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version 1.18, 2002/02/20 17:17:09 version 1.121, 2006/03/16 17:45:01
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.121  2006/03/16 17:45:01  lievre
   individuals from different ages are interviewed on their health status    * imach.c (Module): Comments concerning covariates added
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    * imach.c (Module): refinements in the computation of lli if
   Health expectancies are computed from the transistions observed between    status=-2 in order to have more reliable computation if stepm is
   waves and are computed for each degree of severity of disability (number    not 1 month. Version 0.98f
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.120  2006/03/16 15:10:38  lievre
   The simplest model is the multinomial logistic model where pij is    (Module): refinements in the computation of lli if
   the probabibility to be observed in state j at the second wave conditional    status=-2 in order to have more reliable computation if stepm is
   to be observed in state i at the first wave. Therefore the model is:    not 1 month. Version 0.98f
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.119  2006/03/15 17:42:26  brouard
   age", you should modify the program where the markup    (Module): Bug if status = -2, the loglikelihood was
     *Covariates have to be included here again* invites you to do it.    computed as likelihood omitting the logarithm. Version O.98e
   More covariates you add, less is the speed of the convergence.  
     Revision 1.118  2006/03/14 18:20:07  brouard
   The advantage that this computer programme claims, comes from that if the    (Module): varevsij Comments added explaining the second
   delay between waves is not identical for each individual, or if some    table of variances if popbased=1 .
   individual missed an interview, the information is not rounded or lost, but    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   taken into account using an interpolation or extrapolation.    (Module): Function pstamp added
   hPijx is the probability to be    (Module): Version 0.98d
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.117  2006/03/14 17:16:22  brouard
   unobserved intermediate  states. This elementary transition (by month or    (Module): varevsij Comments added explaining the second
   quarter trimester, semester or year) is model as a multinomial logistic.    table of variances if popbased=1 .
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   and the contribution of each individual to the likelihood is simply 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 FILENAMELENGTH 80    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 /*#define DEBUG*/  
 #define windows    Revision 1.111  2006/01/25 20:38:18  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Lots of cleaning and bugs added (Gompertz)
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.109  2006/01/24 19:37:15  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): Comments (lines starting with a #) are allowed in data.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.108  2006/01/19 18:05:42  lievre
 #define YEARM 12. /* Number of months per year */    Gnuplot problem appeared...
 #define AGESUP 130    To be fixed
 #define AGEBASE 40  
     Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.106  2006/01/19 13:24:36  brouard
 int npar=NPARMAX;    Some cleaning and links added in html output
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.105  2006/01/05 20:23:19  lievre
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    *** empty log message ***
 int popbased=0;  
     Revision 1.104  2005/09/30 16:11:43  lievre
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): sump fixed, loop imx fixed, and simplifications.
 int maxwav; /* Maxim number of waves */    (Module): If the status is missing at the last wave but we know
 int jmin, jmax; /* min, max spacing between 2 waves */    that the person is alive, then we can code his/her status as -2
 int mle, weightopt;    (instead of missing=-1 in earlier versions) and his/her
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    contributions to the likelihood is 1 - Prob of dying from last
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double jmean; /* Mean space between 2 waves */    the healthy state at last known wave). Version is 0.98
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.103  2005/09/30 15:54:49  lievre
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    (Module): sump fixed, loop imx fixed, and simplifications.
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.102  2004/09/15 17:31:30  brouard
   char filerese[FILENAMELENGTH];    Add the possibility to read data file including tab characters.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.101  2004/09/15 10:38:38  brouard
  FILE  *ficresvpl;    Fix on curr_time
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.100  2004/07/12 18:29:06  brouard
 #define NR_END 1    Add version for Mac OS X. Just define UNIX in Makefile
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 #define NRANSI  
 #define ITMAX 200    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 #define TOL 2.0e-4    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 CGOLD 0.3819660    This is the basic analysis of mortality and should be done before any
 #define ZEPS 1.0e-10    other analysis, in order to test if the mortality estimated from the
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    The same imach parameter file can be used but the option for mle should be -3.
 #define TINY 1.0e-20  
     Agnès, who wrote this part of the code, tried to keep most of the
 static double maxarg1,maxarg2;    former routines in order to include the new code within the former code.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    The output is very simple: only an estimate of the intercept and of
      the slope with 95% confident intervals.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Current limitations:
     A) Even if you enter covariates, i.e. with the
 static double sqrarg;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    B) There is no computation of Life Expectancy nor Life Table.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.97  2004/02/20 13:25:42  lievre
 int imx;    Version 0.96d. Population forecasting command line is (temporarily)
 int stepm;    suppressed.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.96  2003/07/15 15:38:55  brouard
 int m,nb;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    rewritten within the same printf. Workaround: many printfs.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 double *weight;    (Repository): Using imachwizard code to output a more meaningful covariance
 int **s; /* Status */    matrix (cov(a12,c31) instead of numbers.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /**************** split *************************/    exist so I changed back to asctime which exists.
 static  int split( char *path, char *dirc, char *name )    (Module): Version 0.96b
 {  
    char *s;                             /* pointer */    Revision 1.92  2003/06/25 16:30:45  brouard
    int  l1, l2;                         /* length counters */    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.91  2003/06/25 15:30:29  brouard
    s = strrchr( path, '\\' );           /* find last / */    * imach.c (Repository): Duplicated warning errors corrected.
    if ( s == NULL ) {                   /* no directory, so use current */    (Repository): Elapsed time after each iteration is now output. It
 #if     defined(__bsd__)                /* get current working directory */    helps to forecast when convergence will be reached. Elapsed time
       extern char       *getwd( );    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.90  2003/06/24 12:34:15  brouard
       extern char       *getcwd( );    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    of the covariance matrix to be input.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.89  2003/06/24 12:30:52  brouard
       }    (Module): Some bugs corrected for windows. Also, when
       strcpy( name, path );             /* we've got it */    mle=-1 a template is output in file "or"mypar.txt with the design
    } else {                             /* strip direcotry from path */    of the covariance matrix to be input.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.88  2003/06/23 17:54:56  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    * 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.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.87  2003/06/18 12:26:01  brouard
       dirc[l1-l2] = 0;                  /* add zero */    Version 0.96
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.86  2003/06/17 20:04:08  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Change position of html and gnuplot routines and added
    return( 0 );                         /* we're done */    routine fileappend.
 }  
     Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 /******************************************/    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 void replace(char *s, char*t)    was wrong (infinity). We still send an "Error" but patch by
 {    assuming that the date of death was just one stepm after the
   int i;    interview.
   int lg=20;    (Repository): Because some people have very long ID (first column)
   i=0;    we changed int to long in num[] and we added a new lvector for
   lg=strlen(t);    memory allocation. But we also truncated to 8 characters (left
   for(i=0; i<= lg; i++) {    truncation)
     (s[i] = t[i]);    (Repository): No more line truncation errors.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.84  2003/06/13 21:44:43  brouard
 }    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 int nbocc(char *s, char occ)    many times. Probs is memory consuming and must be used with
 {    parcimony.
   int i,j=0;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   int lg=20;  
   i=0;    Revision 1.83  2003/06/10 13:39:11  lievre
   lg=strlen(s);    *** empty log message ***
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.82  2003/06/05 15:57:20  brouard
   }    Add log in  imach.c and  fullversion number is now printed.
   return j;  
 }  */
   /*
 void cutv(char *u,char *v, char*t, char occ)     Interpolated Markov Chain
 {  
   int i,lg,j,p=0;    Short summary of the programme:
   i=0;    
   for(j=0; j<=strlen(t)-1; j++) {    This program computes Healthy Life Expectancies from
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   }    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
   lg=strlen(t);    case of a health survey which is our main interest) -2- at least a
   for(j=0; j<p; j++) {    second wave of interviews ("longitudinal") which measure each change
     (u[j] = t[j]);    (if any) in individual health status.  Health expectancies are
   }    computed from the time spent in each health state according to a
      u[p]='\0';    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
    for(j=0; j<= lg; j++) {    simplest model is the multinomial logistic model where pij is the
     if (j>=(p+1))(v[j-p-1] = t[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
     'age' is age and 'sex' is a covariate. If you want to have a more
 /********************** nrerror ********************/    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 void nrerror(char error_text[])    you to do it.  More covariates you add, slower the
 {    convergence.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    The advantage of this computer programme, compared to a simple
   exit(1);    multinomial logistic model, is clear when the delay between waves is not
 }    identical for each individual. Also, if a individual missed an
 /*********************** vector *******************/    intermediate interview, the information is lost, but taken into
 double *vector(int nl, int nh)    account using an interpolation or extrapolation.  
 {  
   double *v;    hPijx is the probability to be observed in state i at age x+h
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    conditional to the observed state i at age x. The delay 'h' can be
   if (!v) nrerror("allocation failure in vector");    split into an exact number (nh*stepm) of unobserved intermediate
   return v-nl+NR_END;    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
 /************************ free vector ******************/    and the contribution of each individual to the likelihood is simply
 void free_vector(double*v, int nl, int nh)    hPijx.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /************************ivector *******************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int *ivector(long nl,long nh)             Institut national d'études démographiques, Paris.
 {    This software have been partly granted by Euro-REVES, a concerted action
   int *v;    from the European Union.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!v) nrerror("allocation failure in ivector");    software can be distributed freely for non commercial use. Latest version
   return v-nl+NR_END;    can be accessed at http://euroreves.ined.fr/imach .
 }  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /******************free ivector **************************/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 void free_ivector(int *v, long nl, long nh)    
 {    **********************************************************************/
   free((FREE_ARG)(v+nl-NR_END));  /*
 }    main
     read parameterfile
 /******************* imatrix *******************************/    read datafile
 int **imatrix(long nrl, long nrh, long ncl, long nch)    concatwav
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    freqsummary
 {    if (mle >= 1)
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;      mlikeli
   int **m;    print results files
      if mle==1 
   /* allocate pointers to rows */       computes hessian
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    read end of parameter file: agemin, agemax, bage, fage, estepm
   if (!m) nrerror("allocation failure 1 in matrix()");        begin-prev-date,...
   m += NR_END;    open gnuplot file
   m -= nrl;    open html file
      period (stable) prevalence
       for age prevalim()
   /* allocate rows and set pointers to them */    h Pij x
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    variance of p varprob
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    forecasting if prevfcast==1 prevforecast call prevalence()
   m[nrl] += NR_END;    health expectancies
   m[nrl] -= ncl;    Variance-covariance of DFLE
      prevalence()
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;     movingaverage()
      varevsij() 
   /* return pointer to array of pointers to rows */    if popbased==1 varevsij(,popbased)
   return m;    total life expectancies
 }    Variance of period (stable) prevalence
    end
 /****************** free_imatrix *************************/  */
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */   
 {  #include <math.h>
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #include <stdio.h>
   free((FREE_ARG) (m+nrl-NR_END));  #include <stdlib.h>
 }  #include <string.h>
   #include <unistd.h>
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  #include <limits.h>
 {  #include <sys/types.h>
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #include <sys/stat.h>
   double **m;  #include <errno.h>
   extern int errno;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  /* #include <sys/time.h> */
   m += NR_END;  #include <time.h>
   m -= nrl;  #include "timeval.h"
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /* #include <libintl.h> */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /* #define _(String) gettext (String) */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #define MAXLINE 256
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define GNUPLOTPROGRAM "gnuplot"
   return m;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 }  #define FILENAMELENGTH 132
   
 /*************************free matrix ************************/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   free((FREE_ARG)(m+nrl-NR_END));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /******************* ma3x *******************************/  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 {  #define NCOVMAX 8 /* Maximum number of covariates */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define MAXN 20000
   double ***m;  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define AGEBASE 40
   if (!m) nrerror("allocation failure 1 in matrix()");  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m += NR_END;  #ifdef UNIX
   m -= nrl;  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define ODIRSEPARATOR '\\'
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #else
   m[nrl] += NR_END;  #define DIRSEPARATOR '\\'
   m[nrl] -= ncl;  #define CHARSEPARATOR "\\"
   #define ODIRSEPARATOR '/'
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #endif
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /* $Id$ */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  /* $State$ */
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
   for (j=ncl+1; j<=nch; j++)  char fullversion[]="$Revision$ $Date$"; 
     m[nrl][j]=m[nrl][j-1]+nlay;  char strstart[80];
    char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int nvar;
     for (j=ncl+1; j<=nch; j++)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
       m[i][j]=m[i][j-1]+nlay;  int npar=NPARMAX;
   }  int nlstate=2; /* Number of live states */
   return m;  int ndeath=1; /* Number of dead states */
 }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int *wav; /* Number of waves for this individuual 0 is possible */
 {  int maxwav; /* Maxim number of waves */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int jmin, jmax; /* min, max spacing between 2 waves */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   free((FREE_ARG)(m+nrl-NR_END));  int gipmx, gsw; /* Global variables on the number of contributions 
 }                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
 /***************** f1dim *************************/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 extern int ncom;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 extern double *pcom,*xicom;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 extern double (*nrfunc)(double []);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
    double jmean; /* Mean space between 2 waves */
 double f1dim(double x)  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   int j;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   double f;  FILE *ficlog, *ficrespow;
   double *xt;  int globpr; /* Global variable for printing or not */
    double fretone; /* Only one call to likelihood */
   xt=vector(1,ncom);  long ipmx; /* Number of contributions */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double sw; /* Sum of weights */
   f=(*nrfunc)(xt);  char filerespow[FILENAMELENGTH];
   free_vector(xt,1,ncom);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   return f;  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /*****************brent *************************/  FILE *fichtm, *fichtmcov; /* Html File */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   int iter;  FILE *ficresstdeij;
   double a,b,d,etemp;  char fileresstde[FILENAMELENGTH];
   double fu,fv,fw,fx;  FILE *ficrescveij;
   double ftemp;  char filerescve[FILENAMELENGTH];
   double p,q,r,tol1,tol2,u,v,w,x,xm;  FILE  *ficresvij;
   double e=0.0;  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
   a=(ax < cx ? ax : cx);  char fileresvpl[FILENAMELENGTH];
   b=(ax > cx ? ax : cx);  char title[MAXLINE];
   x=w=v=bx;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   fw=fv=fx=(*f)(x);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   for (iter=1;iter<=ITMAX;iter++) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     xm=0.5*(a+b);  char command[FILENAMELENGTH];
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int  outcmd=0;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  char filelog[FILENAMELENGTH]; /* Log file */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char filerest[FILENAMELENGTH];
 #endif  char fileregp[FILENAMELENGTH];
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char popfile[FILENAMELENGTH];
       *xmin=x;  
       return fx;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     }  
     ftemp=fu;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     if (fabs(e) > tol1) {  struct timezone tzp;
       r=(x-w)*(fx-fv);  extern int gettimeofday();
       q=(x-v)*(fx-fw);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       p=(x-v)*q-(x-w)*r;  long time_value;
       q=2.0*(q-r);  extern long time();
       if (q > 0.0) p = -p;  char strcurr[80], strfor[80];
       q=fabs(q);  
       etemp=e;  char *endptr;
       e=d;  long lval;
       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));  #define NR_END 1
       else {  #define FREE_ARG char*
         d=p/q;  #define FTOL 1.0e-10
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  #define NRANSI 
           d=SIGN(tol1,xm-x);  #define ITMAX 200 
       }  
     } else {  #define TOL 2.0e-4 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  #define CGOLD 0.3819660 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define ZEPS 1.0e-10 
     fu=(*f)(u);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  #define GOLD 1.618034 
       SHFT(v,w,x,u)  #define GLIMIT 100.0 
         SHFT(fv,fw,fx,fu)  #define TINY 1.0e-20 
         } else {  
           if (u < x) a=u; else b=u;  static double maxarg1,maxarg2;
           if (fu <= fw || w == x) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
             v=w;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
             w=u;    
             fv=fw;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
             fw=fu;  #define rint(a) floor(a+0.5)
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  static double sqrarg;
             fv=fu;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
           }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         }  int agegomp= AGEGOMP;
   }  
   nrerror("Too many iterations in brent");  int imx; 
   *xmin=x;  int stepm=1;
   return fx;  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /****************** mnbrak ***********************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  int m,nb;
             double (*func)(double))  long *num;
 {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double ulim,u,r,q, dum;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double fu;  double **pmmij, ***probs;
    double *ageexmed,*agecens;
   *fa=(*func)(*ax);  double dateintmean=0;
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  double *weight;
     SHFT(dum,*ax,*bx,dum)  int **s; /* Status */
       SHFT(dum,*fb,*fa,dum)  double *agedc, **covar, idx;
       }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   *cx=(*bx)+GOLD*(*bx-*ax);  double *lsurv, *lpop, *tpop;
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     r=(*bx-*ax)*(*fb-*fc);  double ftolhess; /* Tolerance for computing hessian */
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /**************** split *************************/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       fu=(*func)(u);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     } else if ((*cx-u)*(u-ulim) > 0.0) {    */ 
       fu=(*func)(u);    char  *ss;                            /* pointer */
       if (fu < *fc) {    int   l1, l2;                         /* length counters */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    l1 = strlen(path );                   /* length of path */
           }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       u=ulim;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       fu=(*func)(u);      strcpy( name, path );               /* we got the fullname name because no directory */
     } else {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       u=(*cx)+GOLD*(*cx-*bx);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       fu=(*func)(u);      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
     SHFT(*ax,*bx,*cx,u)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       SHFT(*fa,*fb,*fc,fu)        return( GLOCK_ERROR_GETCWD );
       }      }
 }      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
 /*************** linmin ************************/    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 int ncom;      l2 = strlen( ss );                  /* length of filename */
 double *pcom,*xicom;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 double (*nrfunc)(double []);      strcpy( name, ss );         /* save file name */
        strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      dirc[l1-l2] = 0;                    /* add zero */
 {      printf(" DIRC2 = %s \n",dirc);
   double brent(double ax, double bx, double cx,    }
                double (*f)(double), double tol, double *xmin);    /* We add a separator at the end of dirc if not exists */
   double f1dim(double x);    l1 = strlen( dirc );                  /* length of directory */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    if( dirc[l1-1] != DIRSEPARATOR ){
               double *fc, double (*func)(double));      dirc[l1] =  DIRSEPARATOR;
   int j;      dirc[l1+1] = 0; 
   double xx,xmin,bx,ax;      printf(" DIRC3 = %s \n",dirc);
   double fx,fb,fa;    }
      ss = strrchr( name, '.' );            /* find last / */
   ncom=n;    if (ss >0){
   pcom=vector(1,n);      ss++;
   xicom=vector(1,n);      strcpy(ext,ss);                     /* save extension */
   nrfunc=func;      l1= strlen( name);
   for (j=1;j<=n;j++) {      l2= strlen(ss)+1;
     pcom[j]=p[j];      strncpy( finame, name, l1-l2);
     xicom[j]=xi[j];      finame[l1-l2]= 0;
   }    }
   ax=0.0;  
   xx=1.0;    return( 0 );                          /* we're done */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /******************************************/
 #endif  
   for (j=1;j<=n;j++) {  void replace_back_to_slash(char *s, char*t)
     xi[j] *= xmin;  {
     p[j] += xi[j];    int i;
   }    int lg=0;
   free_vector(xicom,1,n);    i=0;
   free_vector(pcom,1,n);    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /*************** powell ************************/      if (t[i]== '\\') s[i]='/';
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    }
             double (*func)(double []))  }
 {  
   void linmin(double p[], double xi[], int n, double *fret,  int nbocc(char *s, char occ)
               double (*func)(double []));  {
   int i,ibig,j;    int i,j=0;
   double del,t,*pt,*ptt,*xit;    int lg=20;
   double fp,fptt;    i=0;
   double *xits;    lg=strlen(s);
   pt=vector(1,n);    for(i=0; i<= lg; i++) {
   ptt=vector(1,n);    if  (s[i] == occ ) j++;
   xit=vector(1,n);    }
   xits=vector(1,n);    return j;
   *fret=(*func)(p);  }
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  void cutv(char *u,char *v, char*t, char occ)
     fp=(*fret);  {
     ibig=0;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     del=0.0;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);       gives u="abcedf" and v="ghi2j" */
     for (i=1;i<=n;i++)    int i,lg,j,p=0;
       printf(" %d %.12f",i, p[i]);    i=0;
     printf("\n");    for(j=0; j<=strlen(t)-1; j++) {
     for (i=1;i<=n;i++) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    }
       fptt=(*fret);  
 #ifdef DEBUG    lg=strlen(t);
       printf("fret=%lf \n",*fret);    for(j=0; j<p; j++) {
 #endif      (u[j] = t[j]);
       printf("%d",i);fflush(stdout);    }
       linmin(p,xit,n,fret,func);       u[p]='\0';
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));     for(j=0; j<= lg; j++) {
         ibig=i;      if (j>=(p+1))(v[j-p-1] = t[j]);
       }    }
 #ifdef DEBUG  }
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  /********************** nrerror ********************/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  void nrerror(char error_text[])
       }  {
       for(j=1;j<=n;j++)    fprintf(stderr,"ERREUR ...\n");
         printf(" p=%.12e",p[j]);    fprintf(stderr,"%s\n",error_text);
       printf("\n");    exit(EXIT_FAILURE);
 #endif  }
     }  /*********************** vector *******************/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double *vector(int nl, int nh)
 #ifdef DEBUG  {
       int k[2],l;    double *v;
       k[0]=1;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       k[1]=-1;    if (!v) nrerror("allocation failure in vector");
       printf("Max: %.12e",(*func)(p));    return v-nl+NR_END;
       for (j=1;j<=n;j++)  }
         printf(" %.12e",p[j]);  
       printf("\n");  /************************ free vector ******************/
       for(l=0;l<=1;l++) {  void free_vector(double*v, int nl, int nh)
         for (j=1;j<=n;j++) {  {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free((FREE_ARG)(v+nl-NR_END));
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  }
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /************************ivector *******************************/
       }  int *ivector(long nl,long nh)
 #endif  {
     int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       free_vector(xit,1,n);    if (!v) nrerror("allocation failure in ivector");
       free_vector(xits,1,n);    return v-nl+NR_END;
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  
       return;  /******************free ivector **************************/
     }  void free_ivector(int *v, long nl, long nh)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  {
     for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
       ptt[j]=2.0*p[j]-pt[j];  }
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  /************************lvector *******************************/
     }  long *lvector(long nl,long nh)
     fptt=(*func)(ptt);  {
     if (fptt < fp) {    long *v;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       if (t < 0.0) {    if (!v) nrerror("allocation failure in ivector");
         linmin(p,xit,n,fret,func);    return v-nl+NR_END;
         for (j=1;j<=n;j++) {  }
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /******************free lvector **************************/
         }  void free_lvector(long *v, long nl, long nh)
 #ifdef DEBUG  {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    free((FREE_ARG)(v+nl-NR_END));
         for(j=1;j<=n;j++)  }
           printf(" %.12e",xit[j]);  
         printf("\n");  /******************* imatrix *******************************/
 #endif  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     }  { 
   }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 }    int **m; 
     
 /**** Prevalence limit ****************/    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    if (!m) nrerror("allocation failure 1 in matrix()"); 
 {    m += NR_END; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    m -= nrl; 
      matrix by transitions matrix until convergence is reached */    
     
   int i, ii,j,k;    /* allocate rows and set pointers to them */ 
   double min, max, maxmin, maxmax,sumnew=0.;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double **matprod2();    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double **out, cov[NCOVMAX], **pmij();    m[nrl] += NR_END; 
   double **newm;    m[nrl] -= ncl; 
   double agefin, delaymax=50 ; /* Max number of years to converge */    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    
     for (j=1;j<=nlstate+ndeath;j++){    /* return pointer to array of pointers to rows */ 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return m; 
     }  } 
   
    cov[1]=1.;  /****************** free_imatrix *************************/
    void free_imatrix(m,nrl,nrh,ncl,nch)
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        int **m;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        long nch,ncl,nrh,nrl; 
     newm=savm;       /* free an int matrix allocated by imatrix() */ 
     /* Covariates have to be included here again */  { 
      cov[2]=agefin;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
       for (k=1; k<=cptcovn;k++) {  } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       for (k=1; k<=cptcovprod;k++)    double **m;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    if (!m) nrerror("allocation failure 1 in matrix()");
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    m += NR_END;
     m -= nrl;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     savm=oldm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     oldm=newm;    m[nrl] += NR_END;
     maxmax=0.;    m[nrl] -= ncl;
     for(j=1;j<=nlstate;j++){  
       min=1.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       max=0.;    return m;
       for(i=1; i<=nlstate; i++) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         sumnew=0;     */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  }
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /*************************free matrix ************************/
         min=FMIN(min,prlim[i][j]);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
       maxmin=max-min;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       maxmax=FMAX(maxmax,maxmin);    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     if(maxmax < ftolpl){  
       return prlim;  /******************* ma3x *******************************/
     }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   }  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /*************** transition probabilities ***************/  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   double s1, s2;    m -= nrl;
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(i=1; i<= nlstate; i++){    m[nrl] += NR_END;
     for(j=1; j<i;j++){    m[nrl] -= ncl;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         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);*/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       ps[i][j]=s2;    m[nrl][ncl] += NR_END;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
     for(j=i+1; j<=nlstate+ndeath;j++){      m[nrl][j]=m[nrl][j-1]+nlay;
       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];    for (i=nrl+1; i<=nrh; i++) {
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
       ps[i][j]=(s2);        m[i][j]=m[i][j-1]+nlay;
     }    }
   }    return m; 
     /*ps[3][2]=1;*/    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   for(i=1; i<= nlstate; i++){    */
      s1=0;  }
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);  /*************************free ma3x ************************/
     for(j=i+1; j<=nlstate+ndeath; j++)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       s1+=exp(ps[i][j]);  {
     ps[i][i]=1./(s1+1.);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for(j=1; j<i; j++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       ps[i][j]= exp(ps[i][j])*ps[i][i];    free((FREE_ARG)(m+nrl-NR_END));
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /*************** function subdirf ***********/
   } /* end i */  char *subdirf(char fileres[])
   {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    /* Caution optionfilefiname is hidden */
     for(jj=1; jj<= nlstate+ndeath; jj++){    strcpy(tmpout,optionfilefiname);
       ps[ii][jj]=0;    strcat(tmpout,"/"); /* Add to the right */
       ps[ii][ii]=1;    strcat(tmpout,fileres);
     }    return tmpout;
   }  }
   
   /*************** function subdirf2 ***********/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  char *subdirf2(char fileres[], char *preop)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
      printf("%lf ",ps[ii][jj]);    
    }    /* Caution optionfilefiname is hidden */
     printf("\n ");    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     printf("\n ");printf("%lf ",cov[2]);*/    strcat(tmpout,preop);
 /*    strcat(tmpout,fileres);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    return tmpout;
   goto end;*/  }
     return ps;  
 }  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
 /**************** Product of 2 matrices ******************/  {
     
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcat(tmpout,"/");
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,preop);
   /* in, b, out are matrice of pointers which should have been initialized    strcat(tmpout,preop2);
      before: only the contents of out is modified. The function returns    strcat(tmpout,fileres);
      a pointer to pointers identical to out */    return tmpout;
   long i, j, k;  }
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /***************** f1dim *************************/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  extern int ncom; 
         out[i][k] +=in[i][j]*b[j][k];  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
   return out;   
 }  double f1dim(double x) 
   { 
     int j; 
 /************* Higher Matrix Product ***************/    double f;
     double *xt; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )   
 {    xt=vector(1,ncom); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
      duration (i.e. until    f=(*nrfunc)(xt); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    free_vector(xt,1,ncom); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    return f; 
      (typically every 2 years instead of every month which is too big).  } 
      Model is determined by parameters x and covariates have to be  
      included manually here.  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
      */  { 
     int iter; 
   int i, j, d, h, k;    double a,b,d,etemp;
   double **out, cov[NCOVMAX];    double fu,fv,fw,fx;
   double **newm;    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
   /* Hstepm could be zero and should return the unit matrix */    double e=0.0; 
   for (i=1;i<=nlstate+ndeath;i++)   
     for (j=1;j<=nlstate+ndeath;j++){    a=(ax < cx ? ax : cx); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    b=(ax > cx ? ax : cx); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    x=w=v=bx; 
     }    fw=fv=fx=(*f)(x); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (iter=1;iter<=ITMAX;iter++) { 
   for(h=1; h <=nhstepm; h++){      xm=0.5*(a+b); 
     for(d=1; d <=hstepm; d++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       newm=savm;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       /* Covariates have to be included here again */      printf(".");fflush(stdout);
       cov[1]=1.;      fprintf(ficlog,".");fflush(ficlog);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  #ifdef DEBUG
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[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);
       for (k=1; k<=cptcovage;k++)      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);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for (k=1; k<=cptcovprod;k++)  #endif
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
         return fx; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      } 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      ftemp=fu;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      if (fabs(e) > tol1) { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        r=(x-w)*(fx-fv); 
       savm=oldm;        q=(x-v)*(fx-fw); 
       oldm=newm;        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     for(i=1; i<=nlstate+ndeath; i++)        if (q > 0.0) p = -p; 
       for(j=1;j<=nlstate+ndeath;j++) {        q=fabs(q); 
         po[i][j][h]=newm[i][j];        etemp=e; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        e=d; 
          */        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)); 
   } /* end h */        else { 
   return po;          d=p/q; 
 }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 /*************** log-likelihood *************/        } 
 double func( double *x)      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i, ii, j, k, mi, d, kk;      } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double **out;      fu=(*f)(u); 
   double sw; /* Sum of weights */      if (fu <= fx) { 
   double lli; /* Individual log likelihood */        if (u >= x) a=x; else b=x; 
   long ipmx;        SHFT(v,w,x,u) 
   /*extern weight */          SHFT(fv,fw,fx,fu) 
   /* We are differentiating ll according to initial status */          } else { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/            if (u < x) a=u; else b=u; 
   /*for(i=1;i<imx;i++)            if (fu <= fw || w == x) { 
     printf(" %d\n",s[4][i]);              v=w; 
   */              w=u; 
   cov[1]=1.;              fv=fw; 
               fw=fu; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;            } else if (fu <= fv || v == x || v == w) { 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){              v=u; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];              fv=fu; 
     for(mi=1; mi<= wav[i]-1; mi++){            } 
       for (ii=1;ii<=nlstate+ndeath;ii++)          } 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    } 
       for(d=0; d<dh[mi][i]; d++){    nrerror("Too many iterations in brent"); 
         newm=savm;    *xmin=x; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    return fx; 
         for (kk=1; kk<=cptcovage;kk++) {  } 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  /****************** mnbrak ***********************/
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));              double (*func)(double)) 
         savm=oldm;  { 
         oldm=newm;    double ulim,u,r,q, dum;
            double fu; 
           
       } /* end mult */    *fa=(*func)(*ax); 
          *fb=(*func)(*bx); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    if (*fb > *fa) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      SHFT(dum,*ax,*bx,dum) 
       ipmx +=1;        SHFT(dum,*fb,*fa,dum) 
       sw += weight[i];        } 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    *cx=(*bx)+GOLD*(*bx-*ax); 
     } /* end of wave */    *fc=(*func)(*cx); 
   } /* end of individual */    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      q=(*bx-*cx)*(*fb-*fa); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   return -l;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 }      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
 /*********** Maximum Likelihood Estimation ***************/        fu=(*func)(u); 
         if (fu < *fc) { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 {            SHFT(*fb,*fc,fu,(*func)(u)) 
   int i,j, iter;            } 
   double **xi,*delti;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double fret;        u=ulim; 
   xi=matrix(1,npar,1,npar);        fu=(*func)(u); 
   for (i=1;i<=npar;i++)      } else { 
     for (j=1;j<=npar;j++)        u=(*cx)+GOLD*(*cx-*bx); 
       xi[i][j]=(i==j ? 1.0 : 0.0);        fu=(*func)(u); 
   printf("Powell\n");      } 
   powell(p,xi,npar,ftol,&iter,&fret,func);      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        } 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  } 
   
 }  /*************** linmin ************************/
   
 /**** Computes Hessian and covariance matrix ***/  int ncom; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  double *pcom,*xicom;
 {  double (*nrfunc)(double []); 
   double  **a,**y,*x,pd;   
   double **hess;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   int i, j,jk;  { 
   int *indx;    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
   double hessii(double p[], double delta, int theta, double delti[]);    double f1dim(double x); 
   double hessij(double p[], double delti[], int i, int j);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   void lubksb(double **a, int npar, int *indx, double b[]) ;                double *fc, double (*func)(double)); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    int j; 
     double xx,xmin,bx,ax; 
   hess=matrix(1,npar,1,npar);    double fx,fb,fa;
    
   printf("\nCalculation of the hessian matrix. Wait...\n");    ncom=n; 
   for (i=1;i<=npar;i++){    pcom=vector(1,n); 
     printf("%d",i);fflush(stdout);    xicom=vector(1,n); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    nrfunc=func; 
     /*printf(" %f ",p[i]);*/    for (j=1;j<=n;j++) { 
     /*printf(" %lf ",hess[i][i]);*/      pcom[j]=p[j]; 
   }      xicom[j]=xi[j]; 
      } 
   for (i=1;i<=npar;i++) {    ax=0.0; 
     for (j=1;j<=npar;j++)  {    xx=1.0; 
       if (j>i) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         printf(".%d%d",i,j);fflush(stdout);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         hess[i][j]=hessij(p,delti,i,j);  #ifdef DEBUG
         hess[j][i]=hess[i][j];        printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         /*printf(" %lf ",hess[i][j]);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }  #endif
     }    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
   printf("\n");      p[j] += xi[j]; 
     } 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    free_vector(xicom,1,n); 
      free_vector(pcom,1,n); 
   a=matrix(1,npar,1,npar);  } 
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  char *asc_diff_time(long time_sec, char ascdiff[])
   indx=ivector(1,npar);  {
   for (i=1;i<=npar;i++)    long sec_left, days, hours, minutes;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    days = (time_sec) / (60*60*24);
   ludcmp(a,npar,indx,&pd);    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
   for (j=1;j<=npar;j++) {    sec_left = (sec_left) %(60*60);
     for (i=1;i<=npar;i++) x[i]=0;    minutes = (sec_left) /60;
     x[j]=1;    sec_left = (sec_left) % (60);
     lubksb(a,npar,indx,x);    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for (i=1;i<=npar;i++){    return ascdiff;
       matcov[i][j]=x[i];  }
     }  
   }  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   printf("\n#Hessian matrix#\n");              double (*func)(double [])) 
   for (i=1;i<=npar;i++) {  { 
     for (j=1;j<=npar;j++) {    void linmin(double p[], double xi[], int n, double *fret, 
       printf("%.3e ",hess[i][j]);                double (*func)(double [])); 
     }    int i,ibig,j; 
     printf("\n");    double del,t,*pt,*ptt,*xit;
   }    double fp,fptt;
     double *xits;
   /* Recompute Inverse */    int niterf, itmp;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    pt=vector(1,n); 
   ludcmp(a,npar,indx,&pd);    ptt=vector(1,n); 
     xit=vector(1,n); 
   /*  printf("\n#Hessian matrix recomputed#\n");    xits=vector(1,n); 
     *fret=(*func)(p); 
   for (j=1;j<=npar;j++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (i=1;i<=npar;i++) x[i]=0;    for (*iter=1;;++(*iter)) { 
     x[j]=1;      fp=(*fret); 
     lubksb(a,npar,indx,x);      ibig=0; 
     for (i=1;i<=npar;i++){      del=0.0; 
       y[i][j]=x[i];      last_time=curr_time;
       printf("%.3e ",y[i][j]);      (void) gettimeofday(&curr_time,&tzp);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     printf("\n");      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   }      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   */      */
      for (i=1;i<=n;i++) {
   free_matrix(a,1,npar,1,npar);        printf(" %d %.12f",i, p[i]);
   free_matrix(y,1,npar,1,npar);        fprintf(ficlog," %d %.12lf",i, p[i]);
   free_vector(x,1,npar);        fprintf(ficrespow," %.12lf", p[i]);
   free_ivector(indx,1,npar);      }
   free_matrix(hess,1,npar,1,npar);      printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
 }      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
 /*************** hessian matrix ****************/        strcpy(strcurr,asctime(&tm));
 double hessii( double x[], double delta, int theta, double delti[])  /*       asctime_r(&tm,strcurr); */
 {        forecast_time=curr_time; 
   int i;        itmp = strlen(strcurr);
   int l=1, lmax=20;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double k1,k2;          strcurr[itmp-1]='\0';
   double p2[NPARMAX+1];        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double res;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for(niterf=10;niterf<=30;niterf+=10){
   double fx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   int k=0,kmax=10;          tmf = *localtime(&forecast_time.tv_sec);
   double l1;  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
   fx=func(x);          itmp = strlen(strfor);
   for (i=1;i<=npar;i++) p2[i]=x[i];          if(strfor[itmp-1]=='\n')
   for(l=0 ; l <=lmax; l++){          strfor[itmp-1]='\0';
     l1=pow(10,l);          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);
     delts=delt;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for(k=1 ; k <kmax; k=k+1){        }
       delt = delta*(l1*k);      }
       p2[theta]=x[theta] +delt;      for (i=1;i<=n;i++) { 
       k1=func(p2)-fx;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       p2[theta]=x[theta]-delt;        fptt=(*fret); 
       k2=func(p2)-fx;  #ifdef DEBUG
       /*res= (k1-2.0*fx+k2)/delt/delt; */        printf("fret=%lf \n",*fret);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        fprintf(ficlog,"fret=%lf \n",*fret);
        #endif
 #ifdef DEBUG        printf("%d",i);fflush(stdout);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif        linmin(p,xit,n,fret,func); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        if (fabs(fptt-(*fret)) > del) { 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          del=fabs(fptt-(*fret)); 
         k=kmax;          ibig=i; 
       }        } 
       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.;        printf("%d %.12e",i,(*fret));
       }        fprintf(ficlog,"%d %.12e",i,(*fret));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        for (j=1;j<=n;j++) {
         delts=delt;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
   delti[theta]=delts;        for(j=1;j<=n;j++) {
   return res;          printf(" p=%.12e",p[j]);
            fprintf(ficlog," p=%.12e",p[j]);
 }        }
         printf("\n");
 double hessij( double x[], double delti[], int thetai,int thetaj)        fprintf(ficlog,"\n");
 {  #endif
   int i;      } 
   int l=1, l1, lmax=20;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double k1,k2,k3,k4,res,fx;  #ifdef DEBUG
   double p2[NPARMAX+1];        int k[2],l;
   int k;        k[0]=1;
         k[1]=-1;
   fx=func(x);        printf("Max: %.12e",(*func)(p));
   for (k=1; k<=2; k++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for (i=1;i<=npar;i++) p2[i]=x[i];        for (j=1;j<=n;j++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;          printf(" %.12e",p[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog," %.12e",p[j]);
     k1=func(p2)-fx;        }
          printf("\n");
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(l=0;l<=1;l++) {
     k2=func(p2)-fx;          for (j=1;j<=n;j++) {
              ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     p2[thetai]=x[thetai]-delti[thetai]/k;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     k3=func(p2)-fx;          }
            printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     p2[thetai]=x[thetai]-delti[thetai]/k;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k4=func(p2)-fx;  #endif
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        free_vector(xit,1,n); 
 #endif        free_vector(xits,1,n); 
   }        free_vector(ptt,1,n); 
   return res;        free_vector(pt,1,n); 
 }        return; 
       } 
 /************** Inverse of matrix **************/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 void ludcmp(double **a, int n, int *indx, double *d)      for (j=1;j<=n;j++) { 
 {        ptt[j]=2.0*p[j]-pt[j]; 
   int i,imax,j,k;        xit[j]=p[j]-pt[j]; 
   double big,dum,sum,temp;        pt[j]=p[j]; 
   double *vv;      } 
        fptt=(*func)(ptt); 
   vv=vector(1,n);      if (fptt < fp) { 
   *d=1.0;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for (i=1;i<=n;i++) {        if (t < 0.0) { 
     big=0.0;          linmin(p,xit,n,fret,func); 
     for (j=1;j<=n;j++)          for (j=1;j<=n;j++) { 
       if ((temp=fabs(a[i][j])) > big) big=temp;            xi[j][ibig]=xi[j][n]; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            xi[j][n]=xit[j]; 
     vv[i]=1.0/big;          }
   }  #ifdef DEBUG
   for (j=1;j<=n;j++) {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (i=1;i<j;i++) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       sum=a[i][j];          for(j=1;j<=n;j++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            printf(" %.12e",xit[j]);
       a[i][j]=sum;            fprintf(ficlog," %.12e",xit[j]);
     }          }
     big=0.0;          printf("\n");
     for (i=j;i<=n;i++) {          fprintf(ficlog,"\n");
       sum=a[i][j];  #endif
       for (k=1;k<j;k++)        }
         sum -= a[i][k]*a[k][j];      } 
       a[i][j]=sum;    } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  } 
         big=dum;  
         imax=i;  /**** Prevalence limit (stable or period prevalence)  ****************/
       }  
     }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     if (j != imax) {  {
       for (k=1;k<=n;k++) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         dum=a[imax][k];       matrix by transitions matrix until convergence is reached */
         a[imax][k]=a[j][k];  
         a[j][k]=dum;    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
       *d = -(*d);    double **matprod2();
       vv[imax]=vv[j];    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     indx[j]=imax;    double agefin, delaymax=50 ; /* Max number of years to converge */
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {    for (ii=1;ii<=nlstate+ndeath;ii++)
       dum=1.0/(a[j][j]);      for (j=1;j<=nlstate+ndeath;j++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
   }  
   free_vector(vv,1,n);  /* Doesn't work */     cov[1]=1.;
 ;   
 }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 void lubksb(double **a, int n, int *indx, double b[])      newm=savm;
 {      /* Covariates have to be included here again */
   int i,ii=0,ip,j;       cov[2]=agefin;
   double sum;    
          for (k=1; k<=cptcovn;k++) {
   for (i=1;i<=n;i++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     ip=indx[i];          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     sum=b[ip];        }
     b[ip]=b[i];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     if (ii)        for (k=1; k<=cptcovprod;k++)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     else if (sum) ii=i;  
     b[i]=sum;        /*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]);*/
   for (i=n;i>=1;i--) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     sum=b[i];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];      savm=oldm;
   }      oldm=newm;
 }      maxmax=0.;
       for(j=1;j<=nlstate;j++){
 /************ Frequencies ********************/        min=1.;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint, int boolprev, double dateprev1,double dateprev2)        max=0.;
 {  /* Some frequencies */        for(i=1; i<=nlstate; i++) {
            sumnew=0;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   double ***freq; /* Frequencies */          prlim[i][j]= newm[i][j]/(1-sumnew);
   double *pp;          max=FMAX(max,prlim[i][j]);
   double pos, k2;          min=FMIN(min,prlim[i][j]);
   FILE *ficresp;        }
   char fileresp[FILENAMELENGTH];        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   pp=vector(1,nlstate);      }
   probs= ma3x(1,130 ,1,8, 1,8);      if(maxmax < ftolpl){
   strcpy(fileresp,"p");        return prlim;
   strcat(fileresp,fileres);      }
   if((ficresp=fopen(fileresp,"w"))==NULL) {    }
     printf("Problem with prevalence resultfile: %s\n", fileresp);  }
     exit(0);  
   }  /*************** transition probabilities ***************/ 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   j=cptcoveff;    double s1, s2;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      for(i=1; i<= nlstate; i++){
        j1++;        for(j=1; j<i;j++){
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
          scanf("%d", i);*/            /*s2 += param[i][j][nc]*cov[nc];*/
         for (i=-1; i<=nlstate+ndeath; i++)              s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
          for (jk=-1; jk<=nlstate+ndeath; jk++)    /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
            for(m=agemin; m <= agemax+3; m++)          }
              freq[i][jk][m]=0;          ps[i][j]=s2;
          /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
        for (i=1; i<=imx; i++) {        }
          bool=1;        for(j=i+1; j<=nlstate+ndeath;j++){
          if  (cptcovn>0) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
            for (z1=1; z1<=cptcoveff; z1++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
                bool=0;          }
          }          ps[i][j]=s2;
          if (bool==1) {        }
            if (boolprev==1){      }
              for(m=fprev1; m<=lprev1; m++){      /*ps[3][2]=1;*/
                if(agev[m][i]==0) agev[m][i]=agemax+1;      
                if(agev[m][i]==1) agev[m][i]=agemax+2;      for(i=1; i<= nlstate; i++){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        s1=0;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for(j=1; j<i; j++)
              }          s1+=exp(ps[i][j]);
            }        for(j=i+1; j<=nlstate+ndeath; j++)
            else {          s1+=exp(ps[i][j]);
             for(m=firstpass; m<=lastpass; m++){        ps[i][i]=1./(s1+1.);
              k2=anint[m][i]+(mint[m][i]/12.);        for(j=1; j<i; j++)
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
              if(agev[m][i]==0) agev[m][i]=agemax+1;        for(j=i+1; j<=nlstate+ndeath; j++)
              if(agev[m][i]==1) agev[m][i]=agemax+2;          ps[i][j]= exp(ps[i][j])*ps[i][i];
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      } /* end i */
              }      
             }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
            }        for(jj=1; jj<= nlstate+ndeath; jj++){
           }          ps[ii][jj]=0;
        }          ps[ii][ii]=1;
         if  (cptcovn>0) {        }
          fprintf(ficresp, "\n#********** Variable ");      }
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      
        fprintf(ficresp, "**********\n#");  
         }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
        for(i=1; i<=nlstate;i++)  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  /*         printf("ddd %lf ",ps[ii][jj]); */
        fprintf(ficresp, "\n");  /*       } */
          /*       printf("\n "); */
   for(i=(int)agemin; i <= (int)agemax+3; i++){  /*        } */
     if(i==(int)agemax+3)  /*        printf("\n ");printf("%lf ",cov[2]); */
       printf("Total");         /*
     else        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       printf("Age %d", i);        goto end;*/
     for(jk=1; jk <=nlstate ; jk++){      return ps;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
         pp[jk] += freq[jk][m][i];  
     }  /**************** Product of 2 matrices ******************/
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         pos += freq[jk][m][i];  {
       if(pp[jk]>=1.e-10)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       else    /* in, b, out are matrice of pointers which should have been initialized 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       before: only the contents of out is modified. The function returns
     }       a pointer to pointers identical to out */
     long i, j, k;
      for(jk=1; jk <=nlstate ; jk++){    for(i=nrl; i<= nrh; i++)
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for(k=ncolol; k<=ncoloh; k++)
         pp[jk] += freq[jk][m][i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
      }          out[i][k] +=in[i][j]*b[j][k];
   
     for(jk=1,pos=0; jk <=nlstate ; jk++)    return out;
       pos += pp[jk];  }
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /************* Higher Matrix Product ***************/
       else  
         printf(" %d.=%.0f prev[%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 )
       if( i <= (int) agemax){  {
         if(pos>=1.e-5){    /* Computes the transition matrix starting at age 'age' over 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);       'nhstepm*hstepm*stepm' months (i.e. until
           probs[i][jk][j1]= pp[jk]/pos;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/       nhstepm*hstepm matrices. 
         }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       else       (typically every 2 years instead of every month which is too big 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);       for the memory).
       }       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)       */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)    int i, j, d, h, k;
       fprintf(ficresp,"\n");    double **out, cov[NCOVMAX];
     printf("\n");    double **newm;
     }  
     }    /* Hstepm could be zero and should return the unit matrix */
  }    for (i=1;i<=nlstate+ndeath;i++)
        for (j=1;j<=nlstate+ndeath;j++){
   fclose(ficresp);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   free_vector(pp,1,nlstate);      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 }  /* End of Freq */    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
 /************ Prevalence ********************/        newm=savm;
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1, double **mint,double **anint,int boolprev, double dateprev1, double dateprev2)        /* Covariates have to be included here again */
 {  /* Some frequencies */        cov[1]=1.;
          cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double ***freq; /* Frequencies */        for (k=1; k<=cptcovage;k++)
   double *pp;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double pos, k2;        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]]];
   pp=vector(1,nlstate);  
   probs= ma3x(1,130 ,1,8, 1,8);  
          /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   j1=0;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                       pmij(pmmij,cov,ncovmodel,x,nlstate));
   j=cptcoveff;        savm=oldm;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        oldm=newm;
        }
  for(k1=1; k1<=j;k1++){      for(i=1; i<=nlstate+ndeath; i++)
     for(i1=1; i1<=ncodemax[k1];i1++){        for(j=1;j<=nlstate+ndeath;j++) {
       j1++;          po[i][j][h]=newm[i][j];
            /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       for (i=-1; i<=nlstate+ndeath; i++)             */
         for (jk=-1; jk<=nlstate+ndeath; jk++)          }
           for(m=agemin; m <= agemax+3; m++)    } /* end h */
           freq[i][jk][m]=0;    return po;
        }
       for (i=1; i<=imx; i++) {  
         bool=1;  
         if  (cptcovn>0) {  /*************** log-likelihood *************/
           for (z1=1; z1<=cptcoveff; z1++)  double func( double *x)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  {
               bool=0;    int i, ii, j, k, mi, d, kk;
               }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if (bool==1) {    double **out;
           if (boolprev==1){    double sw; /* Sum of weights */
             for(m=fprev1; m<=lprev1; m++){    double lli; /* Individual log likelihood */
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int s1, s2;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double bbh, survp;
               freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    long ipmx;
               freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    /*extern weight */
             }    /* We are differentiating ll according to initial status */
           }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           else {    /*for(i=1;i<imx;i++) 
             for(m=firstpass; m<=lastpass; m++){      printf(" %d\n",s[4][i]);
               k2=anint[m][i]+(mint[m][i]/12.);    */
               if ((k2>=dateprev1) && (k2<=dateprev2)) {    cov[1]=1.;
                 if(agev[m][i]==0) agev[m][i]=agemax+1;  
                 if(agev[m][i]==1) agev[m][i]=agemax+2;    for(k=1; k<=nlstate; k++) ll[k]=0.;
                 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];    if(mle==1){
               }      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(i=(int)agemin; i <= (int)agemax+3; i++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            }
               pp[jk] += freq[jk][m][i];          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
           for(jk=1; jk <=nlstate ; jk++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for(m=-1, pos=0; m <=0 ; m++)            for (kk=1; kk<=cptcovage;kk++) {
             pos += freq[jk][m][i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
                    out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            savm=oldm;
              pp[jk] += freq[jk][m][i];            oldm=newm;
          }          } /* end mult */
                  
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          /*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 
            if( i <= (int) agemax){           * (in months) between two waves is not a multiple of stepm, we rounded to 
              if(pos>=1.e-5){           * the nearest (and in case of equal distance, to the lowest) interval but now
                probs[i][jk][j1]= pp[jk]/pos;           * 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
            }           * 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
                     * -stepm/2 to stepm/2 .
         }           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
            s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_vector(pp,1,nlstate);          /* bias bh is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
 }  /* End of Freq */           */
 /************* Waves Concatenation ***************/          /* 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){ 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            /* i.e. if s2 is a death state and if the date of death is known 
 {               then the contribution to the likelihood is the probability to 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.               die between last step unit time and current  step unit time, 
      Death is a valid wave (if date is known).               which is also equal to probability to die before dh 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i               minus probability to die before dh-stepm . 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]               In version up to 0.92 likelihood was computed
      and mw[mi+1][i]. dh depends on stepm.          as if date of death was unknown. Death was treated as any other
      */          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
   int i, mi, m;          to consider that at each interview the state was recorded
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          (healthy, disable or death) and IMaCh was corrected; but when we
      double sum=0., jmean=0.;*/          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
   int j, k=0,jk, ju, jl;          contribution is smaller and very dependent of the step unit
   double sum=0.;          stepm. It is no more the probability to die between last interview
   jmin=1e+5;          and month of death but the probability to survive from last
   jmax=-1;          interview up to one month before death multiplied by the
   jmean=0.;          probability to die within a month. Thanks to Chris
   for(i=1; i<=imx; i++){          Jackson for correcting this bug.  Former versions increased
     mi=0;          mortality artificially. The bad side is that we add another loop
     m=firstpass;          which slows down the processing. The difference can be up to 10%
     while(s[m][i] <= nlstate){          lower mortality.
       if(s[m][i]>=1)            */
         mw[++mi][i]=m;            lli=log(out[s1][s2] - savm[s1][s2]);
       if(m >=lastpass)  
         break;  
       else          } else if  (s2==-2) {
         m++;            for (j=1,survp=0. ; j<=nlstate; j++) 
     }/* end while */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     if (s[m][i] > nlstate){            /*survp += out[s1][j]; */
       mi++;     /* Death is another wave */            lli= log(survp);
       /* if(mi==0)  never been interviewed correctly before death */          }
          /* Only death is a correct wave */          
       mw[mi][i]=m;          else if  (s2==-4) { 
     }            for (j=3,survp=0. ; j<=nlstate; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     wav[i]=mi;            lli= log(survp); 
     if(mi==0)          } 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }          else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
   for(i=1; i<=imx; i++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(mi=1; mi<wav[i];mi++){            lli= log(survp); 
       if (stepm <=0)          } 
         dh[mi][i]=1;          
       else{          else{
         if (s[mw[mi+1][i]][i] > nlstate) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           if (agedc[i] < 2*AGESUP) {            /*  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 */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          } 
           if(j==0) j=1;  /* Survives at least one month after exam */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           k=k+1;          /*if(lli ==000.0)*/
           if (j >= jmax) jmax=j;          /*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); */
           if (j <= jmin) jmin=j;          ipmx +=1;
           sum=sum+j;          sw += weight[i];
           /* if (j<10) printf("j=%d num=%d ",j,i); */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }        } /* end of wave */
         }      } /* end of individual */
         else{    }  else if(mle==2){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           k=k+1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (j >= jmax) jmax=j;        for(mi=1; mi<= wav[i]-1; mi++){
           else if (j <= jmin)jmin=j;          for (ii=1;ii<=nlstate+ndeath;ii++)
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            for (j=1;j<=nlstate+ndeath;j++){
           sum=sum+j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         jk= j/stepm;            }
         jl= j -jk*stepm;          for(d=0; d<=dh[mi][i]; d++){
         ju= j -(jk+1)*stepm;            newm=savm;
         if(jl <= -ju)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           dh[mi][i]=jk;            for (kk=1; kk<=cptcovage;kk++) {
         else              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           dh[mi][i]=jk+1;            }
         if(dh[mi][i]==0)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           dh[mi][i]=1; /* At least one step */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
   }          } /* end mult */
   jmean=sum/k;        
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          s1=s[mw[mi][i]][i];
  }          s2=s[mw[mi+1][i]][i];
 /*********** Tricode ****************************/          bbh=(double)bh[mi][i]/(double)stepm; 
 void tricode(int *Tvar, int **nbcode, int imx)          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;
   int Ndum[20],ij=1, k, j, i;          sw += weight[i];
   int cptcode=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   cptcoveff=0;        } /* end of wave */
        } /* end of individual */
   for (k=0; k<19; k++) Ndum[k]=0;    }  else if(mle==3){  /* exponential inter-extrapolation */
   for (k=1; k<=7; k++) ncodemax[k]=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1; i<=imx; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       ij=(int)(covar[Tvar[j]][i]);            for (j=1;j<=nlstate+ndeath;j++){
       Ndum[ij]++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (ij > cptcode) cptcode=ij;            }
     }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for (i=0; i<=cptcode; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(Ndum[i]!=0) ncodemax[j]++;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     ij=1;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1; i<=ncodemax[j]; i++) {            savm=oldm;
       for (k=0; k<=19; k++) {            oldm=newm;
         if (Ndum[k] != 0) {          } /* end mult */
           nbcode[Tvar[j]][ij]=k;        
           ij++;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         if (ij > ncodemax[j]) break;          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 */
     }          ipmx +=1;
   }            sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  for (k=0; k<19; k++) Ndum[k]=0;        } /* end of wave */
       } /* end of individual */
  for (i=1; i<=ncovmodel-2; i++) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       ij=Tvar[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       Ndum[ij]++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
  ij=1;            for (j=1;j<=nlstate+ndeath;j++){
  for (i=1; i<=10; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    if((Ndum[i]!=0) && (i<=ncov)){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      Tvaraff[ij]=i;            }
      ij++;          for(d=0; d<dh[mi][i]; d++){
    }            newm=savm;
  }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
     cptcoveff=ij-1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }            }
           
 /*********** Health Expectancies ****************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            savm=oldm;
 {            oldm=newm;
   /* Health expectancies */          } /* end mult */
   int i, j, nhstepm, hstepm, h;        
   double age, agelim,hf;          s1=s[mw[mi][i]][i];
   double ***p3mat;          s2=s[mw[mi+1][i]][i];
            if( s2 > nlstate){ 
   fprintf(ficreseij,"# Health expectancies\n");            lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficreseij,"# Age");          }else{
   for(i=1; i<=nlstate;i++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(j=1; j<=nlstate;j++)          }
       fprintf(ficreseij," %1d-%1d",i,j);          ipmx +=1;
   fprintf(ficreseij,"\n");          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=1*YEARM; /*  Every j years of age (in month) */  /*      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]); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } /* end of wave */
       } /* end of individual */
   agelim=AGESUP;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* nhstepm age range expressed in number of stepm */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        for(mi=1; mi<= wav[i]-1; mi++){
     /* Typically if 20 years = 20*12/6=40 stepm */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (stepm >= YEARM) hstepm=1;            for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(d=0; d<dh[mi][i]; d++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          
           eij[i][j][(int)age] +=p3mat[i][j][h];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
     hf=1;            oldm=newm;
     if (stepm >= YEARM) hf=stepm/YEARM;          } /* end mult */
     fprintf(ficreseij,"%.0f",age );        
     for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
       for(j=1; j<=nlstate;j++){          s2=s[mw[mi+1][i]][i];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          ipmx +=1;
     fprintf(ficreseij,"\n");          sw += weight[i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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]);*/
 }        } /* end of wave */
       } /* end of individual */
 /************ Variance ******************/    } /* End of if */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /* Variance of health expectancies */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    return -l;
   double **newm;  }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;  /*************** log-likelihood *************/
   int k, cptcode;  double funcone( double *x)
   double *xp;  {
   double **gp, **gm;    /* Same as likeli but slower because of a lot of printf and if */
   double ***gradg, ***trgradg;    int i, ii, j, k, mi, d, kk;
   double ***p3mat;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double age,agelim;    double **out;
   int theta;    double lli; /* Individual log likelihood */
     double llt;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    int s1, s2;
   fprintf(ficresvij,"# Age");    double bbh, survp;
   for(i=1; i<=nlstate;i++)    /*extern weight */
     for(j=1; j<=nlstate;j++)    /* We are differentiating ll according to initial status */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   fprintf(ficresvij,"\n");    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   xp=vector(1,npar);    */
   dnewm=matrix(1,nlstate,1,npar);    cov[1]=1.;
   doldm=matrix(1,nlstate,1,nlstate);  
      for(k=1; k<=nlstate; k++) ll[k]=0.;
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   agelim = AGESUP;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for(mi=1; mi<= wav[i]-1; mi++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for (ii=1;ii<=nlstate+ndeath;ii++)
     if (stepm >= YEARM) hstepm=1;          for (j=1;j<=nlstate+ndeath;j++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          }
     gp=matrix(0,nhstepm,1,nlstate);        for(d=0; d<dh[mi][i]; d++){
     gm=matrix(0,nhstepm,1,nlstate);          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(theta=1; theta <=npar; theta++){          for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          savm=oldm;
           oldm=newm;
       if (popbased==1) {        } /* end mult */
         for(i=1; i<=nlstate;i++)        
           prlim[i][i]=probs[(int)age][i][ij];        s1=s[mw[mi][i]][i];
       }        s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
       for(j=1; j<= nlstate; j++){        /* bias is positive if real duration
         for(h=0; h<=nhstepm; h++){         * is higher than the multiple of stepm and negative otherwise.
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)         */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         }          lli=log(out[s1][s2] - savm[s1][s2]);
       }        } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
       for(i=1; i<=npar; i++) /* Computes gradient */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          lli= log(survp);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }else if (mle==1){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
       if (popbased==1) {          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<=nlstate;i++)        } else if(mle==3){  /* exponential inter-extrapolation */
           prlim[i][i]=probs[(int)age][i][ij];          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
       for(j=1; j<= nlstate; j++){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         for(h=0; h<=nhstepm; h++){          lli=log(out[s1][s2]); /* Original formula */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        } /* End of if */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        ipmx +=1;
         }        sw += weight[i];
       }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(j=1; j<= nlstate; j++)        if(globpr){
         for(h=0; h<=nhstepm; h++){          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];   %11.6f %11.6f %11.6f ", \
         }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     } /* End theta */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     for(h=0; h<=nhstepm; h++)          }
       for(j=1; j<=nlstate;j++)          fprintf(ficresilk," %10.6f\n", -llt);
         for(theta=1; theta <=npar; theta++)        }
           trgradg[h][j][theta]=gradg[h][theta][j];      } /* end of wave */
     } /* end of individual */
     for(i=1;i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(j=1;j<=nlstate;j++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         vareij[i][j][(int)age] =0.;    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(k=0;k<=nhstepm;k++){      gipmx=ipmx;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      gsw=sw;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    }
         for(i=1;i<=nlstate;i++)    return -l;
           for(j=1;j<=nlstate;j++)  }
             vareij[i][j][(int)age] += doldm[i][j];  
       }  
     }  /*************** function likelione ***********/
     h=1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     if (stepm >= YEARM) h=stepm/YEARM;  {
     fprintf(ficresvij,"%.0f ",age );    /* 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.
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);       Plotting could be done.
       }     */
     fprintf(ficresvij,"\n");    int k;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    if(*globpri !=0){ /* Just counts and sums, no printings */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      strcpy(fileresilk,"ilk"); 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      strcat(fileresilk,fileres);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   } /* End age */        printf("Problem with resultfile: %s\n", fileresilk);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   free_vector(xp,1,npar);      }
   free_matrix(doldm,1,nlstate,1,npar);      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(dnewm,1,nlstate,1,nlstate);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 }      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 /************ Variance of prevlim ******************/      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    }
 {  
   /* Variance of prevalence limit */    *fretone=(*funcone)(p);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    if(*globpri !=0){
   double **newm;      fclose(ficresilk);
   double **dnewm,**doldm;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   int i, j, nhstepm, hstepm;      fflush(fichtm); 
   int k, cptcode;    } 
   double *xp;    return;
   double *gp, *gm;  }
   double **gradg, **trgradg;  
   double age,agelim;  
   int theta;  /*********** Maximum Likelihood Estimation ***************/
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   fprintf(ficresvpl,"# Age");  {
   for(i=1; i<=nlstate;i++)    int i,j, iter;
       fprintf(ficresvpl," %1d-%1d",i,i);    double **xi;
   fprintf(ficresvpl,"\n");    double fret;
     double fretone; /* Only one call to likelihood */
   xp=vector(1,npar);    /*  char filerespow[FILENAMELENGTH];*/
   dnewm=matrix(1,nlstate,1,npar);    xi=matrix(1,npar,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
   hstepm=1*YEARM; /* Every year of age */        xi[i][j]=(i==j ? 1.0 : 0.0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   agelim = AGESUP;    strcpy(filerespow,"pow"); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    strcat(filerespow,fileres);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     if (stepm >= YEARM) hstepm=1;      printf("Problem with resultfile: %s\n", filerespow);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     gradg=matrix(1,npar,1,nlstate);    }
     gp=vector(1,nlstate);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     gm=vector(1,nlstate);    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
     for(theta=1; theta <=npar; theta++){        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       for(i=1; i<=npar; i++){ /* Computes gradient */    fprintf(ficrespow,"\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    powell(p,xi,npar,ftol,&iter,&fret,func);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    free_matrix(xi,1,npar,1,npar);
         gp[i] = prlim[i][i];    fclose(ficrespow);
        printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       for(i=1; i<=npar; i++) /* Computes gradient */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  }
         gm[i] = prlim[i][i];  
   /**** Computes Hessian and covariance matrix ***/
       for(i=1;i<=nlstate;i++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  {
     } /* End theta */    double  **a,**y,*x,pd;
     double **hess;
     trgradg =matrix(1,nlstate,1,npar);    int i, j,jk;
     int *indx;
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         trgradg[j][theta]=gradg[theta][j];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
     for(i=1;i<=nlstate;i++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
       varpl[i][(int)age] =0.;    double gompertz(double p[]);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    hess=matrix(1,npar,1,npar);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)    printf("\nCalculation of the hessian matrix. Wait...\n");
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
     fprintf(ficresvpl,"%.0f ",age );      printf("%d",i);fflush(stdout);
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));     
     fprintf(ficresvpl,"\n");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     free_vector(gp,1,nlstate);      
     free_vector(gm,1,nlstate);      /*  printf(" %f ",p[i]);
     free_matrix(gradg,1,npar,1,nlstate);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     free_matrix(trgradg,1,nlstate,1,npar);    }
   } /* End age */    
     for (i=1;i<=npar;i++) {
   free_vector(xp,1,npar);      for (j=1;j<=npar;j++)  {
   free_matrix(doldm,1,nlstate,1,npar);        if (j>i) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 }          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
 /************ Variance of one-step probabilities  ******************/          hess[j][i]=hess[i][j];    
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          /*printf(" %lf ",hess[i][j]);*/
 {        }
   int i, j;      }
   int k=0, cptcode;    }
   double **dnewm,**doldm;    printf("\n");
   double *xp;    fprintf(ficlog,"\n");
   double *gp, *gm;  
   double **gradg, **trgradg;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double age,agelim, cov[NCOVMAX];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   int theta;    
   char fileresprob[FILENAMELENGTH];    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
   strcpy(fileresprob,"prob");    x=vector(1,npar);
   strcat(fileresprob,fileres);    indx=ivector(1,npar);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    for (i=1;i<=npar;i++)
     printf("Problem with resultfile: %s\n", fileresprob);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   }    ludcmp(a,npar,indx,&pd);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  
      for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   xp=vector(1,npar);      x[j]=1;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      lubksb(a,npar,indx,x);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1;i<=npar;i++){ 
          matcov[i][j]=x[i];
   cov[1]=1;      }
   for (age=bage; age<=fage; age ++){    }
     cov[2]=age;  
     gradg=matrix(1,npar,1,9);    printf("\n#Hessian matrix#\n");
     trgradg=matrix(1,9,1,npar);    fprintf(ficlog,"\n#Hessian matrix#\n");
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=1;i<=npar;i++) { 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=npar;j++) { 
            printf("%.3e ",hess[i][j]);
     for(theta=1; theta <=npar; theta++){        fprintf(ficlog,"%.3e ",hess[i][j]);
       for(i=1; i<=npar; i++)      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      printf("\n");
            fprintf(ficlog,"\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    }
      
       k=0;    /* Recompute Inverse */
       for(i=1; i<= (nlstate+ndeath); i++){    for (i=1;i<=npar;i++)
         for(j=1; j<=(nlstate+ndeath);j++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
            k=k+1;    ludcmp(a,npar,indx,&pd);
           gp[k]=pmmij[i][j];  
         }    /*  printf("\n#Hessian matrix recomputed#\n");
       }  
     for (j=1;j<=npar;j++) {
       for(i=1; i<=npar; i++)      for (i=1;i<=npar;i++) x[i]=0;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      x[j]=1;
          lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        y[i][j]=x[i];
       k=0;        printf("%.3e ",y[i][j]);
       for(i=1; i<=(nlstate+ndeath); i++){        fprintf(ficlog,"%.3e ",y[i][j]);
         for(j=1; j<=(nlstate+ndeath);j++){      }
           k=k+1;      printf("\n");
           gm[k]=pmmij[i][j];      fprintf(ficlog,"\n");
         }    }
       }    */
        
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    free_matrix(a,1,npar,1,npar);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      free_matrix(y,1,npar,1,npar);
     }    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    free_matrix(hess,1,npar,1,npar);
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];  
    }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);  
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
      pmij(pmmij,cov,ncovmodel,x,nlstate);  {
     int i;
      k=0;    int l=1, lmax=20;
      for(i=1; i<=(nlstate+ndeath); i++){    double k1,k2;
        for(j=1; j<=(nlstate+ndeath);j++){    double p2[NPARMAX+1];
          k=k+1;    double res;
          gm[k]=pmmij[i][j];    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         }    double fx;
      }    int k=0,kmax=10;
          double l1;
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    fx=func(x);
            for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      l1=pow(10,l);
      }*/      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
   fprintf(ficresprob,"\n%d ",(int)age);        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        k1=func(p2)-fx;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        p2[theta]=x[theta]-delt;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        k2=func(p2)-fx;
   }        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  #ifdef DEBUG
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        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);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 }  #endif
  free_vector(xp,1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 fclose(ficresprob);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
  exit(0);          k=kmax;
 }        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 /***********************************************/          k=kmax; l=lmax*10.;
 /**************** Main Program *****************/        }
 /***********************************************/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
 /*int main(int argc, char *argv[])*/        }
 int main()      }
 {    }
     delti[theta]=delts;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    return res; 
   double agedeb, agefin,hf;    
   double agemin=1.e20, agemax=-1.e20;  }
   
   double fret;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   double **xi,tmp,delta;  {
     int i;
   double dum; /* Dummy variable */    int l=1, l1, lmax=20;
   double ***p3mat;    double k1,k2,k3,k4,res,fx;
   int *indx;    double p2[NPARMAX+1];
   char line[MAXLINE], linepar[MAXLINE];    int k;
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    fx=func(x);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];    for (k=1; k<=2; k++) {
   char filerest[FILENAMELENGTH];      for (i=1;i<=npar;i++) p2[i]=x[i];
   char fileregp[FILENAMELENGTH];      p2[thetai]=x[thetai]+delti[thetai]/k;
   char popfile[FILENAMELENGTH];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      k1=func(p2)-fx;
   int firstobs=1, lastobs=10;    
   int sdeb, sfin; /* Status at beginning and end */      p2[thetai]=x[thetai]+delti[thetai]/k;
   int c,  h , cpt,l;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   int ju,jl, mi;      k2=func(p2)-fx;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      p2[thetai]=x[thetai]-delti[thetai]/k;
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int hstepm, nhstepm;      k3=func(p2)-fx;
   int *popage,boolprev=0;/*boolprev=0 if date and zero if wave*/    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   double bage, fage, age, agelim, agebase;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double ftolpl=FTOL;      k4=func(p2)-fx;
   double **prlim;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   double *severity;  #ifdef DEBUG
   double ***param; /* Matrix of parameters */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   double  *p;      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);
   double **matcov; /* Matrix of covariance */  #endif
   double ***delti3; /* Scale */    }
   double *delti; /* Scale */    return res;
   double ***eij, ***vareij;  }
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;  /************** Inverse of matrix **************/
   double kk1, kk2;  void ludcmp(double **a, int n, int *indx, double *d) 
   double *popeffectif,*popcount;  { 
   double dateprev1, dateprev2;    int i,imax,j,k; 
     double big,dum,sum,temp; 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    double *vv; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];   
     vv=vector(1,n); 
     *d=1.0; 
   char z[1]="c", occ;    for (i=1;i<=n;i++) { 
 #include <sys/time.h>      big=0.0; 
 #include <time.h>      for (j=1;j<=n;j++) 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        if ((temp=fabs(a[i][j])) > big) big=temp; 
   char strfprev[10], strlprev[10];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   char strfprevfore[10], strlprevfore[10];      vv[i]=1.0/big; 
   /* long total_usecs;    } 
   struct timeval start_time, end_time;    for (j=1;j<=n;j++) { 
        for (i=1;i<j;i++) { 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   printf("\nIMACH, Version 0.7");      } 
   printf("\nEnter the parameter file name: ");      big=0.0; 
       for (i=j;i<=n;i++) { 
 #ifdef windows        sum=a[i][j]; 
   scanf("%s",pathtot);        for (k=1;k<j;k++) 
   getcwd(pathcd, size);          sum -= a[i][k]*a[k][j]; 
   /*cygwin_split_path(pathtot,path,optionfile);        a[i][j]=sum; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   /* cutv(path,optionfile,pathtot,'\\');*/          big=dum; 
           imax=i; 
 split(pathtot, path,optionfile);        } 
   chdir(path);      } 
   replace(pathc,path);      if (j != imax) { 
 #endif        for (k=1;k<=n;k++) { 
 #ifdef unix          dum=a[imax][k]; 
   scanf("%s",optionfile);          a[imax][k]=a[j][k]; 
 #endif          a[j][k]=dum; 
         } 
 /*-------- arguments in the command line --------*/        *d = -(*d); 
         vv[imax]=vv[j]; 
   strcpy(fileres,"r");      } 
   strcat(fileres, optionfile);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
   /*---------arguments file --------*/      if (j != n) { 
         dum=1.0/(a[j][j]); 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     printf("Problem with optionfile %s\n",optionfile);      } 
     goto end;    } 
   }    free_vector(vv,1,n);  /* Doesn't work */
   ;
   strcpy(filereso,"o");  } 
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {  void lubksb(double **a, int n, int *indx, double b[]) 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  { 
   }    int i,ii=0,ip,j; 
     double sum; 
   /* Reads comments: lines beginning with '#' */   
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=n;i++) { 
     ungetc(c,ficpar);      ip=indx[i]; 
     fgets(line, MAXLINE, ficpar);      sum=b[ip]; 
     puts(line);      b[ip]=b[i]; 
     fputs(line,ficparo);      if (ii) 
   }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   ungetc(c,ficpar);      else if (sum) ii=i; 
       b[i]=sum; 
   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);    for (i=n;i>=1;i--) { 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);      sum=b[i]; 
 while((c=getc(ficpar))=='#' && c!= EOF){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     ungetc(c,ficpar);      b[i]=sum/a[i][i]; 
     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,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,&popbased);  }
   fprintf(ficparo,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);  
    /************ Frequencies ********************/
   /* printf("%s %s",strfprev,strlprev);  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[])
      exit(0);*/  {  /* Some frequencies */
  while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     fgets(line, MAXLINE, ficpar);    int first;
     puts(line);    double ***freq; /* Frequencies */
     fputs(line,ficparo);    double *pp, **prop;
   }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   ungetc(c,ficpar);    char fileresp[FILENAMELENGTH];
      
   fscanf(ficpar,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,&nforecast,&mobilav);    pp=vector(1,nlstate);
   fprintf(ficparo,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);    prop=matrix(1,nlstate,iagemin,iagemax+3);
          strcpy(fileresp,"p");
      strcat(fileresp,fileres);
 while((c=getc(ficpar))=='#' && c!= EOF){    if((ficresp=fopen(fileresp,"w"))==NULL) {
     ungetc(c,ficpar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fgets(line, MAXLINE, ficpar);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     puts(line);      exit(0);
     fputs(line,ficparo);    }
   }    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   ungetc(c,ficpar);    j1=0;
      
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);    j=cptcoveff;
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;    first=1;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
     for(k1=1; k1<=j;k1++){
   ncovmodel=2+cptcovn;      for(i1=1; i1<=ncodemax[k1];i1++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        j1++;
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   /* Read guess parameters */          scanf("%d", i);*/
   /* Reads comments: lines beginning with '#' */        for (i=-5; i<=nlstate+ndeath; i++)  
   while((c=getc(ficpar))=='#' && c!= EOF){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     ungetc(c,ficpar);            for(m=iagemin; m <= iagemax+3; m++)
     fgets(line, MAXLINE, ficpar);              freq[i][jk][m]=0;
     puts(line);  
     fputs(line,ficparo);      for (i=1; i<=nlstate; i++)  
   }        for(m=iagemin; m <= iagemax+3; m++)
   ungetc(c,ficpar);          prop[i][m]=0;
          
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        dateintsum=0;
     for(i=1; i <=nlstate; i++)        k2cpt=0;
     for(j=1; j <=nlstate+ndeath-1; j++){        for (i=1; i<=imx; i++) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);          bool=1;
       fprintf(ficparo,"%1d%1d",i1,j1);          if  (cptcovn>0) {
       printf("%1d%1d",i,j);            for (z1=1; z1<=cptcoveff; z1++) 
       for(k=1; k<=ncovmodel;k++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         fscanf(ficpar," %lf",&param[i][j][k]);                bool=0;
         printf(" %lf",param[i][j][k]);          }
         fprintf(ficparo," %lf",param[i][j][k]);          if (bool==1){
       }            for(m=firstpass; m<=lastpass; m++){
       fscanf(ficpar,"\n");              k2=anint[m][i]+(mint[m][i]/12.);
       printf("\n");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       fprintf(ficparo,"\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                  if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   p=param[1][1];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
   /* Reads comments: lines beginning with '#' */                
   while((c=getc(ficpar))=='#' && c!= EOF){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     ungetc(c,ficpar);                  dateintsum=dateintsum+k2;
     fgets(line, MAXLINE, ficpar);                  k2cpt++;
     puts(line);                }
     fputs(line,ficparo);                /*}*/
   }            }
   ungetc(c,ficpar);          }
         }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   for(i=1; i <=nlstate; i++){        pstamp(ficresp);
     for(j=1; j <=nlstate+ndeath-1; j++){        if  (cptcovn>0) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficresp, "\n#********** Variable "); 
       printf("%1d%1d",i,j);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficresp, "**********\n#");
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar,"%le",&delti3[i][j][k]);        for(i=1; i<=nlstate;i++) 
         printf(" %le",delti3[i][j][k]);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficparo," %le",delti3[i][j][k]);        fprintf(ficresp, "\n");
       }        
       fscanf(ficpar,"\n");        for(i=iagemin; i <= iagemax+3; i++){
       printf("\n");          if(i==iagemax+3){
       fprintf(ficparo,"\n");            fprintf(ficlog,"Total");
     }          }else{
   }            if(first==1){
   delti=delti3[1][1];              first=0;
                printf("See log file for details...\n");
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficlog,"Age %d", i);
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          for(jk=1; jk <=nlstate ; jk++){
     puts(line);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     fputs(line,ficparo);              pp[jk] += freq[jk][m][i]; 
   }          }
   ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pos=0; m <=0 ; m++)
   matcov=matrix(1,npar,1,npar);              pos += freq[jk][m][i];
   for(i=1; i <=npar; i++){            if(pp[jk]>=1.e-10){
     fscanf(ficpar,"%s",&str);              if(first==1){
     printf("%s",str);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fprintf(ficparo,"%s",str);              }
     for(j=1; j <=i; j++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fscanf(ficpar," %le",&matcov[i][j]);            }else{
       printf(" %.5le",matcov[i][j]);              if(first==1)
       fprintf(ficparo," %.5le",matcov[i][j]);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fscanf(ficpar,"\n");            }
     printf("\n");          }
     fprintf(ficparo,"\n");  
   }          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i <=npar; i++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     for(j=i+1;j<=npar;j++)              pp[jk] += freq[jk][m][i];
       matcov[i][j]=matcov[j][i];          }       
              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   printf("\n");            pos += pp[jk];
             posprop += prop[jk][i];
           }
     /*-------- data file ----------*/          for(jk=1; jk <=nlstate ; jk++){
     if((ficres =fopen(fileres,"w"))==NULL) {            if(pos>=1.e-5){
       printf("Problem with resultfile: %s\n", fileres);goto end;              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     fprintf(ficres,"#%s\n",version);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                }else{
     if((fic=fopen(datafile,"r"))==NULL)    {              if(first==1)
       printf("Problem with datafile: %s\n", datafile);goto end;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
     n= lastobs;            if( i <= iagemax){
     severity = vector(1,maxwav);              if(pos>=1.e-5){
     outcome=imatrix(1,maxwav+1,1,n);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     num=ivector(1,n);                /*probs[i][jk][j1]= pp[jk]/pos;*/
     moisnais=vector(1,n);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     annais=vector(1,n);              }
     moisdc=vector(1,n);              else
     andc=vector(1,n);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     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 */          for(jk=-1; jk <=nlstate+ndeath; jk++)
     mint=matrix(1,maxwav,1,n);            for(m=-1; m <=nlstate+ndeath; m++)
     anint=matrix(1,maxwav,1,n);              if(freq[jk][m][i] !=0 ) {
     s=imatrix(1,maxwav+1,1,n);              if(first==1)
     adl=imatrix(1,maxwav+1,1,n);                    printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     tab=ivector(1,NCOVMAX);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     ncodemax=ivector(1,8);              }
           if(i <= iagemax)
     i=1;            fprintf(ficresp,"\n");
     while (fgets(line, MAXLINE, fic) != NULL)    {          if(first==1)
       if ((i >= firstobs) && (i <=lastobs)) {            printf("Others in log...\n");
                  fprintf(ficlog,"\n");
         for (j=maxwav;j>=1;j--){        }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      }
           strcpy(line,stra);    }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    dateintmean=dateintsum/k2cpt; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);   
         }    fclose(ficresp);
            free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(pp,1,nlstate);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
   /************ Prevalence ********************/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  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 (j=ncov;j>=1;j--){  {  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         }       in each health status at the date of interview (if between dateprev1 and dateprev2).
         num[i]=atol(stra);       We still use firstpass and lastpass as another selection.
            */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){   
           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;}*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
         i=i+1;    double *pp, **prop;
       }    double pos,posprop; 
     }    double  y2; /* in fractional years */
     /* printf("ii=%d", ij);    int iagemin, iagemax;
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */    iagemin= (int) agemin;
     iagemax= (int) agemax;
   /* for (i=1; i<=imx; i++){    /*pp=vector(1,nlstate);*/
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    j1=0;
     }    
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   /* Calculation of the number of parameter from char model*/    
   Tvar=ivector(1,15);    for(k1=1; k1<=j;k1++){
   Tprod=ivector(1,15);      for(i1=1; i1<=ncodemax[k1];i1++){
   Tvaraff=ivector(1,15);        j1++;
   Tvard=imatrix(1,15,1,2);        
   Tage=ivector(1,15);              for (i=1; i<=nlstate; i++)  
              for(m=iagemin; m <= iagemax+3; m++)
   if (strlen(model) >1){            prop[i][m]=0.0;
     j=0, j1=0, k1=1, k2=1;       
     j=nbocc(model,'+');        for (i=1; i<=imx; i++) { /* Each individual */
     j1=nbocc(model,'*');          bool=1;
     cptcovn=j+1;          if  (cptcovn>0) {
     cptcovprod=j1;            for (z1=1; z1<=cptcoveff; z1++) 
                  if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
     strcpy(modelsav,model);          } 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          if (bool==1) { 
       printf("Error. Non available option model=%s ",model);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       goto end;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for(i=(j+1); i>=1;i--){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       cutv(stra,strb,modelsav,'+');                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 (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                  /*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]]);*/
       /*scanf("%d",i);*/                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       if (strchr(strb,'*')) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
         cutv(strd,strc,strb,'*');                } 
         if (strcmp(strc,"age")==0) {              }
           cptcovprod--;            } /* end selection of waves */
           cutv(strb,stre,strd,'V');          }
           Tvar[i]=atoi(stre);        }
           cptcovage++;        for(i=iagemin; i <= iagemax+3; i++){  
             Tage[cptcovage]=i;          
             /*printf("stre=%s ", stre);*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         }            posprop += prop[jk][i]; 
         else if (strcmp(strd,"age")==0) {          } 
           cptcovprod--;  
           cutv(strb,stre,strc,'V');          for(jk=1; jk <=nlstate ; jk++){     
           Tvar[i]=atoi(stre);            if( i <=  iagemax){ 
           cptcovage++;              if(posprop>=1.e-5){ 
           Tage[cptcovage]=i;                probs[i][jk][j1]= prop[jk][i]/posprop;
         }              } 
         else {            } 
           cutv(strb,stre,strc,'V');          }/* end jk */ 
           Tvar[i]=ncov+k1;        }/* end i */ 
           cutv(strb,strc,strd,'V');      } /* end i1 */
           Tprod[k1]=i;    } /* end k1 */
           Tvard[k1][1]=atoi(strc);    
           Tvard[k1][2]=atoi(stre);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           Tvar[cptcovn+k2]=Tvard[k1][1];    /*free_vector(pp,1,nlstate);*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           for (k=1; k<=lastobs;k++)  }  /* End of prevalence */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;  /************* Waves Concatenation ***************/
           k2=k2+2;  
         }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       }  {
       else {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       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
       cutv(strd,strc,strb,'V');       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       Tvar[i]=atoi(strc);       and mw[mi+1][i]. dh depends on stepm.
       }       */
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    int i, mi, m;
         scanf("%d",i);*/    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     }       double sum=0., jmean=0.;*/
 }    int first;
      int j, k=0,jk, ju, jl;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double sum=0.;
   printf("cptcovprod=%d ", cptcovprod);    first=0;
   scanf("%d ",i);*/    jmin=1e+5;
     fclose(fic);    jmax=-1;
     jmean=0.;
     /*  if(mle==1){*/    for(i=1; i<=imx; i++){
     if (weightopt != 1) { /* Maximisation without weights*/      mi=0;
       for(i=1;i<=n;i++) weight[i]=1.0;      m=firstpass;
     }      while(s[m][i] <= nlstate){
     /*-calculation of age at interview from date of interview and age at death -*/        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     agev=matrix(1,maxwav,1,imx);          mw[++mi][i]=m;
         if(m >=lastpass)
    for (i=1; i<=imx; i++)          break;
      for(m=2; (m<= maxwav); m++)        else
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          m++;
          anint[m][i]=9999;      }/* end while */
          s[m][i]=-1;      if (s[m][i] > nlstate){
        }        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
     for (i=1; i<=imx; i++)  {           /* Only death is a correct wave */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        mw[mi][i]=m;
       for(m=1; (m<= maxwav); m++){      }
         if(s[m][i] >0){  
           if (s[m][i] == nlstate+1) {      wav[i]=mi;
             if(agedc[i]>0)      if(mi==0){
               if(moisdc[i]!=99 && andc[i]!=9999)        nbwarn++;
               agev[m][i]=agedc[i];        if(first==0){
             else {          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
               if (andc[i]!=9999){          first=1;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        }
               agev[m][i]=-1;        if(first==1){
               }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
             }        }
           }      } /* end mi==0 */
           else if(s[m][i] !=9){ /* Should no more exist */    } /* End individuals */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    for(i=1; i<=imx; i++){
               agev[m][i]=1;      for(mi=1; mi<wav[i];mi++){
             else if(agev[m][i] <agemin){        if (stepm <=0)
               agemin=agev[m][i];          dh[mi][i]=1;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        else{
             }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             else if(agev[m][i] >agemax){            if (agedc[i] < 2*AGESUP) {
               agemax=agev[m][i];              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/              if(j==0) j=1;  /* Survives at least one month after exam */
             }              else if(j<0){
             /*agev[m][i]=anint[m][i]-annais[i];*/                nberr++;
             /*   agev[m][i] = age[i]+2*m;*/                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }                j=1; /* Temporary Dangerous patch */
           else { /* =9 */                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);
             agev[m][i]=1;                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]);
             s[m][i]=-1;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
           }              }
         }              k=k+1;
         else /*= 0 Unknown */              if (j >= jmax){
           agev[m][i]=1;                jmax=j;
       }                ijmax=i;
                  }
     }              if (j <= jmin){
     for (i=1; i<=imx; i++)  {                jmin=j;
       for(m=1; (m<= maxwav); m++){                ijmin=i;
         if (s[m][i] > (nlstate+ndeath)) {              }
           printf("Error: Wrong value in nlstate or ndeath\n");                sum=sum+j;
           goto end;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       }            }
     }          }
           else{
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);            k=k+1;
     free_vector(moisnais,1,n);            if (j >= jmax) {
     free_vector(annais,1,n);              jmax=j;
     /* free_matrix(mint,1,maxwav,1,n);              ijmax=i;
        free_matrix(anint,1,maxwav,1,n);*/            }
     free_vector(moisdc,1,n);            else if (j <= jmin){
     free_vector(andc,1,n);              jmin=j;
               ijmin=i;
                }
     wav=ivector(1,imx);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            /*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]);*/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            if(j<0){
                  nberr++;
     /* Concatenates waves */              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]);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
             sum=sum+j;
       Tcode=ivector(1,100);          }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          jk= j/stepm;
       ncodemax[1]=1;          jl= j -jk*stepm;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          ju= j -(jk+1)*stepm;
                if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    codtab=imatrix(1,100,1,10);            if(jl==0){
    h=0;              dh[mi][i]=jk;
    m=pow(2,cptcoveff);              bh[mi][i]=0;
              }else{ /* We want a negative bias in order to only have interpolation ie
    for(k=1;k<=cptcoveff; k++){                    * at the price of an extra matrix product in likelihood */
      for(i=1; i <=(m/pow(2,k));i++){              dh[mi][i]=jk+1;
        for(j=1; j <= ncodemax[k]; j++){              bh[mi][i]=ju;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            }
            h++;          }else{
            if (h>m) h=1;codtab[h][k]=j;            if(jl <= -ju){
          }              dh[mi][i]=jk;
        }              bh[mi][i]=jl;       /* bias is positive if real duration
      }                                   * is higher than the multiple of stepm and negative otherwise.
    }                                   */
                }
    /* Calculates basic frequencies. Computes observed prevalence at single age            else{
        and prints on file fileres'p'. */              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
     if ((nbocc(strfprev,'/')==1) && (nbocc(strlprev,'/')==1)){            }
      boolprev=0;            if(dh[mi][i]==0){
      cutv(stra,strb,strfprev,'/');              dh[mi][i]=1; /* At least one step */
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);              bh[mi][i]=ju; /* At least one step */
      cutv(stra,strb,strlprev,'/');              /*  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);*/
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);            }
    }          } /* end if mle */
            }
    else if ((nbocc(strfprev,'/')==0) &&(nbocc(strlprev,'/')==0)){      } /* end wave */
      boolprev=1;    }
      fprev=atoi(strfprev); lprev=atoi(strlprev);    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);
     else {    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);
       printf("Error in statement lprevalence or fprevalence\n");   }
       goto end;  
     }  /*********** Tricode ****************************/
      void tricode(int *Tvar, int **nbcode, int imx)
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint,boolprev,dateprev1,dateprev2);  {
      
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int Ndum[20],ij=1, k, j, i, maxncov=19;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int cptcode=0;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    cptcoveff=0; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    for (k=0; k<maxncov; k++) Ndum[k]=0;
          for (k=1; k<=7; k++) ncodemax[k]=0;
     /* 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] */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
     if(mle==1){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        Ndum[ij]++; /*store the modality */
     }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
            if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     /*--------- results files --------------*/                                         Tvar[j]. If V=sex and male is 0 and 
     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);                                         female is 1, then  cptcode=1.*/
    fprintf(ficres,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);      }
    fprintf(ficres,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);  
       for (i=0; i<=cptcode; i++) {
    jk=1;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
    fprintf(ficres,"# Parameters\n");      }
    printf("# Parameters\n");  
    for(i=1,jk=1; i <=nlstate; i++){      ij=1; 
      for(k=1; k <=(nlstate+ndeath); k++){      for (i=1; i<=ncodemax[j]; i++) {
        if (k != i)        for (k=0; k<= maxncov; k++) {
          {          if (Ndum[k] != 0) {
            printf("%d%d ",i,k);            nbcode[Tvar[j]][ij]=k; 
            fprintf(ficres,"%1d%1d ",i,k);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
            for(j=1; j <=ncovmodel; j++){            
              printf("%f ",p[jk]);            ij++;
              fprintf(ficres,"%f ",p[jk]);          }
              jk++;          if (ij > ncodemax[j]) break; 
            }        }  
            printf("\n");      } 
            fprintf(ficres,"\n");    }  
          }  
      }   for (k=0; k< maxncov; k++) Ndum[k]=0;
    }  
  if(mle==1){   for (i=1; i<=ncovmodel-2; i++) { 
     /* Computing hessian and covariance matrix */     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     ftolhess=ftol; /* Usually correct */     ij=Tvar[i];
     hesscov(matcov, p, npar, delti, ftolhess, func);     Ndum[ij]++;
  }   }
     fprintf(ficres,"# Scales\n");  
     printf("# Scales\n");   ij=1;
      for(i=1,jk=1; i <=nlstate; i++){   for (i=1; i<= maxncov; i++) {
       for(j=1; j <=nlstate+ndeath; j++){     if((Ndum[i]!=0) && (i<=ncovcol)){
         if (j!=i) {       Tvaraff[ij]=i; /*For printing */
           fprintf(ficres,"%1d%1d",i,j);       ij++;
           printf("%1d%1d",i,j);     }
           for(k=1; k<=ncovmodel;k++){   }
             printf(" %.5e",delti[jk]);   
             fprintf(ficres," %.5e",delti[jk]);   cptcoveff=ij-1; /*Number of simple covariates*/
             jk++;  }
           }  
           printf("\n");  /*********** Health Expectancies ****************/
           fprintf(ficres,"\n");  
         }  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       }  
      }  {
        /* Health expectancies, no variances */
     k=1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     fprintf(ficres,"# Covariance\n");    double age, agelim, hf;
     printf("# Covariance\n");    double ***p3mat;
     for(i=1;i<=npar;i++){    double eip;
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;    pstamp(ficreseij);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficreseij,"# Age");
       fprintf(ficres,"%3d",i);    for(i=1; i<=nlstate;i++){
       printf("%3d",i);      for(j=1; j<=nlstate;j++){
       for(j=1; j<=i;j++){        fprintf(ficreseij," e%1d%1d ",i,j);
         fprintf(ficres," %.5e",matcov[i][j]);      }
         printf(" %.5e",matcov[i][j]);      fprintf(ficreseij," e%1d. ",i);
       }    }
       fprintf(ficres,"\n");    fprintf(ficreseij,"\n");
       printf("\n");  
       k++;    
     }    if(estepm < stepm){
          printf ("Problem %d lower than %d\n",estepm, stepm);
     while((c=getc(ficpar))=='#' && c!= EOF){    }
       ungetc(c,ficpar);    else  hstepm=estepm;   
       fgets(line, MAXLINE, ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
       puts(line);     * This is mainly to measure the difference between two models: for example
       fputs(line,ficparo);     * 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 
     ungetc(c,ficpar);     * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);     * 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 
     if (fage <= 2) {     * hypothesis. A more precise result, taking into account a more precise
       bage = agemin;     * curvature will be obtained if estepm is as small as stepm. */
       fage = agemax;  
     }    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       nhstepm is the number of hstepm from age to agelim 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
           and note for a fixed period like estepm months */
 /*------------ gnuplot -------------*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 chdir(pathcd);       survival function given by stepm (the optimization length). Unfortunately it
   if((ficgp=fopen("graph.plt","w"))==NULL) {       means that if the survival funtion is printed only each two years of age and if
     printf("Problem with file graph.gp");goto end;       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.
 #ifdef windows    */
   fprintf(ficgp,"cd \"%s\" \n",pathc);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #endif  
 m=pow(2,cptcoveff);    agelim=AGESUP;
      /* nhstepm age range expressed in number of stepm */
  /* 1eme*/    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   for (cpt=1; cpt<= nlstate ; cpt ++) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    for (k1=1; k1<= m ; k1 ++) {    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 #ifdef windows    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);  
 #endif    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #ifdef unix      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 #endif      
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 for (i=1; i<= nlstate ; i ++) {      
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      
 }      printf("%d|",(int)age);fflush(stdout);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for (i=1; i<= nlstate ; i ++) {      
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /* Computing expectancies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<=nlstate;i++)
 }        for(j=1; j<=nlstate;j++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
      for (i=1; i<= nlstate ; i ++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            
   else fprintf(ficgp," \%%*lf (\%%*lf)");            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          }
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");      fprintf(ficreseij,"%3.0f",age );
 #endif      for(i=1; i<=nlstate;i++){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        eip=0;
    }        for(j=1; j<=nlstate;j++){
   }          eip +=eij[i][j][(int)age];
   /*2 eme*/          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
   for (k1=1; k1<= m ; k1 ++) {        fprintf(ficreseij,"%9.4f", eip );
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      }
          fprintf(ficreseij,"\n");
     for (i=1; i<= nlstate+1 ; i ++) {      
       k=2*i;    }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (j=1; j<= nlstate+1 ; j ++) {    printf("\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficlog,"\n");
   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);  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[] )
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* Covariances of health expectancies eij and of total life expectancies according
         else fprintf(ficgp," \%%*lf (\%%*lf)");     to initial status i, ei. .
 }      */
       fprintf(ficgp,"\" t\"\" w l 0,");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double age, agelim, hf;
       for (j=1; j<= nlstate+1 ; j ++) {    double ***p3matp, ***p3matm, ***varhe;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double **dnewm,**doldm;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *xp, *xm;
 }      double **gp, **gm;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    double ***gradg, ***trgradg;
       else fprintf(ficgp,"\" t\"\" w l 0,");    int theta;
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double eip, vip;
   }  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   /*3eme*/    xp=vector(1,npar);
     xm=vector(1,npar);
   for (k1=1; k1<= m ; k1 ++) {    dnewm=matrix(1,nlstate*nlstate,1,npar);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       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);    pstamp(ficresstdeij);
       for (i=1; i< nlstate ; i ++) {    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         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);    fprintf(ficresstdeij,"# Age");
       }    for(i=1; i<=nlstate;i++){
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   }      fprintf(ficresstdeij," e%1d. ",i);
      }
   /* CV preval stat */    fprintf(ficresstdeij,"\n");
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {    pstamp(ficrescveij);
       k=3;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    fprintf(ficrescveij,"# Age");
       for (i=1; i< nlstate ; i ++)    for(i=1; i<=nlstate;i++)
         fprintf(ficgp,"+$%d",k+i+1);      for(j=1; j<=nlstate;j++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        cptj= (j-1)*nlstate+i;
              for(i2=1; i2<=nlstate;i2++)
       l=3+(nlstate+ndeath)*cpt;          for(j2=1; j2<=nlstate;j2++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            cptj2= (j2-1)*nlstate+i2;
       for (i=1; i< nlstate ; i ++) {            if(cptj2 <= cptj)
         l=3+(nlstate+ndeath)*cpt;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         fprintf(ficgp,"+$%d",l+i+1);          }
       }      }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      fprintf(ficrescveij,"\n");
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
     }    if(estepm < stepm){
   }        printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   /* proba elementaires */    else  hstepm=estepm;   
    for(i=1,jk=1; i <=nlstate; i++){    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(k=1; k <=(nlstate+ndeath); k++){     * This is mainly to measure the difference between two models: for example
       if (k != i) {     * if stepm=24 months pijx are given only every 2 years and by summing them
         for(j=1; j <=ncovmodel; j++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/     * progression in between and thus overestimating or underestimating according
           /*fprintf(ficgp,"%s",alph[1]);*/     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           jk++;     * to compare the new estimate of Life expectancy with the same linear 
           fprintf(ficgp,"\n");     * hypothesis. A more precise result, taking into account a more precise
         }     * curvature will be obtained if estepm is as small as stepm. */
       }  
     }    /* For example we decided to compute the life expectancy with the smallest unit */
     }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   for(jk=1; jk <=m; jk++) {       nstepm is the number of stepm from age to agelin. 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);       Look at hpijx to understand the reason of that which relies in memory size
    i=1;       and note for a fixed period like estepm months */
    for(k2=1; k2<=nlstate; k2++) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      k3=i;       survival function given by stepm (the optimization length). Unfortunately it
      for(k=1; k<=(nlstate+ndeath); k++) {       means that if the survival funtion is printed only each two years of age and if
        if (k != k2){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       results. So we changed our mind and took the option of the best precision.
 ij=1;    */
         for(j=3; j <=ncovmodel; j++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           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]]]);    /* If stepm=6 months */
             ij++;    /* nhstepm age range expressed in number of stepm */
           }    agelim=AGESUP;
           else    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         }    /* if (stepm >= YEARM) hstepm=1;*/
           fprintf(ficgp,")/(1");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
            
         for(k1=1; k1 <=nlstate; k1++){      p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 ij=1;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           for(j=3; j <=ncovmodel; j++){    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    gp=matrix(0,nhstepm,1,nlstate*nlstate);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
             ij++;  
           }    for (age=bage; age<=fage; age ++){ 
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           fprintf(ficgp,")");   
         }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      /* Computing  Variances of health expectancies */
         i=i+ncovmodel;      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        }         decrease memory allocation */
      }      for(theta=1; theta <=npar; theta++){
    }        for(i=1; i<=npar; i++){ 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
            }
   fclose(ficgp);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
            hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
 chdir(path);    
            for(j=1; j<= nlstate; j++){
     free_ivector(wav,1,imx);          for(i=1; i<=nlstate; i++){
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            for(h=0; h<=nhstepm-1; h++){
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     free_ivector(num,1,n);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     free_vector(agedc,1,n);            }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          }
     fclose(ficparo);        }
     fclose(ficres);       
     /*  }*/        for(ij=1; ij<= nlstate*nlstate; ij++)
              for(h=0; h<=nhstepm-1; h++){
    /*________fin mle=1_________*/            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
              }
       }/* End theta */
        
     /* No more information from the sample is required now */      
   /* Reads comments: lines beginning with '#' */      for(h=0; h<=nhstepm-1; h++)
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<=nlstate*nlstate;j++)
     ungetc(c,ficpar);          for(theta=1; theta <=npar; theta++)
     fgets(line, MAXLINE, ficpar);            trgradg[h][j][theta]=gradg[h][theta][j];
     puts(line);      
     fputs(line,ficparo);  
   }       for(ij=1;ij<=nlstate*nlstate;ij++)
   ungetc(c,ficpar);        for(ji=1;ji<=nlstate*nlstate;ji++)
            varhe[ij][ji][(int)age] =0.;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);       printf("%d|",(int)age);fflush(stdout);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 /*--------- index.htm --------*/       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
   strcpy(optionfilehtm,optionfile);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   strcat(optionfilehtm,".htm");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for(ij=1;ij<=nlstate*nlstate;ij++)
     printf("Problem with %s \n",optionfilehtm);goto end;            for(ji=1;ji<=nlstate*nlstate;ji++)
   }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">      }
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      /* Computing expectancies */
 Total number of observations=%d <br>      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 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          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>            
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            /* 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]);*/
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>          }
         - 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>      fprintf(ficresstdeij,"%3.0f",age );
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      for(i=1; i<=nlstate;i++){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>        eip=0.;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>        vip=0.;
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
  fprintf(fichtm," <li>Graphs</li><p>");          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
  m=cptcoveff;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
  j1=0;      }
  for(k1=1; k1<=m;k1++){      fprintf(ficresstdeij,"\n");
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;      fprintf(ficrescveij,"%3.0f",age );
        if (cptcovn > 0) {      for(i=1; i<=nlstate;i++)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(j=1; j<=nlstate;j++){
          for (cpt=1; cpt<=cptcoveff;cpt++)          cptj= (j-1)*nlstate+i;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          for(i2=1; i2<=nlstate;i2++)
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            for(j2=1; j2<=nlstate;j2++){
        }              cptj2= (j2-1)*nlstate+i2;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              if(cptj2 <= cptj)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                    fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
        for(cpt=1; cpt<nlstate;cpt++){            }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      fprintf(ficrescveij,"\n");
        }     
     for(cpt=1; cpt<=nlstate;cpt++) {    }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 interval) in state (%d): v%s%d%d.gif <br>    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
      }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      for(cpt=1; cpt<=nlstate;cpt++) {    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    printf("\n");
      }    fprintf(ficlog,"\n");
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.gif<br>    free_vector(xm,1,npar);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    free_vector(xp,1,npar);
 fprintf(fichtm,"\n</body>");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
  }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 fclose(fichtm);  }
   
   /*--------------- Prevalence limit --------------*/  /************ Variance ******************/
    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   strcpy(filerespl,"pl");  {
   strcat(filerespl,fileres);    /* Variance of health expectancies */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    /* double **newm;*/
   }    double **dnewm,**doldm;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double **dnewmp,**doldmp;
   fprintf(ficrespl,"#Prevalence limit\n");    int i, j, nhstepm, hstepm, h, nstepm ;
   fprintf(ficrespl,"#Age ");    int k, cptcode;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    double *xp;
   fprintf(ficrespl,"\n");    double **gp, **gm;  /* for var eij */
      double ***gradg, ***trgradg; /*for var eij */
   prlim=matrix(1,nlstate,1,nlstate);    double **gradgp, **trgradgp; /* for var p point j */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *gpp, *gmp; /* for var p point j */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***p3mat;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double age,agelim, hf;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double ***mobaverage;
   k=0;    int theta;
   agebase=agemin;    char digit[4];
   agelim=agemax;    char digitp[25];
   ftolpl=1.e-10;  
   i1=cptcoveff;    char fileresprobmorprev[FILENAMELENGTH];
   if (cptcovn < 1){i1=1;}  
     if(popbased==1){
   for(cptcov=1;cptcov<=i1;cptcov++){      if(mobilav!=0)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        strcpy(digitp,"-populbased-mobilav-");
         k=k+1;      else strcpy(digitp,"-populbased-nomobil-");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    else 
         for(j=1;j<=cptcoveff;j++)      strcpy(digitp,"-stablbased-");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");    if (mobilav!=0) {
              mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for (age=agebase; age<=agelim; age++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficrespl,"%.0f",age );        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           for(i=1; i<=nlstate;i++)      }
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");  
         }    strcpy(fileresprobmorprev,"prmorprev"); 
       }    sprintf(digit,"%-d",ij);
     }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   fclose(ficrespl);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   /*------------- h Pij x at various ages ------------*/    strcat(fileresprobmorprev,fileres);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    }
   }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   printf("Computing pij: result on file '%s' \n", filerespij);   
      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    pstamp(ficresprobmorprev);
   /*if (stepm<=24) stepsize=2;*/    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   agelim=AGESUP;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   hstepm=stepsize*YEARM; /* Every year of age */      fprintf(ficresprobmorprev," p.%-d SE",j);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      for(i=1; i<=nlstate;i++)
          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   k=0;    }  
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresprobmorprev,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\n# Routine varevsij");
       k=k+1;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
         fprintf(ficrespij,"\n#****** ");    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");
         for(j=1;j<=cptcoveff;j++)    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   } */
         fprintf(ficrespij,"******\n");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            pstamp(ficresvij);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    if(popbased==1)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    else
           oldm=oldms;savm=savms;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresvij,"# Age");
           fprintf(ficrespij,"# Age");    for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)      for(j=1; j<=nlstate;j++)
             for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficresvij,"\n");
           fprintf(ficrespij,"\n");  
           for (h=0; h<=nhstepm; h++){    xp=vector(1,npar);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    dnewm=matrix(1,nlstate,1,npar);
             for(i=1; i<=nlstate;i++)    doldm=matrix(1,nlstate,1,nlstate);
               for(j=1; j<=nlstate+ndeath;j++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             fprintf(ficrespij,"\n");  
           }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    gpp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficrespij,"\n");    gmp=vector(nlstate+1,nlstate+ndeath);
         }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     }    
   }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    }
     else  hstepm=estepm;   
   fclose(ficrespij);    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /*---------- Forecasting ------------------*/       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   strcpy(fileresf,"f");       Look at hpijx to understand the reason of that which relies in memory size
   strcat(fileresf,fileres);       and note for a fixed period like k years */
   if((ficresf=fopen(fileresf,"w"))==NULL) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;       survival function given by stepm (the optimization length). Unfortunately it
   }       means that if the survival funtion is printed every two years of age and if
   printf("Computing forecasting: result on file '%s' \n", fileresf);       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.
  if ((nbocc(strfprevfore,'/')==1) && (nbocc(strlprevfore,'/')==1)){    */
      boolprev=0;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      cutv(stra,strb,strfprevfore,'/');    agelim = AGESUP;
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      cutv(stra,strb,strlprevfore,'/');      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
    else if ((nbocc(strfprevfore,'/')==0) &&(nbocc(strlprevfore,'/')==0)){      gp=matrix(0,nhstepm,1,nlstate);
      boolprev=1;      gm=matrix(0,nhstepm,1,nlstate);
      fprev=atoi(strfprevfore); lprev=atoi(strlprevfore);  
    }  
     else {      for(theta=1; theta <=npar; theta++){
       printf("Error in statement lprevalence or fprevalence\n");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       goto end;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     }        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore,mint,anint,boolprev,dateprev1,dateprev2);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   free_matrix(mint,1,maxwav,1,n);        if (popbased==1) {
   free_matrix(anint,1,maxwav,1,n);          if(mobilav ==0){
   free_matrix(agev,1,maxwav,1,imx);            for(i=1; i<=nlstate;i++)
   /* Mobile average */              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
   if (mobilav==1) {          }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    
       for (i=1; i<=nlstate;i++)        for(j=1; j<= nlstate; j++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for(h=0; h<=nhstepm; h++){
           mobaverage[(int)agedeb][i][cptcod]=0.;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                  gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     for (agedeb=bage+4; agedeb<=fage; agedeb++){          }
       for (i=1; i<=nlstate;i++){        }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        /* This for computing probability of death (h=1 means
           for (cpt=0;cpt<=4;cpt++){           computed over hstepm matrices product = hstepm*stepm months) 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];           as a weighted average of prlim.
           }        */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }          }    
   }        /* end probability of death */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   if (stepm<=12) stepsize=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   agelim=AGESUP;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   hstepm=stepsize*YEARM; /* Every year of age */   
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        if (popbased==1) {
            if(mobilav ==0){
   if (popforecast==1) {            for(i=1; i<=nlstate;i++)
     if((ficpop=fopen(popfile,"r"))==NULL)    {              prlim[i][i]=probs[(int)age][i][ij];
       printf("Problem with population file : %s\n",popfile);goto end;          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     popage=ivector(0,AGESUP);              prlim[i][i]=mobaverage[(int)age][i][ij];
     popeffectif=vector(0,AGESUP);          }
     popcount=vector(0,AGESUP);        }
   
     i=1;          for(j=1; j<= nlstate; j++){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)          for(h=0; h<=nhstepm; h++){
       {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         i=i+1;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       }          }
     imx=i;        }
          /* This for computing probability of death (h=1 means
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
         */
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       k=k+1;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       fprintf(ficresf,"\n#****** ");        }    
       for(j=1;j<=cptcoveff;j++) {        /* end probability of death */
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }        for(j=1; j<= nlstate; j++) /* vareij */
       fprintf(ficresf,"******\n");          for(h=0; h<=nhstepm; h++){
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          }
       if (popforecast==1)  fprintf(ficresf," [Population]");  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       for (agedeb=fage; agedeb>=bage; agedeb--){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);        }
        if (mobilav==1) {  
         for(j=1; j<=nlstate;j++)      } /* End theta */
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);  
         }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         else {  
           for(j=1; j<=nlstate;j++)      for(h=0; h<=nhstepm; h++) /* veij */
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);        for(j=1; j<=nlstate;j++)
         }            for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");  
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       }        for(theta=1; theta <=npar; theta++)
                trgradgp[j][theta]=gradgp[theta][j];
       for (cpt=1; cpt<=nforecast;cpt++) {    
         fprintf(ficresf,"\n");  
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(i=1;i<=nlstate;i++)
         nhstepm = nhstepm/hstepm;        for(j=1;j<=nlstate;j++)
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/          vareij[i][j][(int)age] =0.;
   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(h=0;h<=nhstepm;h++){
         oldm=oldms;savm=savms;        for(k=0;k<=nhstepm;k++){
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
                          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         for (h=0; h<=nhstepm; h++){          for(i=1;i<=nlstate;i++)
                    for(j=1;j<=nlstate;j++)
          if (h*hstepm/YEARM*stepm==cpt)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);        }
                }
              
          for(j=1; j<=nlstate+ndeath;j++) {      /* pptj */
            kk1=0.;kk2=0;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            for(i=1; i<=nlstate;i++) {              matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
              if (mobilav==1)      for(j=nlstate+1;j<=nlstate+ndeath;j++)
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];        for(i=nlstate+1;i<=nlstate+ndeath;i++)
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];          varppt[j][i]=doldmp[j][i];
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];      /* end ppptj */
             }      /*  x centered again */
            if (h*hstepm/YEARM*stepm==cpt) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
              fprintf(ficresf," %.3f", kk1);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);   
            }      if (popbased==1) {
           }        if(mobilav ==0){
         }          for(i=1; i<=nlstate;i++)
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            prlim[i][i]=probs[(int)age][i][ij];
                }else{ /* mobilav */ 
       }          for(i=1; i<=nlstate;i++)
       }            prlim[i][i]=mobaverage[(int)age][i][ij];
     }        }
   }      }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);               
   if (popforecast==1) {      /* This for computing probability of death (h=1 means
     free_ivector(popage,0,AGESUP);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     free_vector(popeffectif,0,AGESUP);         as a weighted average of prlim.
     free_vector(popcount,0,AGESUP);      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_imatrix(s,1,maxwav+1,1,n);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   free_vector(weight,1,n);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   fclose(ficresf);      }    
   /*---------- Health expectancies and variances ------------*/      /* end probability of death */
   
   strcpy(filerest,"t");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   strcat(filerest,fileres);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if((ficrest=fopen(filerest,"w"))==NULL) {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        }
       } 
       fprintf(ficresprobmorprev,"\n");
   strcpy(filerese,"e");  
   strcat(filerese,fileres);      fprintf(ficresvij,"%.0f ",age );
   if((ficreseij=fopen(filerese,"w"))==NULL) {      for(i=1; i<=nlstate;i++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        for(j=1; j<=nlstate;j++){
   }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        }
       fprintf(ficresvij,"\n");
  strcpy(fileresv,"v");      free_matrix(gp,0,nhstepm,1,nlstate);
   strcat(fileresv,fileres);      free_matrix(gm,0,nhstepm,1,nlstate);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
   k=0;    free_vector(gmp,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       k=k+1;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       fprintf(ficrest,"\n#****** ");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficrest,"******\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficreseij,"\n#****** ");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       fprintf(ficreseij,"******\n");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       fprintf(ficresvij,"\n#****** ");    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       for(j=1;j<=cptcoveff;j++)  */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       fprintf(ficresvij,"******\n");    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_vector(xp,1,npar);
       oldm=oldms;savm=savms;    free_matrix(doldm,1,nlstate,1,nlstate);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      free_matrix(dnewm,1,nlstate,1,npar);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       oldm=oldms;savm=savms;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fclose(ficresprobmorprev);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fflush(ficgp);
       fprintf(ficrest,"\n");    fflush(fichtm); 
          }  /* end varevsij */
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;  /************ Variance of prevlim ******************/
       epj=vector(1,nlstate+1);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
       for(age=bage; age <=fage ;age++){  {
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* Variance of prevalence limit */
         if (popbased==1) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           for(i=1; i<=nlstate;i++)    double **newm;
             prlim[i][i]=probs[(int)age][i][k];    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
            int k, cptcode;
         fprintf(ficrest," %.0f",age);    double *xp;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double *gp, *gm;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    double **gradg, **trgradg;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    double age,agelim;
           }    int theta;
           epj[nlstate+1] +=epj[j];    
         }    pstamp(ficresvpl);
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
           for(j=1;j <=nlstate;j++)    fprintf(ficresvpl,"# Age");
             vepp += vareij[i][j][(int)age];    for(i=1; i<=nlstate;i++)
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        fprintf(ficresvpl," %1d-%1d",i,i);
         for(j=1;j <=nlstate;j++){    fprintf(ficresvpl,"\n");
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }    xp=vector(1,npar);
         fprintf(ficrest,"\n");    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
     }    
   }    hstepm=1*YEARM; /* Every year of age */
            hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
            agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  fclose(ficreseij);      if (stepm >= YEARM) hstepm=1;
  fclose(ficresvij);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   fclose(ficrest);      gradg=matrix(1,npar,1,nlstate);
   fclose(ficpar);      gp=vector(1,nlstate);
   free_vector(epj,1,nlstate+1);      gm=vector(1,nlstate);
   /*  scanf("%d ",i); */  
       for(theta=1; theta <=npar; theta++){
   /*------- Variance limit prevalence------*/          for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
 strcpy(fileresvpl,"vpl");        }
   strcat(fileresvpl,fileres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        for(i=1;i<=nlstate;i++)
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          gp[i] = prlim[i][i];
     exit(0);      
   }        for(i=1; i<=npar; i++) /* Computes gradient */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  k=0;        for(i=1;i<=nlstate;i++)
  for(cptcov=1;cptcov<=i1;cptcov++){          gm[i] = prlim[i][i];
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;        for(i=1;i<=nlstate;i++)
      fprintf(ficresvpl,"\n#****** ");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
      for(j=1;j<=cptcoveff;j++)      } /* End theta */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\n");      trgradg =matrix(1,nlstate,1,npar);
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      for(j=1; j<=nlstate;j++)
      oldm=oldms;savm=savms;        for(theta=1; theta <=npar; theta++)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          trgradg[j][theta]=gradg[theta][j];
    }  
  }      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
   fclose(ficresvpl);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   /*---------- End : free ----------------*/      for(i=1;i<=nlstate;i++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fprintf(ficresvpl,"%.0f ",age );
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        fprintf(ficresvpl,"\n");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_vector(gp,1,nlstate);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_vector(gm,1,nlstate);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(gradg,1,npar,1,nlstate);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(trgradg,1,nlstate,1,npar);
      } /* End age */
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,npar);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   printf("End of Imach\n");  }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
    /************ Variance of one-step probabilities  ******************/
   /* 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);*/  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   /*printf("Total time was %d uSec.\n", total_usecs);*/  {
   /*------ End -----------*/    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
  end:    int first=1, first1;
 #ifdef windows    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
  chdir(pathcd);    double **dnewm,**doldm;
 #endif    double *xp;
      double *gp, *gm;
  system("..\\gp37mgw\\wgnuplot graph.plt");    double **gradg, **trgradg;
     double **mu;
 #ifdef windows    double age,agelim, cov[NCOVMAX];
   while (z[0] != 'q') {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     chdir(pathcd);    int theta;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    char fileresprob[FILENAMELENGTH];
     scanf("%s",z);    char fileresprobcov[FILENAMELENGTH];
     if (z[0] == 'c') system("./imach");    char fileresprobcor[FILENAMELENGTH];
     else if (z[0] == 'e') {  
       chdir(path);    double ***varpij;
       system(optionfilehtm);  
     }    strcpy(fileresprob,"prob"); 
     else if (z[0] == 'q') exit(0);    strcat(fileresprob,fileres);
   }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 #endif      printf("Problem with resultfile: %s\n", fileresprob);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
           cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.18  
changed lines
  Added in v.1.121

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