-------- arguments in the command line --------*/  ;
   } 
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);  void lubksb(double **a, int n, int *indx, double b[]) 
   strcat(fileres,".txt");    /* Other files have txt extension */  { 
     int i,ii=0,ip,j; 
   /*---------arguments file --------*/    double sum; 
    
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for (i=1;i<=n;i++) { 
     printf("Problem with optionfile %s\n",optionfile);      ip=indx[i]; 
     goto end;      sum=b[ip]; 
   }      b[ip]=b[i]; 
       if (ii) 
   strcpy(filereso,"o");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   strcat(filereso,fileres);      else if (sum) ii=i; 
   if((ficparo=fopen(filereso,"w"))==NULL) {      b[i]=sum; 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    } 
   }    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   /* Reads comments: lines beginning with '#' */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   while((c=getc(ficpar))=='#' && c!= EOF){      b[i]=sum/a[i][i]; 
     ungetc(c,ficpar);    } 
     fgets(line, MAXLINE, ficpar);  } 
     puts(line);  
     fputs(line,ficparo);  void pstamp(FILE *fichier)
   }  {
   ungetc(c,ficpar);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);  /************ Frequencies ********************/
   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);  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[])
 while((c=getc(ficpar))=='#' && c!= EOF){  {  /* Some frequencies */
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     puts(line);    int first;
     fputs(line,ficparo);    double ***freq; /* Frequencies */
   }    double *pp, **prop;
   ungetc(c,ficpar);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      char fileresp[FILENAMELENGTH];
        
   covar=matrix(0,NCOVMAX,1,n);    pp=vector(1,nlstate);
   cptcovn=0;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
   ncovmodel=2+cptcovn;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   /* Read guess parameters */      exit(0);
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     ungetc(c,ficpar);    j1=0;
     fgets(line, MAXLINE, ficpar);    
     puts(line);    j=cptcoveff;
     fputs(line,ficparo);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }  
   ungetc(c,ficpar);    first=1;
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for(k1=1; k1<=j;k1++){
     for(i=1; i <=nlstate; i++)      for(i1=1; i1<=ncodemax[k1];i1++){
     for(j=1; j <=nlstate+ndeath-1; j++){        j1++;
       fscanf(ficpar,"%1d%1d",&i1,&j1);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       fprintf(ficparo,"%1d%1d",i1,j1);          scanf("%d", i);*/
       printf("%1d%1d",i,j);        for (i=-5; i<=nlstate+ndeath; i++)  
       for(k=1; k<=ncovmodel;k++){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         fscanf(ficpar," %lf",&param[i][j][k]);            for(m=iagemin; m <= iagemax+3; m++)
         printf(" %lf",param[i][j][k]);              freq[i][jk][m]=0;
         fprintf(ficparo," %lf",param[i][j][k]);  
       }      for (i=1; i<=nlstate; i++)  
       fscanf(ficpar,"\n");        for(m=iagemin; m <= iagemax+3; m++)
       printf("\n");          prop[i][m]=0;
       fprintf(ficparo,"\n");        
     }        dateintsum=0;
          k2cpt=0;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        for (i=1; i<=imx; i++) {
           bool=1;
   p=param[1][1];          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   /* Reads comments: lines beginning with '#' */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   while((c=getc(ficpar))=='#' && c!= EOF){                bool=0;
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          if (bool==1){
     puts(line);            for(m=firstpass; m<=lastpass; m++){
     fputs(line,ficparo);              k2=anint[m][i]+(mint[m][i]/12.);
   }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   ungetc(c,ficpar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                if (m<lastpass) {
   for(i=1; i <=nlstate; i++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     for(j=1; j <=nlstate+ndeath-1; j++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       fscanf(ficpar,"%1d%1d",&i1,&j1);                }
       printf("%1d%1d",i,j);                
       fprintf(ficparo,"%1d%1d",i1,j1);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       for(k=1; k<=ncovmodel;k++){                  dateintsum=dateintsum+k2;
         fscanf(ficpar,"%le",&delti3[i][j][k]);                  k2cpt++;
         printf(" %le",delti3[i][j][k]);                }
         fprintf(ficparo," %le",delti3[i][j][k]);                /*}*/
       }            }
       fscanf(ficpar,"\n");          }
       printf("\n");        }
       fprintf(ficparo,"\n");         
     }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   }        pstamp(ficresp);
   delti=delti3[1][1];        if  (cptcovn>0) {
            fprintf(ficresp, "\n#********** Variable "); 
   /* Reads comments: lines beginning with '#' */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresp, "**********\n#");
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=nlstate;i++) 
     puts(line);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fputs(line,ficparo);        fprintf(ficresp, "\n");
   }        
   ungetc(c,ficpar);        for(i=iagemin; i <= iagemax+3; i++){
            if(i==iagemax+3){
   matcov=matrix(1,npar,1,npar);            fprintf(ficlog,"Total");
   for(i=1; i <=npar; i++){          }else{
     fscanf(ficpar,"%s",&str);            if(first==1){
     printf("%s",str);              first=0;
     fprintf(ficparo,"%s",str);              printf("See log file for details...\n");
     for(j=1; j <=i; j++){            }
       fscanf(ficpar," %le",&matcov[i][j]);            fprintf(ficlog,"Age %d", i);
       printf(" %.5le",matcov[i][j]);          }
       fprintf(ficparo," %.5le",matcov[i][j]);          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     fscanf(ficpar,"\n");              pp[jk] += freq[jk][m][i]; 
     printf("\n");          }
     fprintf(ficparo,"\n");          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pos=0; m <=0 ; m++)
   for(i=1; i <=npar; i++)              pos += freq[jk][m][i];
     for(j=i+1;j<=npar;j++)            if(pp[jk]>=1.e-10){
       matcov[i][j]=matcov[j][i];              if(first==1){
                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   printf("\n");              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
     /*-------- data file ----------*/              if(first==1)
     if((ficres =fopen(fileres,"w"))==NULL) {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       printf("Problem with resultfile: %s\n", fileres);goto end;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     }            }
     fprintf(ficres,"#%s\n",version);          }
      
     if((fic=fopen(datafile,"r"))==NULL)    {          for(jk=1; jk <=nlstate ; jk++){
       printf("Problem with datafile: %s\n", datafile);goto end;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     }              pp[jk] += freq[jk][m][i];
           }       
     n= lastobs;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     severity = vector(1,maxwav);            pos += pp[jk];
     outcome=imatrix(1,maxwav+1,1,n);            posprop += prop[jk][i];
     num=ivector(1,n);          }
     moisnais=vector(1,n);          for(jk=1; jk <=nlstate ; jk++){
     annais=vector(1,n);            if(pos>=1.e-5){
     moisdc=vector(1,n);              if(first==1)
     andc=vector(1,n);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     agedc=vector(1,n);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     cod=ivector(1,n);            }else{
     weight=vector(1,n);              if(first==1)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     mint=matrix(1,maxwav,1,n);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     anint=matrix(1,maxwav,1,n);            }
     s=imatrix(1,maxwav+1,1,n);            if( i <= iagemax){
     adl=imatrix(1,maxwav+1,1,n);                  if(pos>=1.e-5){
     tab=ivector(1,NCOVMAX);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     ncodemax=ivector(1,8);                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     i=1;              }
     while (fgets(line, MAXLINE, fic) != NULL)    {              else
       if ((i >= firstobs) && (i <=lastobs)) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                    }
         for (j=maxwav;j>=1;j--){          }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          
           strcpy(line,stra);          for(jk=-1; jk <=nlstate+ndeath; jk++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(m=-1; m <=nlstate+ndeath; m++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              if(freq[jk][m][i] !=0 ) {
         }              if(first==1)
                        printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              }
           if(i <= iagemax)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            fprintf(ficresp,"\n");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          if(first==1)
             printf("Others in log...\n");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficlog,"\n");
         for (j=ncov;j>=1;j--){        }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }
         }    }
         num[i]=atol(stra);    dateintmean=dateintsum/k2cpt; 
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    fclose(ficresp);
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
         i=i+1;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       }    /* End of Freq */
     }  }
     /* printf("ii=%d", ij);  
        scanf("%d",i);*/  /************ Prevalence ********************/
   imx=i-1; /* Number of individuals */  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
   /* for (i=1; i<=imx; i++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;       in each health status at the date of interview (if between dateprev1 and dateprev2).
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;       We still use firstpass and lastpass as another selection.
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    */
     }   
     int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     for (i=1; i<=imx; i++)    double ***freq; /* Frequencies */
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    double *pp, **prop;
     double pos,posprop; 
   /* Calculation of the number of parameter from char model*/    double  y2; /* in fractional years */
   Tvar=ivector(1,15);    int iagemin, iagemax;
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    iagemin= (int) agemin;
   Tvard=imatrix(1,15,1,2);    iagemax= (int) agemax;
   Tage=ivector(1,15);          /*pp=vector(1,nlstate);*/
        prop=matrix(1,nlstate,iagemin,iagemax+3); 
   if (strlen(model) >1){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j=0, j1=0, k1=1, k2=1;    j1=0;
     j=nbocc(model,'+');    
     j1=nbocc(model,'*');    j=cptcoveff;
     cptcovn=j+1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     cptcovprod=j1;    
        for(k1=1; k1<=j;k1++){
          for(i1=1; i1<=ncodemax[k1];i1++){
     strcpy(modelsav,model);        j1++;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        
       printf("Error. Non available option model=%s ",model);        for (i=1; i<=nlstate; i++)  
       goto end;          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0.0;
           
     for(i=(j+1); i>=1;i--){        for (i=1; i<=imx; i++) { /* Each individual */
       cutv(stra,strb,modelsav,'+');          bool=1;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          if  (cptcovn>0) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/            for (z1=1; z1<=cptcoveff; z1++) 
       /*scanf("%d",i);*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       if (strchr(strb,'*')) {                bool=0;
         cutv(strd,strc,strb,'*');          } 
         if (strcmp(strc,"age")==0) {          if (bool==1) { 
           cptcovprod--;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           cutv(strb,stre,strd,'V');              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           Tvar[i]=atoi(stre);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           cptcovage++;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             Tage[cptcovage]=i;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             /*printf("stre=%s ", stre);*/                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) { 
         else if (strcmp(strd,"age")==0) {                  /*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]]);*/
           cptcovprod--;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           cutv(strb,stre,strc,'V');                  prop[s[m][i]][iagemax+3] += weight[i]; 
           Tvar[i]=atoi(stre);                } 
           cptcovage++;              }
           Tage[cptcovage]=i;            } /* end selection of waves */
         }          }
         else {        }
           cutv(strb,stre,strc,'V');        for(i=iagemin; i <= iagemax+3; i++){  
           Tvar[i]=ncov+k1;          
           cutv(strb,strc,strd,'V');          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           Tprod[k1]=i;            posprop += prop[jk][i]; 
           Tvard[k1][1]=atoi(strc);          } 
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];          for(jk=1; jk <=nlstate ; jk++){     
           Tvar[cptcovn+k2+1]=Tvard[k1][2];            if( i <=  iagemax){ 
           for (k=1; k<=lastobs;k++)              if(posprop>=1.e-5){ 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                probs[i][jk][j1]= prop[jk][i]/posprop;
           k1++;              } 
           k2=k2+2;            } 
         }          }/* end jk */ 
       }        }/* end i */ 
       else {      } /* end i1 */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    } /* end k1 */
        /*  scanf("%d",i);*/    
       cutv(strd,strc,strb,'V');    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       Tvar[i]=atoi(strc);    /*free_vector(pp,1,nlstate);*/
       }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       strcpy(modelsav,stra);    }  /* End of prevalence */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/  /************* Waves Concatenation ***************/
     }  
 }  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)
    {
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   printf("cptcovprod=%d ", cptcovprod);       Death is a valid wave (if date is known).
   scanf("%d ",i);*/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     fclose(fic);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
     /*  if(mle==1){*/       */
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     /*-calculation of age at interview from date of interview and age at death -*/       double sum=0., jmean=0.;*/
     agev=matrix(1,maxwav,1,imx);    int first;
     int j, k=0,jk, ju, jl;
    for (i=1; i<=imx; i++)    double sum=0.;
      for(m=2; (m<= maxwav); m++)    first=0;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    jmin=1e+5;
          anint[m][i]=9999;    jmax=-1;
          s[m][i]=-1;    jmean=0.;
        }    for(i=1; i<=imx; i++){
          mi=0;
     for (i=1; i<=imx; i++)  {      m=firstpass;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      while(s[m][i] <= nlstate){
       for(m=1; (m<= maxwav); m++){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         if(s[m][i] >0){          mw[++mi][i]=m;
           if (s[m][i] == nlstate+1) {        if(m >=lastpass)
             if(agedc[i]>0)          break;
               if(moisdc[i]!=99 && andc[i]!=9999)        else
               agev[m][i]=agedc[i];          m++;
             else {      }/* end while */
               if (andc[i]!=9999){      if (s[m][i] > nlstate){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        mi++;     /* Death is another wave */
               agev[m][i]=-1;        /* if(mi==0)  never been interviewed correctly before death */
               }           /* Only death is a correct wave */
             }        mw[mi][i]=m;
           }      }
           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]);      wav[i]=mi;
             if(mint[m][i]==99 || anint[m][i]==9999)      if(mi==0){
               agev[m][i]=1;        nbwarn++;
             else if(agev[m][i] <agemin){        if(first==0){
               agemin=agev[m][i];          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          first=1;
             }        }
             else if(agev[m][i] >agemax){        if(first==1){
               agemax=agev[m][i];          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        }
             }      } /* end mi==0 */
             /*agev[m][i]=anint[m][i]-annais[i];*/    } /* End individuals */
             /*   agev[m][i] = age[i]+2*m;*/  
           }    for(i=1; i<=imx; i++){
           else { /* =9 */      for(mi=1; mi<wav[i];mi++){
             agev[m][i]=1;        if (stepm <=0)
             s[m][i]=-1;          dh[mi][i]=1;
           }        else{
         }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         else /*= 0 Unknown */            if (agedc[i] < 2*AGESUP) {
           agev[m][i]=1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       }              if(j==0) j=1;  /* Survives at least one month after exam */
                  else if(j<0){
     }                nberr++;
     for (i=1; i<=imx; i++)  {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for(m=1; (m<= maxwav); m++){                j=1; /* Temporary Dangerous patch */
         if (s[m][i] > (nlstate+ndeath)) {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           printf("Error: Wrong value in nlstate or ndeath\n");                  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]);
           goto end;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
         }              }
       }              k=k+1;
     }              if (j >= jmax){
                 jmax=j;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                ijmax=i;
               }
     free_vector(severity,1,maxwav);              if (j <= jmin){
     free_imatrix(outcome,1,maxwav+1,1,n);                jmin=j;
     free_vector(moisnais,1,n);                ijmin=i;
     free_vector(annais,1,n);              }
     /* free_matrix(mint,1,maxwav,1,n);              sum=sum+j;
        free_matrix(anint,1,maxwav,1,n);*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     free_vector(moisdc,1,n);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     free_vector(andc,1,n);            }
           }
              else{
     wav=ivector(1,imx);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  /*        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]); */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
                k=k+1;
     /* Concatenates waves */            if (j >= jmax) {
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              jmax=j;
               ijmax=i;
             }
       Tcode=ivector(1,100);            else if (j <= jmin){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              jmin=j;
       ncodemax[1]=1;              ijmin=i;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            }
                  /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
    codtab=imatrix(1,100,1,10);            /*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]);*/
    h=0;            if(j<0){
    m=pow(2,cptcoveff);              nberr++;
                printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
    for(k=1;k<=cptcoveff; k++){              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      for(i=1; i <=(m/pow(2,k));i++){            }
        for(j=1; j <= ncodemax[k]; j++){            sum=sum+j;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          }
            h++;          jk= j/stepm;
            if (h>m) h=1;codtab[h][k]=j;          jl= j -jk*stepm;
          }          ju= j -(jk+1)*stepm;
        }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
      }            if(jl==0){
    }              dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
    /*for(i=1; i <=m ;i++){                    * at the price of an extra matrix product in likelihood */
      for(k=1; k <=cptcovn; k++){              dh[mi][i]=jk+1;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);              bh[mi][i]=ju;
      }            }
      printf("\n");          }else{
    }            if(jl <= -ju){
    scanf("%d",i);*/              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
    /* Calculates basic frequencies. Computes observed prevalence at single age                                   * is higher than the multiple of stepm and negative otherwise.
        and prints on file fileres'p'. */                                   */
             }
                else{
                  dh[mi][i]=jk+1;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              bh[mi][i]=ju;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(dh[mi][i]==0){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              dh[mi][i]=1; /* At least one step */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              bh[mi][i]=ju; /* At least one step */
                    /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
     /* For 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] */          } /* end if mle */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        }
       } /* end wave */
     if(mle==1){    }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    jmean=sum/k;
     }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
        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);
     /*--------- results files --------------*/   }
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  
    /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
    jk=1;  {
    fprintf(ficres,"# Parameters\n");    
    printf("# Parameters\n");    int Ndum[20],ij=1, k, j, i, maxncov=19;
    for(i=1,jk=1; i <=nlstate; i++){    int cptcode=0;
      for(k=1; k <=(nlstate+ndeath); k++){    cptcoveff=0; 
        if (k != i)   
          {    for (k=0; k<maxncov; k++) Ndum[k]=0;
            printf("%d%d ",i,k);    for (k=1; k<=7; k++) ncodemax[k]=0;
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
              printf("%f ",p[jk]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
              fprintf(ficres,"%f ",p[jk]);                                 modality*/ 
              jk++;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            }        Ndum[ij]++; /*store the modality */
            printf("\n");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
            fprintf(ficres,"\n");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
          }                                         Tvar[j]. If V=sex and male is 0 and 
      }                                         female is 1, then  cptcode=1.*/
    }      }
  if(mle==1){  
     /* Computing hessian and covariance matrix */      for (i=0; i<=cptcode; i++) {
     ftolhess=ftol; /* Usually correct */        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 */
     hesscov(matcov, p, npar, delti, ftolhess, func);      }
  }  
     fprintf(ficres,"# Scales\n");      ij=1; 
     printf("# Scales\n");      for (i=1; i<=ncodemax[j]; i++) {
      for(i=1,jk=1; i <=nlstate; i++){        for (k=0; k<= maxncov; k++) {
       for(j=1; j <=nlstate+ndeath; j++){          if (Ndum[k] != 0) {
         if (j!=i) {            nbcode[Tvar[j]][ij]=k; 
           fprintf(ficres,"%1d%1d",i,j);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           printf("%1d%1d",i,j);            
           for(k=1; k<=ncovmodel;k++){            ij++;
             printf(" %.5e",delti[jk]);          }
             fprintf(ficres," %.5e",delti[jk]);          if (ij > ncodemax[j]) break; 
             jk++;        }  
           }      } 
           printf("\n");    }  
           fprintf(ficres,"\n");  
         }   for (k=0; k< maxncov; k++) Ndum[k]=0;
       }  
      }   for (i=1; i<=ncovmodel-2; i++) { 
         /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     k=1;     ij=Tvar[i];
     fprintf(ficres,"# Covariance\n");     Ndum[ij]++;
     printf("# Covariance\n");   }
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;   ij=1;
       i1=(i-1)/(ncovmodel*nlstate)+1;   for (i=1; i<= maxncov; i++) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     if((Ndum[i]!=0) && (i<=ncovcol)){
       printf("%s%d%d",alph[k],i1,tab[i]);*/       Tvaraff[ij]=i; /*For printing */
       fprintf(ficres,"%3d",i);       ij++;
       printf("%3d",i);     }
       for(j=1; j<=i;j++){   }
         fprintf(ficres," %.5e",matcov[i][j]);   
         printf(" %.5e",matcov[i][j]);   cptcoveff=ij-1; /*Number of simple covariates*/
       }  }
       fprintf(ficres,"\n");  
       printf("\n");  /*********** Health Expectancies ****************/
       k++;  
     }  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[] )
      
     while((c=getc(ficpar))=='#' && c!= EOF){  {
       ungetc(c,ficpar);    /* Health expectancies, no variances */
       fgets(line, MAXLINE, ficpar);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       puts(line);    double age, agelim, hf;
       fputs(line,ficparo);    double ***p3mat;
     }    double eip;
     ungetc(c,ficpar);  
      pstamp(ficreseij);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
        fprintf(ficreseij,"# Age");
     if (fage <= 2) {    for(i=1; i<=nlstate;i++){
       bage = agemin;      for(j=1; j<=nlstate;j++){
       fage = agemax;        fprintf(ficreseij," e%1d%1d ",i,j);
     }      }
          fprintf(ficreseij," e%1d. ",i);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    }
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficreseij,"\n");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
      
     while((c=getc(ficpar))=='#' && c!= EOF){    if(estepm < stepm){
     ungetc(c,ficpar);      printf ("Problem %d lower than %d\n",estepm, stepm);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    else  hstepm=estepm;   
     fputs(line,ficparo);    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * This is mainly to measure the difference between two models: for example
   ungetc(c,ficpar);     * if stepm=24 months pijx are given only every 2 years and by summing them
       * we are calculating an estimate of the Life Expectancy assuming a linear 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);     * progression in between and thus overestimating or underestimating according
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);     * to the curvature of the survival function. If, for the same date, we 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           * to compare the new estimate of Life expectancy with the same linear 
   while((c=getc(ficpar))=='#' && c!= EOF){     * hypothesis. A more precise result, taking into account a more precise
     ungetc(c,ficpar);     * curvature will be obtained if estepm is as small as stepm. */
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /* For example we decided to compute the life expectancy with the smallest unit */
     fputs(line,ficparo);    /* 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 
   ungetc(c,ficpar);       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 estepm months */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    dateprev2=anprev2+mprev2/12.+jprev2/365.;       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
   fscanf(ficpar,"pop_based=%d\n",&popbased);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    fprintf(ficparo,"pop_based=%d\n",popbased);         results. So we changed our mind and took the option of the best precision.
    fprintf(ficres,"pop_based=%d\n",popbased);      */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    agelim=AGESUP;
     fgets(line, MAXLINE, ficpar);    /* nhstepm age range expressed in number of stepm */
     puts(line);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     fputs(line,ficparo);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }    /* if (stepm >= YEARM) hstepm=1;*/
   ungetc(c,ficpar);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
          hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     /*------------ gnuplot -------------*/      
     /*chdir(pathcd);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     strcpy(optionfilegnuplot,optionfilefiname);      
     strcat(optionfilegnuplot,".plt");      printf("%d|",(int)age);fflush(stdout);
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       printf("Problem with file %s",optionfilegnuplot);goto end;      
     }      /* Computing expectancies */
 #ifdef windows      for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);        for(j=1; j<=nlstate;j++)
 #endif          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 m=pow(2,cptcoveff);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
              
  /* 1eme*/            /* 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]);*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {          }
   
 #ifdef windows      fprintf(ficreseij,"%3.0f",age );
     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);      for(i=1; i<=nlstate;i++){
 #endif        eip=0;
 #ifdef unix        for(j=1; j<=nlstate;j++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          eip +=eij[i][j][(int)age];
 #endif          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
 for (i=1; i<= nlstate ; i ++) {        fprintf(ficreseij,"%9.4f", eip );
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficreseij,"\n");
 }      
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
     for (i=1; i<= nlstate ; i ++) {    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    printf("\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficlog,"\n");
 }    
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  }
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /* Covariances of health expectancies eij and of total life expectancies according
 #ifdef unix     to initial status i, ei. .
 fprintf(ficgp,"\nset ter gif small size 400,300");    */
 #endif    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double age, agelim, hf;
    }    double ***p3matp, ***p3matm, ***varhe;
   }    double **dnewm,**doldm;
   /*2 eme*/    double *xp, *xm;
     double **gp, **gm;
   for (k1=1; k1<= m ; k1 ++) {    double ***gradg, ***trgradg;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    int theta;
      
     for (i=1; i<= nlstate+1 ; i ++) {    double eip, vip;
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for (j=1; j<= nlstate+1 ; j ++) {    xp=vector(1,npar);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    xm=vector(1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    dnewm=matrix(1,nlstate*nlstate,1,npar);
 }      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    pstamp(ficresstdeij);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficresstdeij,"# Age");
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for(i=1; i<=nlstate;i++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=1; j<=nlstate;j++)
 }          fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficresstdeij," e%1d. ",i);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    }
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficresstdeij,"\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    pstamp(ficrescveij);
 }      fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fprintf(ficrescveij,"# Age");
       else fprintf(ficgp,"\" t\"\" w l 0,");    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        cptj= (j-1)*nlstate+i;
   }        for(i2=1; i2<=nlstate;i2++)
            for(j2=1; j2<=nlstate;j2++){
   /*3eme*/            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
   for (k1=1; k1<= m ; k1 ++) {              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     for (cpt=1; cpt<= nlstate ; cpt ++) {          }
       k=2+nlstate*(cpt-1);      }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    fprintf(ficrescveij,"\n");
       for (i=1; i< nlstate ; i ++) {    
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }    else  hstepm=estepm;   
   }    /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
   /* CV preval stat */     * if stepm=24 months pijx are given only every 2 years and by summing them
   for (k1=1; k1<= m ; k1 ++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
     for (cpt=1; cpt<nlstate ; cpt ++) {     * progression in between and thus overestimating or underestimating according
       k=3;     * to the curvature of the survival function. If, for the same date, we 
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       for (i=1; i< nlstate ; i ++)     * to compare the new estimate of Life expectancy with the same linear 
         fprintf(ficgp,"+$%d",k+i+1);     * hypothesis. A more precise result, taking into account a more precise
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);     * curvature will be obtained if estepm is as small as stepm. */
        
       l=3+(nlstate+ndeath)*cpt;    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for (i=1; i< nlstate ; i ++) {       nhstepm is the number of hstepm from age to agelim 
         l=3+(nlstate+ndeath)*cpt;       nstepm is the number of stepm from age to agelin. 
         fprintf(ficgp,"+$%d",l+i+1);       Look at hpijx to understand the reason of that which relies in memory size
       }       and note for a fixed period like estepm months */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       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
   }         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.
   /* proba elementaires */    */
    for(i=1,jk=1; i <=nlstate; i++){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    /* If stepm=6 months */
         for(j=1; j <=ncovmodel; j++){    /* nhstepm age range expressed in number of stepm */
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    agelim=AGESUP;
           /*fprintf(ficgp,"%s",alph[1]);*/    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           jk++;    /* if (stepm >= YEARM) hstepm=1;*/
           fprintf(ficgp,"\n");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }    
       }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   for(jk=1; jk <=m; jk++) {    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {    for (age=bage; age<=fage; age ++){ 
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        if (k != k2){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);   
 ij=1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      /* Computing  Variances of health expectancies */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
             ij++;         decrease memory allocation */
           }      for(theta=1; theta <=npar; theta++){
           else        for(i=1; i<=npar; i++){ 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           fprintf(ficgp,")/(1");        }
                hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         for(k1=1; k1 <=nlstate; k1++){          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    
 ij=1;        for(j=1; j<= nlstate; j++){
           for(j=3; j <=ncovmodel; j++){          for(i=1; i<=nlstate; i++){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            for(h=0; h<=nhstepm-1; h++){
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
             ij++;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           }            }
           else          }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }
           }       
           fprintf(ficgp,")");        for(ij=1; ij<= nlstate*nlstate; ij++)
         }          for(h=0; h<=nhstepm-1; h++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          }
         i=i+ncovmodel;      }/* End theta */
        }      
      }      
    }      for(h=0; h<=nhstepm-1; h++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        for(j=1; j<=nlstate*nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
   fclose(ficgp);      
   /* end gnuplot */  
           for(ij=1;ij<=nlstate*nlstate;ij++)
 chdir(path);        for(ji=1;ji<=nlstate*nlstate;ji++)
              varhe[ij][ji][(int)age] =0.;
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       printf("%d|",(int)age);fflush(stdout);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     free_ivector(num,1,n);       for(h=0;h<=nhstepm-1;h++){
     free_vector(agedc,1,n);        for(k=0;k<=nhstepm-1;k++){
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     fclose(ficparo);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     fclose(ficres);          for(ij=1;ij<=nlstate*nlstate;ij++)
     /*  }*/            for(ji=1;ji<=nlstate*nlstate;ji++)
                  varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
    /*________fin mle=1_________*/        }
          }
       /* Computing expectancies */
        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     /* No more information from the sample is required now */      for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */        for(j=1; j<=nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     ungetc(c,ficpar);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     fgets(line, MAXLINE, ficpar);            
     puts(line);            /* 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]);*/
     fputs(line,ficparo);  
   }          }
   ungetc(c,ficpar);  
        fprintf(ficresstdeij,"%3.0f",age );
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      for(i=1; i<=nlstate;i++){
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        eip=0.;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        vip=0.;
 /*--------- index.htm --------*/        for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
   strcpy(optionfilehtm,optionfile);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   strcat(optionfilehtm,".htm");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     printf("Problem with %s \n",optionfilehtm);goto end;        }
   }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">      fprintf(ficresstdeij,"\n");
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  
 Total number of observations=%d <br>      fprintf(ficrescveij,"%3.0f",age );
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      for(i=1; i<=nlstate;i++)
 <hr  size=\"2\" color=\"#EC5E5E\">        for(j=1; j<=nlstate;j++){
 <li>Outputs files<br><br>\n          cptj= (j-1)*nlstate+i;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          for(i2=1; i2<=nlstate;i2++)
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            for(j2=1; j2<=nlstate;j2++){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>              cptj2= (j2-1)*nlstate+i2;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>              if(cptj2 <= cptj)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         - 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>        }
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      fprintf(ficrescveij,"\n");
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>     
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    }
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
  fprintf(fichtm," <li>Graphs</li><p>");    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
  m=cptcoveff;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
  j1=0;    fprintf(ficlog,"\n");
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    free_vector(xm,1,npar);
        j1++;    free_vector(xp,1,npar);
        if (cptcovn > 0) {    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
          for (cpt=1; cpt<=cptcoveff;cpt++)    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }  /************ Variance ******************/
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  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[])
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      {
        for(cpt=1; cpt<nlstate;cpt++){    /* Variance of health expectancies */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    /* double **newm;*/
        }    double **dnewm,**doldm;
     for(cpt=1; cpt<=nlstate;cpt++) {    double **dnewmp,**doldmp;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    int i, j, nhstepm, hstepm, h, nstepm ;
 interval) in state (%d): v%s%d%d.gif <br>    int k, cptcode;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      double *xp;
      }    double **gp, **gm;  /* for var eij */
      for(cpt=1; cpt<=nlstate;cpt++) {    double ***gradg, ***trgradg; /*for var eij */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    double **gradgp, **trgradgp; /* for var p point j */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    double *gpp, *gmp; /* for var p point j */
      }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    double ***p3mat;
 health expectancies in states (1) and (2): e%s%d.gif<br>    double age,agelim, hf;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    double ***mobaverage;
 fprintf(fichtm,"\n</body>");    int theta;
    }    char digit[4];
  }    char digitp[25];
 fclose(fichtm);  
     char fileresprobmorprev[FILENAMELENGTH];
   /*--------------- Prevalence limit --------------*/  
      if(popbased==1){
   strcpy(filerespl,"pl");      if(mobilav!=0)
   strcat(filerespl,fileres);        strcpy(digitp,"-populbased-mobilav-");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      else strcpy(digitp,"-populbased-nomobil-");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }
   }    else 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      strcpy(digitp,"-stablbased-");
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");    if (mobilav!=0) {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficrespl,"\n");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   prlim=matrix(1,nlstate,1,nlstate);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   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 */    strcpy(fileresprobmorprev,"prmorprev"); 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    sprintf(digit,"%-d",ij);
   k=0;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   agebase=agemin;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   agelim=agemax;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   ftolpl=1.e-10;    strcat(fileresprobmorprev,fileres);
   i1=cptcoveff;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   if (cptcovn < 1){i1=1;}      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         k=k+1;   
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         fprintf(ficrespl,"\n#******");    pstamp(ficresprobmorprev);
         for(j=1;j<=cptcoveff;j++)    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(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         fprintf(ficrespl,"******\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              fprintf(ficresprobmorprev," p.%-d SE",j);
         for (age=agebase; age<=agelim; age++){      for(i=1; i<=nlstate;i++)
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           fprintf(ficrespl,"%.0f",age );    }  
           for(i=1; i<=nlstate;i++)    fprintf(ficresprobmorprev,"\n");
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(ficgp,"\n# Routine varevsij");
           fprintf(ficrespl,"\n");    /* 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);
     }  /*   } */
   fclose(ficrespl);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
   /*------------- h Pij x at various ages ------------*/    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    else
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   }    fprintf(ficresvij,"# Age");
   printf("Computing pij: result on file '%s' \n", filerespij);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   /*if (stepm<=24) stepsize=2;*/    fprintf(ficresvij,"\n");
   
   agelim=AGESUP;    xp=vector(1,npar);
   hstepm=stepsize*YEARM; /* Every year of age */    dnewm=matrix(1,nlstate,1,npar);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   k=0;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       k=k+1;    gpp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficrespij,"\n#****** ");    gmp=vector(nlstate+1,nlstate+ndeath);
         for(j=1;j<=cptcoveff;j++)    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
         fprintf(ficrespij,"******\n");    if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    else  hstepm=estepm;   
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    /* For example we decided to compute the life expectancy with the smallest unit */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           oldm=oldms;savm=savms;       nhstepm is the number of hstepm from age to agelim 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         nstepm is the number of stepm from age to agelin. 
           fprintf(ficrespij,"# Age");       Look at hpijx to understand the reason of that which relies in memory size
           for(i=1; i<=nlstate;i++)       and note for a fixed period like k years */
             for(j=1; j<=nlstate+ndeath;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               fprintf(ficrespij," %1d-%1d",i,j);       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficrespij,"\n");       means that if the survival funtion is printed every two years of age and if
           for (h=0; h<=nhstepm; h++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       results. So we changed our mind and took the option of the best precision.
             for(i=1; i<=nlstate;i++)    */
               for(j=1; j<=nlstate+ndeath;j++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    agelim = AGESUP;
             fprintf(ficrespij,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           fprintf(ficrespij,"\n");      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);
   
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
       for(theta=1; theta <=npar; theta++){
   fclose(ficrespij);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   if(stepm == 1) {        }
   /*---------- Forecasting ------------------*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   /*printf("calage= %f", calagedate);*/        if (popbased==1) {
            if(mobilav ==0){
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   strcpy(fileresf,"f");            for(i=1; i<=nlstate;i++)
   strcat(fileresf,fileres);              prlim[i][i]=mobaverage[(int)age][i][ij];
   if((ficresf=fopen(fileresf,"w"))==NULL) {          }
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;        }
   }    
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   free_matrix(mint,1,maxwav,1,n);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   free_matrix(anint,1,maxwav,1,n);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   free_matrix(agev,1,maxwav,1,imx);          }
   /* Mobile average */        }
         /* This for computing probability of death (h=1 means
   if (cptcoveff==0) ncodemax[cptcoveff]=1;           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   if (mobilav==1) {        */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       for (i=1; i<=nlstate;i++)            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        }    
           mobaverage[(int)agedeb][i][cptcod]=0.;        /* end probability of death */
      
     for (agedeb=bage+4; agedeb<=fage; agedeb++){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       for (i=1; i<=nlstate;i++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           for (cpt=0;cpt<=4;cpt++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];   
           }        if (popbased==1) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          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];
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;        }
   
   agelim=AGESUP;        for(j=1; j<= nlstate; j++){
   /*hstepm=stepsize*YEARM; *//* Every year of age */          for(h=0; h<=nhstepm; h++){
   hstepm=1;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   yp1=modf(dateintmean,&yp);          }
   anprojmean=yp;        }
   yp2=modf((yp1*12),&yp);        /* This for computing probability of death (h=1 means
   mprojmean=yp;           computed over hstepm matrices product = hstepm*stepm months) 
   yp1=modf((yp2*30.5),&yp);           as a weighted average of prlim.
   jprojmean=yp;        */
   if(jprojmean==0) jprojmean=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if(mprojmean==0) jprojmean=1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        }    
         /* end probability of death */
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL)    {        for(j=1; j<= nlstate; j++) /* vareij */
       printf("Problem with population file : %s\n",popfile);goto end;          for(h=0; h<=nhstepm; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     popage=ivector(0,AGESUP);          }
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     i=1;          }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)  
       {      } /* End theta */
         i=i+1;  
       }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     imx=i;  
          for(h=0; h<=nhstepm; h++) /* veij */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        for(j=1; j<=nlstate;j++)
   }          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       k=k+1;        for(theta=1; theta <=npar; theta++)
       fprintf(ficresf,"\n#******");          trgradgp[j][theta]=gradgp[theta][j];
       for(j=1;j<=cptcoveff;j++) {    
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficresf,"******\n");      for(i=1;i<=nlstate;i++)
       fprintf(ficresf,"# StartingAge FinalAge");        for(j=1;j<=nlstate;j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          vareij[i][j][(int)age] =0.;
       if (popforecast==1)  fprintf(ficresf," [Population]");  
          for(h=0;h<=nhstepm;h++){
       for (cpt=0; cpt<4;cpt++) {        for(k=0;k<=nhstepm;k++){
         fprintf(ficresf,"\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */            for(j=1;j<=nlstate;j++)
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         nhstepm = nhstepm/hstepm;        }
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/      }
     
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* pptj */
         oldm=oldms;savm=savms;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
              for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for (h=0; h<=nhstepm; h++){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           if (h==(int) (calagedate+YEARM*cpt)) {          varppt[j][i]=doldmp[j][i];
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);      /* end ppptj */
           }      /*  x centered again */
           for(j=1; j<=nlstate+ndeath;j++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             kk1=0.;kk2=0;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             for(i=1; i<=nlstate;i++) {           
               if (mobilav==1)      if (popbased==1) {
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if(mobilav ==0){
               else {          for(i=1; i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            prlim[i][i]=probs[(int)age][i][ij];
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/        }else{ /* mobilav */ 
               }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];        }
             }      }
                         
             if (h==(int)(calagedate+12*cpt)){      /* This for computing probability of death (h=1 means
               fprintf(ficresf," %.3f", kk1);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                       as a weighted average of prlim.
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);      */
             }      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]; 
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/      }    
       }      /* end probability of death */
       }  
     }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   if (popforecast==1) {        for(i=1; i<=nlstate;i++){
     free_ivector(popage,0,AGESUP);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     free_vector(popeffectif,0,AGESUP);        }
     free_vector(popcount,0,AGESUP);      } 
   }      fprintf(ficresprobmorprev,"\n");
   free_imatrix(s,1,maxwav+1,1,n);  
   free_vector(weight,1,n);*/      fprintf(ficresvij,"%.0f ",age );
   fclose(ficresf);      for(i=1; i<=nlstate;i++)
   }/* End forecasting */        for(j=1; j<=nlstate;j++){
   else{          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     erreur=108;        }
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);      fprintf(ficresvij,"\n");
   }      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
   /*---------- Health expectancies and variances ------------*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   strcpy(filerest,"t");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(filerest,fileres);    } /* End age */
   if((ficrest=fopen(filerest,"w"))==NULL) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    free_vector(gmp,nlstate+1,nlstate+ndeath);
   }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    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 */
   strcpy(filerese,"e");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   strcat(filerese,fileres);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   if((ficreseij=fopen(filerese,"w"))==NULL) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  /*   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));
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    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));
  strcpy(fileresv,"v");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   strcat(fileresv,fileres);    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);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  */
   }  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
   k=0;    free_vector(xp,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(doldm,1,nlstate,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(dnewm,1,nlstate,1,npar);
       k=k+1;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficrest,"\n#****** ");    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       for(j=1;j<=cptcoveff;j++)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficrest,"******\n");    fclose(ficresprobmorprev);
     fflush(ficgp);
       fprintf(ficreseij,"\n#****** ");    fflush(fichtm); 
       for(j=1;j<=cptcoveff;j++)  }  /* end varevsij */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");  /************ 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[])
       fprintf(ficresvij,"\n#****** ");  {
       for(j=1;j<=cptcoveff;j++)    /* Variance of prevalence limit */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       fprintf(ficresvij,"******\n");    double **newm;
     double **dnewm,**doldm;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int i, j, nhstepm, hstepm;
       oldm=oldms;savm=savms;    int k, cptcode;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      double *xp;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double *gp, *gm;
       oldm=oldms;savm=savms;    double **gradg, **trgradg;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double age,agelim;
          int theta;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    pstamp(ficresvpl);
       fprintf(ficrest,"\n");    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
            fprintf(ficresvpl,"# Age");
       hf=1;    for(i=1; i<=nlstate;i++)
       if (stepm >= YEARM) hf=stepm/YEARM;        fprintf(ficresvpl," %1d-%1d",i,i);
       epj=vector(1,nlstate+1);    fprintf(ficresvpl,"\n");
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    xp=vector(1,npar);
         if (popbased==1) {    dnewm=matrix(1,nlstate,1,npar);
           for(i=1; i<=nlstate;i++)    doldm=matrix(1,nlstate,1,nlstate);
             prlim[i][i]=probs[(int)age][i][k];    
         }    hstepm=1*YEARM; /* Every year of age */
            hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         fprintf(ficrest," %.0f",age);    agelim = AGESUP;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      if (stepm >= YEARM) hstepm=1;
           }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           epj[nlstate+1] +=epj[j];      gradg=matrix(1,npar,1,nlstate);
         }      gp=vector(1,nlstate);
         for(i=1, vepp=0.;i <=nlstate;i++)      gm=vector(1,nlstate);
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];      for(theta=1; theta <=npar; theta++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        for(i=1; i<=npar; i++){ /* Computes gradient */
         for(j=1;j <=nlstate;j++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));        }
         }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficrest,"\n");        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];
  fclose(ficreseij);  
  fclose(ficresvij);        for(i=1;i<=nlstate;i++)
   fclose(ficrest);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   fclose(ficpar);      } /* End theta */
   free_vector(epj,1,nlstate+1);  
   /*  scanf("%d ",i); */      trgradg =matrix(1,nlstate,1,npar);
   
   /*------- Variance limit prevalence------*/        for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
 strcpy(fileresvpl,"vpl");          trgradg[j][theta]=gradg[theta][j];
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      for(i=1;i<=nlstate;i++)
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        varpl[i][(int)age] =0.;
     exit(0);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   }      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficresvpl,"%.0f ",age );
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(i=1; i<=nlstate;i++)
      k=k+1;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      fprintf(ficresvpl,"\n#****** ");      fprintf(ficresvpl,"\n");
      for(j=1;j<=cptcoveff;j++)      free_vector(gp,1,nlstate);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      free_vector(gm,1,nlstate);
      fprintf(ficresvpl,"******\n");      free_matrix(gradg,1,npar,1,nlstate);
            free_matrix(trgradg,1,nlstate,1,npar);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    } /* End age */
      oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    free_vector(xp,1,npar);
    }    free_matrix(doldm,1,nlstate,1,npar);
  }    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   fclose(ficresvpl);  }
   
   /*---------- End : free ----------------*/  /************ Variance of one-step probabilities  ******************/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
    {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int i, j=0,  i1, k1, l1, t, tj;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    int k2, l2, j1,  z1;
      int k=0,l, cptcode;
      int first=1, first1;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    double **dnewm,**doldm;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    double *xp;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    double *gp, *gm;
      double **gradg, **trgradg;
   free_matrix(matcov,1,npar,1,npar);    double **mu;
   free_vector(delti,1,npar);    double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int theta;
     char fileresprob[FILENAMELENGTH];
   if(erreur >0)    char fileresprobcov[FILENAMELENGTH];
     printf("End of Imach with error %d\n",erreur);    char fileresprobcor[FILENAMELENGTH];
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double ***varpij;
    
   /* 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);*/    strcpy(fileresprob,"prob"); 
   /*printf("Total time was %d uSec.\n", total_usecs);*/    strcat(fileresprob,fileres);
   /*------ End -----------*/    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
  end:    }
 #ifdef windows    strcpy(fileresprobcov,"probcov"); 
   /* chdir(pathcd);*/    strcat(fileresprobcov,fileres);
 #endif    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
  /*system("wgnuplot graph.plt");*/      printf("Problem with resultfile: %s\n", fileresprobcov);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    strcpy(fileresprobcor,"probcor"); 
  strcpy(plotcmd,GNUPLOTPROGRAM);    strcat(fileresprobcor,fileres);
  strcat(plotcmd," ");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
  strcat(plotcmd,optionfilegnuplot);      printf("Problem with resultfile: %s\n", fileresprobcor);
  system(plotcmd);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
 #ifdef windows    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   while (z[0] != 'q') {    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     chdir(path);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     scanf("%s",z);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     if (z[0] == 'c') system("./imach");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     else if (z[0] == 'e') {    pstamp(ficresprob);
       chdir(path);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       system(optionfilehtm);    fprintf(ficresprob,"# Age");
     }    pstamp(ficresprobcov);
     else if (z[0] == 'q') exit(0);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   }    fprintf(ficresprobcov,"# Age");
 #endif    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.1.23  
changed lines
  Added in v.1.122


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