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version 1.11, 2001/05/17 16:07:14 version 1.111, 2006/01/25 20:38:18
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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 1.111  2006/01/25 20:38:18  brouard
   individuals from different ages are interviewed on their health status    (Module): Lots of cleaning and bugs added (Gompertz)
   or degree of  disability. At least a second wave of interviews    (Module): Comments can be added in data file. Missing date values
   ("longitudinal") should  measure each new individual health status.    can be a simple dot '.'.
   Health expectancies are computed from the transistions observed between  
   waves and are computed for each degree of severity of disability (number    Revision 1.110  2006/01/25 00:51:50  brouard
   of life states). More degrees you consider, more time is necessary to    (Module): Lots of cleaning and bugs added (Gompertz)
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.109  2006/01/24 19:37:15  brouard
   the probabibility to be observed in state j at the second wave conditional    (Module): Comments (lines starting with a #) are allowed in data.
   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'    Revision 1.108  2006/01/19 18:05:42  lievre
   is a covariate. If you want to have a more complex model than "constant and    Gnuplot problem appeared...
   age", you should modify the program where the markup    To be fixed
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.106  2006/01/19 13:24:36  brouard
   individual missed an interview, the information is not rounded or lost, but    Some cleaning and links added in html output
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.105  2006/01/05 20:23:19  lievre
   observed in state i at age x+h conditional to the observed state i at age    *** empty log message ***
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.104  2005/09/30 16:11:43  lievre
   quarter trimester, semester or year) is model as a multinomial logistic.    (Module): sump fixed, loop imx fixed, and simplifications.
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    (Module): If the status is missing at the last wave but we know
   and the contribution of each individual to the likelihood is simply hPijx.    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
   Also this programme outputs the covariance matrix of the parameters but also    contributions to the likelihood is 1 - Prob of dying from last
   of the life expectancies. It also computes the prevalence limits.    health status (= 1-p13= p11+p12 in the easiest case of somebody in
      the healthy state at last known wave). Version is 0.98
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.103  2005/09/30 15:54:49  lievre
   This software have been partly granted by Euro-REVES, a concerted action    (Module): sump fixed, loop imx fixed, and simplifications.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.102  2004/09/15 17:31:30  brouard
   software can be distributed freely for non commercial use. Latest version    Add the possibility to read data file including tab characters.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
 #include <math.h>  
 #include <stdio.h>    Revision 1.100  2004/07/12 18:29:06  brouard
 #include <stdlib.h>    Add version for Mac OS X. Just define UNIX in Makefile
 #include <unistd.h>  
     Revision 1.99  2004/06/05 08:57:40  brouard
 #define MAXLINE 256    *** empty log message ***
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.98  2004/05/16 15:05:56  brouard
 #define windows    New version 0.97 . First attempt to estimate force of mortality
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    directly from the data i.e. without the need of knowing the health
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    other analysis, in order to test if the mortality estimated from the
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    The same imach parameter file can be used but the option for mle should be -3.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Agnès, who wrote this part of the code, tried to keep most of the
 #define MAXN 20000    former routines in order to include the new code within the former code.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    The output is very simple: only an estimate of the intercept and of
 #define AGEBASE 40    the slope with 95% confident intervals.
   
     Current limitations:
 int nvar;    A) Even if you enter covariates, i.e. with the
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 int npar=NPARMAX;    B) There is no computation of Life Expectancy nor Life Table.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.97  2004/02/20 13:25:42  lievre
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.96  2003/07/15 15:38:55  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 int mle, weightopt;    rewritten within the same printf. Workaround: many printfs.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.95  2003/07/08 07:54:34  brouard
 double jmean; /* Mean space between 2 waves */    * imach.c (Repository):
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Repository): Using imachwizard code to output a more meaningful covariance
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    matrix (cov(a12,c31) instead of numbers.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Revision 1.94  2003/06/27 13:00:02  brouard
 FILE *ficreseij;    Just cleaning
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.93  2003/06/25 16:33:55  brouard
   char fileresv[FILENAMELENGTH];    (Module): On windows (cygwin) function asctime_r doesn't
  FILE  *ficresvpl;    exist so I changed back to asctime which exists.
   char fileresvpl[FILENAMELENGTH];    (Module): Version 0.96b
   
 #define NR_END 1    Revision 1.92  2003/06/25 16:30:45  brouard
 #define FREE_ARG char*    (Module): On windows (cygwin) function asctime_r doesn't
 #define FTOL 1.0e-10    exist so I changed back to asctime which exists.
   
 #define NRANSI    Revision 1.91  2003/06/25 15:30:29  brouard
 #define ITMAX 200    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 #define TOL 2.0e-4    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 #define CGOLD 0.3819660    concerning matrix of covariance. It has extension -cov.htm.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 #define GOLD 1.618034    mle=-1 a template is output in file "or"mypar.txt with the design
 #define GLIMIT 100.0    of the covariance matrix to be input.
 #define TINY 1.0e-20  
     Revision 1.89  2003/06/24 12:30:52  brouard
 static double maxarg1,maxarg2;    (Module): Some bugs corrected for windows. Also, when
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    mle=-1 a template is output in file "or"mypar.txt with the design
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    of the covariance matrix to be input.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.88  2003/06/23 17:54:56  brouard
 #define rint(a) floor(a+0.5)    * 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.
   
 static double sqrarg;    Revision 1.87  2003/06/18 12:26:01  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Version 0.96
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.86  2003/06/17 20:04:08  brouard
 int imx;    (Module): Change position of html and gnuplot routines and added
 int stepm;    routine fileappend.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.85  2003/06/17 13:12:43  brouard
 int m,nb;    * imach.c (Repository): Check when date of death was earlier that
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    current date of interview. It may happen when the death was just
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    prior to the death. In this case, dh was negative and likelihood
 double **pmmij;    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 double *weight;    interview.
 int **s; /* Status */    (Repository): Because some people have very long ID (first column)
 double *agedc, **covar, idx;    we changed int to long in num[] and we added a new lvector for
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    memory allocation. But we also truncated to 8 characters (left
     truncation)
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Repository): No more line truncation errors.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.84  2003/06/13 21:44:43  brouard
 /**************** split *************************/    * imach.c (Repository): Replace "freqsummary" at a correct
 static  int split( char *path, char *dirc, char *name )    place. It differs from routine "prevalence" which may be called
 {    many times. Probs is memory consuming and must be used with
    char *s;                             /* pointer */    parcimony.
    int  l1, l2;                         /* length counters */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
    l1 = strlen( path );                 /* length of path */    Revision 1.83  2003/06/10 13:39:11  lievre
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
    s = strrchr( path, '\\' );           /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.82  2003/06/05 15:57:20  brouard
 #if     defined(__bsd__)                /* get current working directory */    Add log in  imach.c and  fullversion number is now printed.
       extern char       *getwd( );  
   */
       if ( getwd( dirc ) == NULL ) {  /*
 #else     Interpolated Markov Chain
       extern char       *getcwd( );  
     Short summary of the programme:
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    
 #endif    This program computes Healthy Life Expectancies from
          return( GLOCK_ERROR_GETCWD );    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
       }    first survey ("cross") where individuals from different ages are
       strcpy( name, path );             /* we've got it */    interviewed on their health status or degree of disability (in the
    } else {                             /* strip direcotry from path */    case of a health survey which is our main interest) -2- at least a
       s++;                              /* after this, the filename */    second wave of interviews ("longitudinal") which measure each change
       l2 = strlen( s );                 /* length of filename */    (if any) in individual health status.  Health expectancies are
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    computed from the time spent in each health state according to a
       strcpy( name, s );                /* save file name */    model. More health states you consider, more time is necessary to reach the
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Maximum Likelihood of the parameters involved in the model.  The
       dirc[l1-l2] = 0;                  /* add zero */    simplest model is the multinomial logistic model where pij is the
    }    probability to be observed in state j at the second wave
    l1 = strlen( dirc );                 /* length of directory */    conditional to be observed in state i at the first wave. Therefore
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
    return( 0 );                         /* we're done */    'age' is age and 'sex' is a covariate. If you want to have a more
 }    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /******************************************/    convergence.
   
 void replace(char *s, char*t)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   int i;    identical for each individual. Also, if a individual missed an
   int lg=20;    intermediate interview, the information is lost, but taken into
   i=0;    account using an interpolation or extrapolation.  
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    hPijx is the probability to be observed in state i at age x+h
     (s[i] = t[i]);    conditional to the observed state i at age x. The delay 'h' can be
     if (t[i]== '\\') s[i]='/';    split into an exact number (nh*stepm) of unobserved intermediate
   }    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
 int nbocc(char *s, char occ)    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   int i,j=0;  
   int lg=20;    Also this programme outputs the covariance matrix of the parameters but also
   i=0;    of the life expectancies. It also computes the stable prevalence. 
   lg=strlen(s);    
   for(i=0; i<= lg; i++) {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   if  (s[i] == occ ) j++;             Institut national d'études démographiques, Paris.
   }    This software have been partly granted by Euro-REVES, a concerted action
   return j;    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 void cutv(char *u,char *v, char*t, char occ)    can be accessed at http://euroreves.ined.fr/imach .
 {  
   int i,lg,j,p=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   i=0;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   for(j=0; j<=strlen(t)-1; j++) {    
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    **********************************************************************/
   }  /*
     main
   lg=strlen(t);    read parameterfile
   for(j=0; j<p; j++) {    read datafile
     (u[j] = t[j]);    concatwav
   }    freqsummary
      u[p]='\0';    if (mle >= 1)
       mlikeli
    for(j=0; j<= lg; j++) {    print results files
     if (j>=(p+1))(v[j-p-1] = t[j]);    if mle==1 
   }       computes hessian
 }    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 /********************** nrerror ********************/    open gnuplot file
     open html file
 void nrerror(char error_text[])    stable prevalence
 {     for age prevalim()
   fprintf(stderr,"ERREUR ...\n");    h Pij x
   fprintf(stderr,"%s\n",error_text);    variance of p varprob
   exit(1);    forecasting if prevfcast==1 prevforecast call prevalence()
 }    health expectancies
 /*********************** vector *******************/    Variance-covariance of DFLE
 double *vector(int nl, int nh)    prevalence()
 {     movingaverage()
   double *v;    varevsij() 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    if popbased==1 varevsij(,popbased)
   if (!v) nrerror("allocation failure in vector");    total life expectancies
   return v-nl+NR_END;    Variance of stable prevalence
 }   end
   */
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  
 {  
   free((FREE_ARG)(v+nl-NR_END));   
 }  #include <math.h>
   #include <stdio.h>
 /************************ivector *******************************/  #include <stdlib.h>
 int *ivector(long nl,long nh)  #include <string.h>
 {  #include <unistd.h>
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #include <limits.h>
   if (!v) nrerror("allocation failure in ivector");  #include <sys/types.h>
   return v-nl+NR_END;  #include <sys/stat.h>
 }  #include <errno.h>
   extern int errno;
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  /* #include <sys/time.h> */
 {  #include <time.h>
   free((FREE_ARG)(v+nl-NR_END));  #include "timeval.h"
 }  
   /* #include <libintl.h> */
 /******************* imatrix *******************************/  /* #define _(String) gettext (String) */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define MAXLINE 256
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define GNUPLOTPROGRAM "gnuplot"
   int **m;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
    #define FILENAMELENGTH 132
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   if (!m) nrerror("allocation failure 1 in matrix()");  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   m += NR_END;  
   m -= nrl;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    
   /* allocate rows and set pointers to them */  #define NINTERVMAX 8
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   m[nrl] += NR_END;  #define NCOVMAX 8 /* Maximum number of covariates */
   m[nrl] -= ncl;  #define MAXN 20000
    #define YEARM 12. /* Number of months per year */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define AGESUP 130
    #define AGEBASE 40
   /* return pointer to array of pointers to rows */  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   return m;  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /****************** free_imatrix *************************/  #define ODIRSEPARATOR '\\'
 void free_imatrix(m,nrl,nrh,ncl,nch)  #else
       int **m;  #define DIRSEPARATOR '\\'
       long nch,ncl,nrh,nrl;  #define CHARSEPARATOR "\\"
      /* free an int matrix allocated by imatrix() */  #define ODIRSEPARATOR '/'
 {  #endif
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  /* $Id$ */
 }  /* $State$ */
   
 /******************* matrix *******************************/  char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
 double **matrix(long nrl, long nrh, long ncl, long nch)  char fullversion[]="$Revision$ $Date$"; 
 {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int nvar;
   double **m;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int nlstate=2; /* Number of live states */
   if (!m) nrerror("allocation failure 1 in matrix()");  int ndeath=1; /* Number of dead states */
   m += NR_END;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m -= nrl;  int popbased=0;
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int *wav; /* Number of waves for this individuual 0 is possible */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int maxwav; /* Maxim number of waves */
   m[nrl] += NR_END;  int jmin, jmax; /* min, max spacing between 2 waves */
   m[nrl] -= ncl;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   int gipmx, gsw; /* Global variables on the number of contributions 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;                     to the likelihood and the sum of weights (done by funcone)*/
   return m;  int mle, weightopt;
 }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 /*************************free matrix ************************/  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 {  double jmean; /* Mean space between 2 waves */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double **oldm, **newm, **savm; /* Working pointers to matrices */
   free((FREE_ARG)(m+nrl-NR_END));  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 /******************* ma3x *******************************/  int globpr; /* Global variable for printing or not */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double fretone; /* Only one call to likelihood */
 {  long ipmx; /* Number of contributions */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  double sw; /* Sum of weights */
   double ***m;  char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  FILE *ficresilk;
   if (!m) nrerror("allocation failure 1 in matrix()");  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m += NR_END;  FILE *ficresprobmorprev;
   m -= nrl;  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char filerese[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE  *ficresvij;
   m[nrl] += NR_END;  char fileresv[FILENAMELENGTH];
   m[nrl] -= ncl;  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   m[nrl][ncl] += NR_END;  char command[FILENAMELENGTH];
   m[nrl][ncl] -= nll;  int  outcmd=0;
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    
   for (i=nrl+1; i<=nrh; i++) {  char filelog[FILENAMELENGTH]; /* Log file */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char filerest[FILENAMELENGTH];
     for (j=ncl+1; j<=nch; j++)  char fileregp[FILENAMELENGTH];
       m[i][j]=m[i][j-1]+nlay;  char popfile[FILENAMELENGTH];
   }  
   return m;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /*************************free ma3x ************************/  struct timezone tzp;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  long time_value;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  extern long time();
   free((FREE_ARG)(m+nrl-NR_END));  char strcurr[80], strfor[80];
 }  
   char *endptr;
 /***************** f1dim *************************/  long lval;
 extern int ncom;  
 extern double *pcom,*xicom;  #define NR_END 1
 extern double (*nrfunc)(double []);  #define FREE_ARG char*
    #define FTOL 1.0e-10
 double f1dim(double x)  
 {  #define NRANSI 
   int j;  #define ITMAX 200 
   double f;  
   double *xt;  #define TOL 2.0e-4 
    
   xt=vector(1,ncom);  #define CGOLD 0.3819660 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define ZEPS 1.0e-10 
   f=(*nrfunc)(xt);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   free_vector(xt,1,ncom);  
   return f;  #define GOLD 1.618034 
 }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   int iter;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double a,b,d,etemp;    
   double fu,fv,fw,fx;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   double ftemp;  #define rint(a) floor(a+0.5)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  static double sqrarg;
    #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   a=(ax < cx ? ax : cx);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   b=(ax > cx ? ax : cx);  int agegomp= AGEGOMP;
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  int imx; 
   for (iter=1;iter<=ITMAX;iter++) {  int stepm=1;
     xm=0.5*(a+b);  /* Stepm, step in month: minimum step interpolation*/
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int estepm;
     printf(".");fflush(stdout);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 #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);  int m,nb;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  long *num;
 #endif  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       *xmin=x;  double **pmmij, ***probs;
       return fx;  double *ageexmed,*agecens;
     }  double dateintmean=0;
     ftemp=fu;  
     if (fabs(e) > tol1) {  double *weight;
       r=(x-w)*(fx-fv);  int **s; /* Status */
       q=(x-v)*(fx-fw);  double *agedc, **covar, idx;
       p=(x-v)*q-(x-w)*r;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       q=2.0*(q-r);  double *lsurv, *lpop, *tpop;
       if (q > 0.0) p = -p;  
       q=fabs(q);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       etemp=e;  double ftolhess; /* Tolerance for computing hessian */
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /**************** split *************************/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       else {  {
         d=p/q;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         u=x+d;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         if (u-a < tol2 || b-u < tol2)    */ 
           d=SIGN(tol1,xm-x);    char  *ss;                            /* pointer */
       }    int   l1, l2;                         /* length counters */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    l1 = strlen(path );                   /* length of path */
     }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     fu=(*f)(u);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     if (fu <= fx) {      strcpy( name, path );               /* we got the fullname name because no directory */
       if (u >= x) a=x; else b=x;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       SHFT(v,w,x,u)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         SHFT(fv,fw,fx,fu)      /* get current working directory */
         } else {      /*    extern  char* getcwd ( char *buf , int len);*/
           if (u < x) a=u; else b=u;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
           if (fu <= fw || w == x) {        return( GLOCK_ERROR_GETCWD );
             v=w;      }
             w=u;      /* got dirc from getcwd*/
             fv=fw;      printf(" DIRC = %s \n",dirc);
             fw=fu;    } else {                              /* strip direcotry from path */
           } else if (fu <= fv || v == x || v == w) {      ss++;                               /* after this, the filename */
             v=u;      l2 = strlen( ss );                  /* length of filename */
             fv=fu;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           }      strcpy( name, ss );         /* save file name */
         }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   }      dirc[l1-l2] = 0;                    /* add zero */
   nrerror("Too many iterations in brent");      printf(" DIRC2 = %s \n",dirc);
   *xmin=x;    }
   return fx;    /* We add a separator at the end of dirc if not exists */
 }    l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
 /****************** mnbrak ***********************/      dirc[l1] =  DIRSEPARATOR;
       dirc[l1+1] = 0; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      printf(" DIRC3 = %s \n",dirc);
             double (*func)(double))    }
 {    ss = strrchr( name, '.' );            /* find last / */
   double ulim,u,r,q, dum;    if (ss >0){
   double fu;      ss++;
        strcpy(ext,ss);                     /* save extension */
   *fa=(*func)(*ax);      l1= strlen( name);
   *fb=(*func)(*bx);      l2= strlen(ss)+1;
   if (*fb > *fa) {      strncpy( finame, name, l1-l2);
     SHFT(dum,*ax,*bx,dum)      finame[l1-l2]= 0;
       SHFT(dum,*fb,*fa,dum)    }
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    return( 0 );                          /* we're done */
   *fc=(*func)(*cx);  }
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  /******************************************/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  void replace_back_to_slash(char *s, char*t)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    int i;
       fu=(*func)(u);    int lg=0;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    i=0;
       fu=(*func)(u);    lg=strlen(t);
       if (fu < *fc) {    for(i=0; i<= lg; i++) {
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      (s[i] = t[i]);
           SHFT(*fb,*fc,fu,(*func)(u))      if (t[i]== '\\') s[i]='/';
           }    }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  int nbocc(char *s, char occ)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    int i,j=0;
       fu=(*func)(u);    int lg=20;
     }    i=0;
     SHFT(*ax,*bx,*cx,u)    lg=strlen(s);
       SHFT(*fa,*fb,*fc,fu)    for(i=0; i<= lg; i++) {
       }    if  (s[i] == occ ) j++;
 }    }
     return j;
 /*************** linmin ************************/  }
   
 int ncom;  void cutv(char *u,char *v, char*t, char occ)
 double *pcom,*xicom;  {
 double (*nrfunc)(double []);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   double brent(double ax, double bx, double cx,    i=0;
                double (*f)(double), double tol, double *xmin);    for(j=0; j<=strlen(t)-1; j++) {
   double f1dim(double x);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    }
               double *fc, double (*func)(double));  
   int j;    lg=strlen(t);
   double xx,xmin,bx,ax;    for(j=0; j<p; j++) {
   double fx,fb,fa;      (u[j] = t[j]);
      }
   ncom=n;       u[p]='\0';
   pcom=vector(1,n);  
   xicom=vector(1,n);     for(j=0; j<= lg; j++) {
   nrfunc=func;      if (j>=(p+1))(v[j-p-1] = t[j]);
   for (j=1;j<=n;j++) {    }
     pcom[j]=p[j];  }
     xicom[j]=xi[j];  
   }  /********************** nrerror ********************/
   ax=0.0;  
   xx=1.0;  void nrerror(char error_text[])
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    fprintf(stderr,"ERREUR ...\n");
 #ifdef DEBUG    fprintf(stderr,"%s\n",error_text);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    exit(EXIT_FAILURE);
 #endif  }
   for (j=1;j<=n;j++) {  /*********************** vector *******************/
     xi[j] *= xmin;  double *vector(int nl, int nh)
     p[j] += xi[j];  {
   }    double *v;
   free_vector(xicom,1,n);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   free_vector(pcom,1,n);    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /************************ free vector ******************/
             double (*func)(double []))  void free_vector(double*v, int nl, int nh)
 {  {
   void linmin(double p[], double xi[], int n, double *fret,    free((FREE_ARG)(v+nl-NR_END));
               double (*func)(double []));  }
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  /************************ivector *******************************/
   double fp,fptt;  int *ivector(long nl,long nh)
   double *xits;  {
   pt=vector(1,n);    int *v;
   ptt=vector(1,n);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   xit=vector(1,n);    if (!v) nrerror("allocation failure in ivector");
   xits=vector(1,n);    return v-nl+NR_END;
   *fret=(*func)(p);  }
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /******************free ivector **************************/
     fp=(*fret);  void free_ivector(int *v, long nl, long nh)
     ibig=0;  {
     del=0.0;    free((FREE_ARG)(v+nl-NR_END));
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  }
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  /************************lvector *******************************/
     printf("\n");  long *lvector(long nl,long nh)
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    long *v;
       fptt=(*fret);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in ivector");
       printf("fret=%lf \n",*fret);    return v-nl+NR_END;
 #endif  }
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  /******************free lvector **************************/
       if (fabs(fptt-(*fret)) > del) {  void free_lvector(long *v, long nl, long nh)
         del=fabs(fptt-(*fret));  {
         ibig=i;    free((FREE_ARG)(v+nl-NR_END));
       }  }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  /******************* imatrix *******************************/
       for (j=1;j<=n;j++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         printf(" x(%d)=%.12e",j,xit[j]);  { 
       }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       for(j=1;j<=n;j++)    int **m; 
         printf(" p=%.12e",p[j]);    
       printf("\n");    /* allocate pointers to rows */ 
 #endif    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m += NR_END; 
 #ifdef DEBUG    m -= nrl; 
       int k[2],l;    
       k[0]=1;    
       k[1]=-1;    /* allocate rows and set pointers to them */ 
       printf("Max: %.12e",(*func)(p));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       for (j=1;j<=n;j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         printf(" %.12e",p[j]);    m[nrl] += NR_END; 
       printf("\n");    m[nrl] -= ncl; 
       for(l=0;l<=1;l++) {    
         for (j=1;j<=n;j++) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    /* return pointer to array of pointers to rows */ 
         }    return m; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  } 
       }  
 #endif  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
       free_vector(xit,1,n);        long nch,ncl,nrh,nrl; 
       free_vector(xits,1,n);       /* free an int matrix allocated by imatrix() */ 
       free_vector(ptt,1,n);  { 
       free_vector(pt,1,n);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       return;    free((FREE_ARG) (m+nrl-NR_END)); 
     }  } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  /******************* matrix *******************************/
       ptt[j]=2.0*p[j]-pt[j];  double **matrix(long nrl, long nrh, long ncl, long nch)
       xit[j]=p[j]-pt[j];  {
       pt[j]=p[j];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     fptt=(*func)(ptt);  
     if (fptt < fp) {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    if (!m) nrerror("allocation failure 1 in matrix()");
       if (t < 0.0) {    m += NR_END;
         linmin(p,xit,n,fret,func);    m -= nrl;
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           xi[j][n]=xit[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         }    m[nrl] += NR_END;
 #ifdef DEBUG    m[nrl] -= ncl;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           printf(" %.12e",xit[j]);    return m;
         printf("\n");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 #endif     */
       }  }
     }  
   }  /*************************free matrix ************************/
 }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 /**** Prevalence limit ****************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  }
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /******************* ma3x *******************************/
      matrix by transitions matrix until convergence is reached */  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
   int i, ii,j,k;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double min, max, maxmin, maxmax,sumnew=0.;    double ***m;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double **newm;    if (!m) nrerror("allocation failure 1 in matrix()");
   double agefin, delaymax=50 ; /* Max number of years to converge */    m += NR_END;
     m -= nrl;
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     m[nrl] -= ncl;
    cov[1]=1.;  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     newm=savm;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     /* Covariates have to be included here again */    m[nrl][ncl] += NR_END;
      cov[2]=agefin;    m[nrl][ncl] -= nll;
      for (j=ncl+1; j<=nch; j++) 
       for (k=1; k<=cptcovn;k++) {      m[nrl][j]=m[nrl][j-1]+nlay;
         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]);*/    for (i=nrl+1; i<=nrh; i++) {
       }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (k=1; k<=cptcovage;k++)      for (j=ncl+1; j<=nch; j++) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        m[i][j]=m[i][j-1]+nlay;
       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]]];    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    */
   }
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   /*************************free ma3x ************************/
     savm=oldm;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     oldm=newm;  {
     maxmax=0.;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for(j=1;j<=nlstate;j++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       min=1.;    free((FREE_ARG)(m+nrl-NR_END));
       max=0.;  }
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /*************** function subdirf ***********/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  char *subdirf(char fileres[])
         prlim[i][j]= newm[i][j]/(1-sumnew);  {
         max=FMAX(max,prlim[i][j]);    /* Caution optionfilefiname is hidden */
         min=FMIN(min,prlim[i][j]);    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/"); /* Add to the right */
       maxmin=max-min;    strcat(tmpout,fileres);
       maxmax=FMAX(maxmax,maxmin);    return tmpout;
     }  }
     if(maxmax < ftolpl){  
       return prlim;  /*************** function subdirf2 ***********/
     }  char *subdirf2(char fileres[], char *preop)
   }  {
 }    
     /* Caution optionfilefiname is hidden */
 /*************** transition probabilities **********/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    strcat(tmpout,preop);
 {    strcat(tmpout,fileres);
   double s1, s2;    return tmpout;
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   /*************** function subdirf3 ***********/
     for(i=1; i<= nlstate; i++){  char *subdirf3(char fileres[], char *preop, char *preop2)
     for(j=1; j<i;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    
         /*s2 += param[i][j][nc]*cov[nc];*/    /* Caution optionfilefiname is hidden */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcpy(tmpout,optionfilefiname);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
       ps[i][j]=s2;    strcat(tmpout,preop2);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    strcat(tmpout,fileres);
     }    return tmpout;
     for(j=i+1; j<=nlstate+ndeath;j++){  }
       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];  /***************** f1dim *************************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  extern int ncom; 
       }  extern double *pcom,*xicom;
       ps[i][j]=s2;  extern double (*nrfunc)(double []); 
     }   
   }  double f1dim(double x) 
   for(i=1; i<= nlstate; i++){  { 
      s1=0;    int j; 
     for(j=1; j<i; j++)    double f;
       s1+=exp(ps[i][j]);    double *xt; 
     for(j=i+1; j<=nlstate+ndeath; j++)   
       s1+=exp(ps[i][j]);    xt=vector(1,ncom); 
     ps[i][i]=1./(s1+1.);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for(j=1; j<i; j++)    f=(*nrfunc)(xt); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    free_vector(xt,1,ncom); 
     for(j=i+1; j<=nlstate+ndeath; j++)    return f; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  } 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  { 
     for(jj=1; jj<= nlstate+ndeath; jj++){    int iter; 
       ps[ii][jj]=0;    double a,b,d,etemp;
       ps[ii][ii]=1;    double fu,fv,fw,fx;
     }    double ftemp;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){   
     for(jj=1; jj<= nlstate+ndeath; jj++){    a=(ax < cx ? ax : cx); 
      printf("%lf ",ps[ii][jj]);    b=(ax > cx ? ax : cx); 
    }    x=w=v=bx; 
     printf("\n ");    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
     printf("\n ");printf("%lf ",cov[2]);*/      xm=0.5*(a+b); 
 /*      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   goto end;*/      printf(".");fflush(stdout);
     return ps;      fprintf(ficlog,".");fflush(ficlog);
 }  #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);
 /**************** Product of 2 matrices ******************/      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  #endif
 {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        *xmin=x; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        return fx; 
   /* in, b, out are matrice of pointers which should have been initialized      } 
      before: only the contents of out is modified. The function returns      ftemp=fu;
      a pointer to pointers identical to out */      if (fabs(e) > tol1) { 
   long i, j, k;        r=(x-w)*(fx-fv); 
   for(i=nrl; i<= nrh; i++)        q=(x-v)*(fx-fw); 
     for(k=ncolol; k<=ncoloh; k++)        p=(x-v)*q-(x-w)*r; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        q=2.0*(q-r); 
         out[i][k] +=in[i][j]*b[j][k];        if (q > 0.0) p = -p; 
         q=fabs(q); 
   return out;        etemp=e; 
 }        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)); 
 /************* Higher Matrix Product ***************/        else { 
           d=p/q; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )          u=x+d; 
 {          if (u-a < tol2 || b-u < tol2) 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month            d=SIGN(tol1,xm-x); 
      duration (i.e. until        } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      } else { 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      (typically every 2 years instead of every month which is too big).      } 
      Model is determined by parameters x and covariates have to be      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
      included manually here.      fu=(*f)(u); 
       if (fu <= fx) { 
      */        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
   int i, j, d, h, k;          SHFT(fv,fw,fx,fu) 
   double **out, cov[NCOVMAX];          } else { 
   double **newm;            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
   /* Hstepm could be zero and should return the unit matrix */              v=w; 
   for (i=1;i<=nlstate+ndeath;i++)              w=u; 
     for (j=1;j<=nlstate+ndeath;j++){              fv=fw; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);              fw=fu; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */              fv=fu; 
   for(h=1; h <=nhstepm; h++){            } 
     for(d=1; d <=hstepm; d++){          } 
       newm=savm;    } 
       /* Covariates have to be included here again */    nrerror("Too many iterations in brent"); 
       cov[1]=1.;    *xmin=x; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return fx; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
 for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /****************** mnbrak ***********************/
    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]]];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double ulim,u,r,q, dum;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double fu; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,   
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    *fa=(*func)(*ax); 
       savm=oldm;    *fb=(*func)(*bx); 
       oldm=newm;    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
     for(i=1; i<=nlstate+ndeath; i++)        SHFT(dum,*fb,*fa,dum) 
       for(j=1;j<=nlstate+ndeath;j++) {        } 
         po[i][j][h]=newm[i][j];    *cx=(*bx)+GOLD*(*bx-*ax); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    *fc=(*func)(*cx); 
          */    while (*fb > *fc) { 
       }      r=(*bx-*ax)*(*fb-*fc); 
   } /* end h */      q=(*bx-*cx)*(*fb-*fa); 
   return po;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 /*************** log-likelihood *************/        fu=(*func)(u); 
 double func( double *x)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 {        fu=(*func)(u); 
   int i, ii, j, k, mi, d, kk;        if (fu < *fc) { 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double **out;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double sw; /* Sum of weights */            } 
   double lli; /* Individual log likelihood */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   long ipmx;        u=ulim; 
   /*extern weight */        fu=(*func)(u); 
   /* We are differentiating ll according to initial status */      } else { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        u=(*cx)+GOLD*(*cx-*bx); 
   /*for(i=1;i<imx;i++)        fu=(*func)(u); 
     printf(" %d\n",s[4][i]);      } 
   */      SHFT(*ax,*bx,*cx,u) 
   cov[1]=1.;        SHFT(*fa,*fb,*fc,fu) 
         } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  } 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*************** linmin ************************/
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  int ncom; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double *pcom,*xicom;
       for(d=0; d<dh[mi][i]; d++){  double (*nrfunc)(double []); 
         newm=savm;   
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         for (kk=1; kk<=cptcovage;kk++) {  { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    double brent(double ax, double bx, double cx, 
         }                 double (*f)(double), double tol, double *xmin); 
            double f1dim(double x); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                double *fc, double (*func)(double)); 
         savm=oldm;    int j; 
         oldm=newm;    double xx,xmin,bx,ax; 
            double fx,fb,fa;
           
       } /* end mult */    ncom=n; 
          pcom=vector(1,n); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    xicom=vector(1,n); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    nrfunc=func; 
       ipmx +=1;    for (j=1;j<=n;j++) { 
       sw += weight[i];      pcom[j]=p[j]; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      xicom[j]=xi[j]; 
     } /* end of wave */    } 
   } /* end of individual */    ax=0.0; 
     xx=1.0; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  #ifdef DEBUG
   return -l;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
     for (j=1;j<=n;j++) { 
 /*********** Maximum Likelihood Estimation ***************/      xi[j] *= xmin; 
       p[j] += xi[j]; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    } 
 {    free_vector(xicom,1,n); 
   int i,j, iter;    free_vector(pcom,1,n); 
   double **xi,*delti;  } 
   double fret;  
   xi=matrix(1,npar,1,npar);  char *asc_diff_time(long time_sec, char ascdiff[])
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++)    long sec_left, days, hours, minutes;
       xi[i][j]=(i==j ? 1.0 : 0.0);    days = (time_sec) / (60*60*24);
   printf("Powell\n");    sec_left = (time_sec) % (60*60*24);
   powell(p,xi,npar,ftol,&iter,&fret,func);    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    minutes = (sec_left) /60;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 }    return ascdiff;
   }
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*************** powell ************************/
 {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double  **a,**y,*x,pd;              double (*func)(double [])) 
   double **hess;  { 
   int i, j,jk;    void linmin(double p[], double xi[], int n, double *fret, 
   int *indx;                double (*func)(double [])); 
     int i,ibig,j; 
   double hessii(double p[], double delta, int theta, double delti[]);    double del,t,*pt,*ptt,*xit;
   double hessij(double p[], double delti[], int i, int j);    double fp,fptt;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double *xits;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    int niterf, itmp;
   
     pt=vector(1,n); 
   hess=matrix(1,npar,1,npar);    ptt=vector(1,n); 
     xit=vector(1,n); 
   printf("\nCalculation of the hessian matrix. Wait...\n");    xits=vector(1,n); 
   for (i=1;i<=npar;i++){    *fret=(*func)(p); 
     printf("%d",i);fflush(stdout);    for (j=1;j<=n;j++) pt[j]=p[j]; 
     hess[i][i]=hessii(p,ftolhess,i,delti);    for (*iter=1;;++(*iter)) { 
     /*printf(" %f ",p[i]);*/      fp=(*fret); 
   }      ibig=0; 
       del=0.0; 
   for (i=1;i<=npar;i++) {      last_time=curr_time;
     for (j=1;j<=npar;j++)  {      (void) gettimeofday(&curr_time,&tzp);
       if (j>i) {      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(".%d%d",i,j);fflush(stdout);      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
         hess[i][j]=hessij(p,delti,i,j);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
         hess[j][i]=hess[i][j];      */
       }     for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
   }        fprintf(ficlog," %d %.12lf",i, p[i]);
   printf("\n");        fprintf(ficrespow," %.12lf", p[i]);
       }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      printf("\n");
        fprintf(ficlog,"\n");
   a=matrix(1,npar,1,npar);      fprintf(ficrespow,"\n");fflush(ficrespow);
   y=matrix(1,npar,1,npar);      if(*iter <=3){
   x=vector(1,npar);        tm = *localtime(&curr_time.tv_sec);
   indx=ivector(1,npar);        strcpy(strcurr,asctime(&tm));
   for (i=1;i<=npar;i++)  /*       asctime_r(&tm,strcurr); */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        forecast_time=curr_time; 
   ludcmp(a,npar,indx,&pd);        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   for (j=1;j<=npar;j++) {          strcurr[itmp-1]='\0';
     for (i=1;i<=npar;i++) x[i]=0;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     x[j]=1;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     lubksb(a,npar,indx,x);        for(niterf=10;niterf<=30;niterf+=10){
     for (i=1;i<=npar;i++){          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       matcov[i][j]=x[i];          tmf = *localtime(&forecast_time.tv_sec);
     }  /*      asctime_r(&tmf,strfor); */
   }          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
   printf("\n#Hessian matrix#\n");          if(strfor[itmp-1]=='\n')
   for (i=1;i<=npar;i++) {          strfor[itmp-1]='\0';
     for (j=1;j<=npar;j++) {          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       printf("%.3e ",hess[i][j]);          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);
     }        }
     printf("\n");      }
   }      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   /* Recompute Inverse */        fptt=(*fret); 
   for (i=1;i<=npar;i++)  #ifdef DEBUG
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        printf("fret=%lf \n",*fret);
   ludcmp(a,npar,indx,&pd);        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
   /*  printf("\n#Hessian matrix recomputed#\n");        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   for (j=1;j<=npar;j++) {        linmin(p,xit,n,fret,func); 
     for (i=1;i<=npar;i++) x[i]=0;        if (fabs(fptt-(*fret)) > del) { 
     x[j]=1;          del=fabs(fptt-(*fret)); 
     lubksb(a,npar,indx,x);          ibig=i; 
     for (i=1;i<=npar;i++){        } 
       y[i][j]=x[i];  #ifdef DEBUG
       printf("%.3e ",y[i][j]);        printf("%d %.12e",i,(*fret));
     }        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf("\n");        for (j=1;j<=n;j++) {
   }          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]);
   free_matrix(a,1,npar,1,npar);        }
   free_matrix(y,1,npar,1,npar);        for(j=1;j<=n;j++) {
   free_vector(x,1,npar);          printf(" p=%.12e",p[j]);
   free_ivector(indx,1,npar);          fprintf(ficlog," p=%.12e",p[j]);
   free_matrix(hess,1,npar,1,npar);        }
         printf("\n");
         fprintf(ficlog,"\n");
 }  #endif
       } 
 /*************** hessian matrix ****************/      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 double hessii( double x[], double delta, int theta, double delti[])  #ifdef DEBUG
 {        int k[2],l;
   int i;        k[0]=1;
   int l=1, lmax=20;        k[1]=-1;
   double k1,k2;        printf("Max: %.12e",(*func)(p));
   double p2[NPARMAX+1];        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double res;        for (j=1;j<=n;j++) {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          printf(" %.12e",p[j]);
   double fx;          fprintf(ficlog," %.12e",p[j]);
   int k=0,kmax=10;        }
   double l1;        printf("\n");
         fprintf(ficlog,"\n");
   fx=func(x);        for(l=0;l<=1;l++) {
   for (i=1;i<=npar;i++) p2[i]=x[i];          for (j=1;j<=n;j++) {
   for(l=0 ; l <=lmax; l++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     l1=pow(10,l);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     delts=delt;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for(k=1 ; k <kmax; k=k+1){          }
       delt = delta*(l1*k);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       p2[theta]=x[theta] +delt;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       k1=func(p2)-fx;        }
       p2[theta]=x[theta]-delt;  #endif
       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(xit,1,n); 
              free_vector(xits,1,n); 
 #ifdef DEBUG        free_vector(ptt,1,n); 
       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_vector(pt,1,n); 
 #endif        return; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      } 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         k=kmax;      for (j=1;j<=n;j++) { 
       }        ptt[j]=2.0*p[j]-pt[j]; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        xit[j]=p[j]-pt[j]; 
         k=kmax; l=lmax*10.;        pt[j]=p[j]; 
       }      } 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      fptt=(*func)(ptt); 
         delts=delt;      if (fptt < fp) { 
       }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     }        if (t < 0.0) { 
   }          linmin(p,xit,n,fret,func); 
   delti[theta]=delts;          for (j=1;j<=n;j++) { 
   return res;            xi[j][ibig]=xi[j][n]; 
              xi[j][n]=xit[j]; 
 }          }
   #ifdef DEBUG
 double hessij( double x[], double delti[], int thetai,int thetaj)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int i;          for(j=1;j<=n;j++){
   int l=1, l1, lmax=20;            printf(" %.12e",xit[j]);
   double k1,k2,k3,k4,res,fx;            fprintf(ficlog," %.12e",xit[j]);
   double p2[NPARMAX+1];          }
   int k;          printf("\n");
           fprintf(ficlog,"\n");
   fx=func(x);  #endif
   for (k=1; k<=2; k++) {        }
     for (i=1;i<=npar;i++) p2[i]=x[i];      } 
     p2[thetai]=x[thetai]+delti[thetai]/k;    } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  } 
     k1=func(p2)-fx;  
    /**** Prevalence limit (stable prevalence)  ****************/
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     k2=func(p2)-fx;  {
      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     p2[thetai]=x[thetai]-delti[thetai]/k;       matrix by transitions matrix until convergence is reached */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;    int i, ii,j,k;
      double min, max, maxmin, maxmax,sumnew=0.;
     p2[thetai]=x[thetai]-delti[thetai]/k;    double **matprod2();
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double **out, cov[NCOVMAX], **pmij();
     k4=func(p2)-fx;    double **newm;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double agefin, delaymax=50 ; /* Max number of years to converge */
 #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);    for (ii=1;ii<=nlstate+ndeath;ii++)
 #endif      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   return res;      }
 }  
      cov[1]=1.;
 /************** Inverse of matrix **************/   
 void ludcmp(double **a, int n, int *indx, double *d)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   int i,imax,j,k;      newm=savm;
   double big,dum,sum,temp;      /* Covariates have to be included here again */
   double *vv;       cov[2]=agefin;
      
   vv=vector(1,n);        for (k=1; k<=cptcovn;k++) {
   *d=1.0;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (i=1;i<=n;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]]);*/
     big=0.0;        }
     for (j=1;j<=n;j++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       if ((temp=fabs(a[i][j])) > big) big=temp;        for (k=1; k<=cptcovprod;k++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     vv[i]=1.0/big;  
   }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for (j=1;j<=n;j++) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for (i=1;i<j;i++) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       sum=a[i][j];      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;      savm=oldm;
     }      oldm=newm;
     big=0.0;      maxmax=0.;
     for (i=j;i<=n;i++) {      for(j=1;j<=nlstate;j++){
       sum=a[i][j];        min=1.;
       for (k=1;k<j;k++)        max=0.;
         sum -= a[i][k]*a[k][j];        for(i=1; i<=nlstate; i++) {
       a[i][j]=sum;          sumnew=0;
       if ( (dum=vv[i]*fabs(sum)) >= big) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         big=dum;          prlim[i][j]= newm[i][j]/(1-sumnew);
         imax=i;          max=FMAX(max,prlim[i][j]);
       }          min=FMIN(min,prlim[i][j]);
     }        }
     if (j != imax) {        maxmin=max-min;
       for (k=1;k<=n;k++) {        maxmax=FMAX(maxmax,maxmin);
         dum=a[imax][k];      }
         a[imax][k]=a[j][k];      if(maxmax < ftolpl){
         a[j][k]=dum;        return prlim;
       }      }
       *d = -(*d);    }
       vv[imax]=vv[j];  }
     }  
     indx[j]=imax;  /*************** transition probabilities ***************/ 
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double s1, s2;
     }    /*double t34;*/
   }    int i,j,j1, nc, ii, jj;
   free_vector(vv,1,n);  /* Doesn't work */  
 ;      for(i=1; i<= nlstate; i++){
 }        for(j=1; j<i;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 void lubksb(double **a, int n, int *indx, double b[])            /*s2 += param[i][j][nc]*cov[nc];*/
 {            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int i,ii=0,ip,j;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   double sum;          }
            ps[i][j]=s2;
   for (i=1;i<=n;i++) {  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     ip=indx[i];        }
     sum=b[ip];        for(j=i+1; j<=nlstate+ndeath;j++){
     b[ip]=b[i];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     if (ii)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     else if (sum) ii=i;          }
     b[i]=sum;          ps[i][j]=s2;
   }        }
   for (i=n;i>=1;i--) {      }
     sum=b[i];      /*ps[3][2]=1;*/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      
     b[i]=sum/a[i][i];      for(i=1; i<= nlstate; i++){
   }        s1=0;
 }        for(j=1; j<i; j++)
           s1+=exp(ps[i][j]);
 /************ Frequencies ********************/        for(j=i+1; j<=nlstate+ndeath; j++)
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          s1+=exp(ps[i][j]);
 {  /* Some frequencies */        ps[i][i]=1./(s1+1.);
          for(j=1; j<i; j++)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   double ***freq; /* Frequencies */        for(j=i+1; j<=nlstate+ndeath; j++)
   double *pp;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   double pos;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   FILE *ficresp;      } /* end i */
   char fileresp[FILENAMELENGTH];      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   pp=vector(1,nlstate);        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
   strcpy(fileresp,"p");          ps[ii][ii]=1;
   strcat(fileresp,fileres);        }
   if((ficresp=fopen(fileresp,"w"))==NULL) {      }
     printf("Problem with prevalence resultfile: %s\n", fileresp);      
     exit(0);  
   }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   j1=0;  /*         printf("ddd %lf ",ps[ii][jj]); */
   /*       } */
   j=cptcoveff;  /*       printf("\n "); */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*        } */
   /*        printf("\n ");printf("%lf ",cov[2]); */
   for(k1=1; k1<=j;k1++){         /*
    for(i1=1; i1<=ncodemax[k1];i1++){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
        j1++;        goto end;*/
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      return ps;
          scanf("%d", i);*/  }
         for (i=-1; i<=nlstate+ndeath; i++)    
          for (jk=-1; jk<=nlstate+ndeath; jk++)    /**************** Product of 2 matrices ******************/
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          {
        for (i=1; i<=imx; i++) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
          bool=1;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
          if  (cptcovn>0) {    /* in, b, out are matrice of pointers which should have been initialized 
            for (z1=1; z1<=cptcoveff; z1++)       before: only the contents of out is modified. The function returns
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       a pointer to pointers identical to out */
                bool=0;    long i, j, k;
          }    for(i=nrl; i<= nrh; i++)
           if (bool==1) {      for(k=ncolol; k<=ncoloh; k++)
            for(m=firstpass; m<=lastpass-1; m++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
              if(agev[m][i]==0) agev[m][i]=agemax+1;          out[i][k] +=in[i][j]*b[j][k];
              if(agev[m][i]==1) agev[m][i]=agemax+2;  
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    return out;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  }
            }  
          }  
        }  /************* Higher Matrix Product ***************/
         if  (cptcovn>0) {  
          fprintf(ficresp, "\n#********** Variable ");  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  {
        fprintf(ficresp, "**********\n#");    /* Computes the transition matrix starting at age 'age' over 
         }       'nhstepm*hstepm*stepm' months (i.e. until
        for(i=1; i<=nlstate;i++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);       nhstepm*hstepm matrices. 
        fprintf(ficresp, "\n");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
               (typically every 2 years instead of every month which is too big 
   for(i=(int)agemin; i <= (int)agemax+3; i++){       for the memory).
     if(i==(int)agemax+3)       Model is determined by parameters x and covariates have to be 
       printf("Total");       included manually here. 
     else  
       printf("Age %d", i);       */
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int i, j, d, h, k;
         pp[jk] += freq[jk][m][i];    double **out, cov[NCOVMAX];
     }    double **newm;
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)    /* Hstepm could be zero and should return the unit matrix */
         pos += freq[jk][m][i];    for (i=1;i<=nlstate+ndeath;i++)
       if(pp[jk]>=1.e-10)      for (j=1;j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        oldm[i][j]=(i==j ? 1.0 : 0.0);
       else        po[i][j][0]=(i==j ? 1.0 : 0.0);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      }
     }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(jk=1; jk <=nlstate ; jk++){    for(h=1; h <=nhstepm; h++){
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)      for(d=1; d <=hstepm; d++){
         pp[jk] += freq[jk][m][i];        newm=savm;
     }        /* Covariates have to be included here again */
     for(jk=1,pos=0; jk <=nlstate ; jk++)        cov[1]=1.;
       pos += pp[jk];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       if(pos>=1.e-5)        for (k=1; k<=cptcovage;k++)
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       else        for (k=1; k<=cptcovprod;k++)
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if( i <= (int) agemax){  
         if(pos>=1.e-5)  
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       else        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
     for(jk=-1; jk <=nlstate+ndeath; jk++)        oldm=newm;
       for(m=-1; m <=nlstate+ndeath; m++)      }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for(i=1; i<=nlstate+ndeath; i++)
     if(i <= (int) agemax)        for(j=1;j<=nlstate+ndeath;j++) {
       fprintf(ficresp,"\n");          po[i][j][h]=newm[i][j];
     printf("\n");          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     }           */
     }        }
  }    } /* end h */
      return po;
   fclose(ficresp);  }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  
   /*************** log-likelihood *************/
 }  /* End of Freq */  double func( double *x)
   {
 /************* Waves Concatenation ***************/    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    double **out;
 {    double sw; /* Sum of weights */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    double lli; /* Individual log likelihood */
      Death is a valid wave (if date is known).    int s1, s2;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    double bbh, survp;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    long ipmx;
      and mw[mi+1][i]. dh depends on stepm.    /*extern weight */
      */    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   int i, mi, m;    /*for(i=1;i<imx;i++) 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      printf(" %d\n",s[4][i]);
      double sum=0., jmean=0.;*/    */
     cov[1]=1.;
   int j, k=0,jk, ju, jl;  
   double sum=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   jmin=1e+5;  
   jmax=-1;    if(mle==1){
   jmean=0.;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=imx; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     mi=0;        for(mi=1; mi<= wav[i]-1; mi++){
     m=firstpass;          for (ii=1;ii<=nlstate+ndeath;ii++)
     while(s[m][i] <= nlstate){            for (j=1;j<=nlstate+ndeath;j++){
       if(s[m][i]>=1)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         mw[++mi][i]=m;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(m >=lastpass)            }
         break;          for(d=0; d<dh[mi][i]; d++){
       else            newm=savm;
         m++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }/* end while */            for (kk=1; kk<=cptcovage;kk++) {
     if (s[m][i] > nlstate){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       mi++;     /* Death is another wave */            }
       /* if(mi==0)  never been interviewed correctly before death */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          /* Only death is a correct wave */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       mw[mi][i]=m;            savm=oldm;
     }            oldm=newm;
           } /* end mult */
     wav[i]=mi;        
     if(mi==0)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          /* But now since version 0.9 we anticipate for bias at large stepm.
   }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
   for(i=1; i<=imx; i++){           * the nearest (and in case of equal distance, to the lowest) interval but now
     for(mi=1; mi<wav[i];mi++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       if (stepm <=0)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         dh[mi][i]=1;           * probability in order to take into account the bias as a fraction of the way
       else{           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         if (s[mw[mi+1][i]][i] > nlstate) {           * -stepm/2 to stepm/2 .
           if (agedc[i] < 2*AGESUP) {           * For stepm=1 the results are the same as for previous versions of Imach.
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);           * For stepm > 1 the results are less biased than in previous versions. 
           if(j==0) j=1;  /* Survives at least one month after exam */           */
           k=k+1;          s1=s[mw[mi][i]][i];
           if (j >= jmax) jmax=j;          s2=s[mw[mi+1][i]][i];
           if (j <= jmin) jmin=j;          bbh=(double)bh[mi][i]/(double)stepm; 
           sum=sum+j;          /* bias bh is positive if real duration
           if (j<0) printf("j=%d num=%d ",j,i);           * is higher than the multiple of stepm and negative otherwise.
           }           */
         }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         else{          if( s2 > nlstate){ 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            /* i.e. if s2 is a death state and if the date of death is known 
           k=k+1;               then the contribution to the likelihood is the probability to 
           if (j >= jmax) jmax=j;               die between last step unit time and current  step unit time, 
           else if (j <= jmin)jmin=j;               which is also equal to probability to die before dh 
           sum=sum+j;               minus probability to die before dh-stepm . 
         }               In version up to 0.92 likelihood was computed
         jk= j/stepm;          as if date of death was unknown. Death was treated as any other
         jl= j -jk*stepm;          health state: the date of the interview describes the actual state
         ju= j -(jk+1)*stepm;          and not the date of a change in health state. The former idea was
         if(jl <= -ju)          to consider that at each interview the state was recorded
           dh[mi][i]=jk;          (healthy, disable or death) and IMaCh was corrected; but when we
         else          introduced the exact date of death then we should have modified
           dh[mi][i]=jk+1;          the contribution of an exact death to the likelihood. This new
         if(dh[mi][i]==0)          contribution is smaller and very dependent of the step unit
           dh[mi][i]=1; /* At least one step */          stepm. It is no more the probability to die between last interview
       }          and month of death but the probability to survive from last
     }          interview up to one month before death multiplied by the
   }          probability to die within a month. Thanks to Chris
   jmean=sum/k;          Jackson for correcting this bug.  Former versions increased
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          mortality artificially. The bad side is that we add another loop
 }          which slows down the processing. The difference can be up to 10%
 /*********** Tricode ****************************/          lower mortality.
 void tricode(int *Tvar, int **nbcode, int imx)            */
 {            lli=log(out[s1][s2] - savm[s1][s2]);
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;  
   cptcoveff=0;          } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
   for (k=0; k<19; k++) Ndum[k]=0;              survp += out[s1][j];
   for (k=1; k<=7; k++) ncodemax[k]=0;            lli= survp;
           }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          
     for (i=1; i<=imx; i++) {          else if  (s2==-4) {
       ij=(int)(covar[Tvar[j]][i]);            for (j=3,survp=0. ; j<=nlstate; j++) 
       Ndum[ij]++;              survp += out[s1][j];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            lli= survp;
       if (ij > cptcode) cptcode=ij;          }
     }          
           else if  (s2==-5) {
     for (i=0; i<=cptcode; i++) {            for (j=1,survp=0. ; j<=2; j++) 
       if(Ndum[i]!=0) ncodemax[j]++;              survp += out[s1][j];
     }            lli= survp;
     ij=1;          }
   
   
     for (i=1; i<=ncodemax[j]; i++) {          else{
       for (k=0; k<=19; k++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         if (Ndum[k] != 0) {            /*  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 */
           nbcode[Tvar[j]][ij]=k;          } 
           ij++;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         }          /*if(lli ==000.0)*/
         if (ij > ncodemax[j]) break;          /*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); */
       }            ipmx +=1;
     }          sw += weight[i];
   }            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
  for (k=0; k<19; k++) Ndum[k]=0;      } /* end of individual */
     }  else if(mle==2){
  for (i=1; i<=ncovmodel; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       ij=Tvar[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       Ndum[ij]++;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
  ij=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (i=1; i<=10; i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    if((Ndum[i]!=0) && (i<=ncov)){            }
      Tvaraff[ij]=i;          for(d=0; d<=dh[mi][i]; d++){
      ij++;            newm=savm;
    }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  }            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     cptcoveff=ij-1;            }
 }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*********** Health Expectancies ****************/            savm=oldm;
             oldm=newm;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          } /* end mult */
 {        
   /* Health expectancies */          s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm, h;          s2=s[mw[mi+1][i]][i];
   double age, agelim,hf;          bbh=(double)bh[mi][i]/(double)stepm; 
   double ***p3mat;          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;
   fprintf(ficreseij,"# Health expectancies\n");          sw += weight[i];
   fprintf(ficreseij,"# Age");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for(i=1; i<=nlstate;i++)        } /* end of wave */
     for(j=1; j<=nlstate;j++)      } /* end of individual */
       fprintf(ficreseij," %1d-%1d",i,j);    }  else if(mle==3){  /* exponential inter-extrapolation */
   fprintf(ficreseij,"\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   hstepm=1*YEARM; /*  Every j years of age (in month) */        for(mi=1; mi<= wav[i]-1; mi++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   agelim=AGESUP;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* nhstepm age range expressed in number of stepm */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          for(d=0; d<dh[mi][i]; d++){
     /* Typically if 20 years = 20*12/6=40 stepm */            newm=savm;
     if (stepm >= YEARM) hstepm=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            for (kk=1; kk<=cptcovage;kk++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
     for(i=1; i<=nlstate;i++)          } /* end mult */
       for(j=1; j<=nlstate;j++)        
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          s1=s[mw[mi][i]][i];
           eij[i][j][(int)age] +=p3mat[i][j][h];          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
              lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     hf=1;          ipmx +=1;
     if (stepm >= YEARM) hf=stepm/YEARM;          sw += weight[i];
     fprintf(ficreseij,"%.0f",age );          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1; i<=nlstate;i++)        } /* end of wave */
       for(j=1; j<=nlstate;j++){      } /* end of individual */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficreseij,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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);
 /************ Variance ******************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            }
 {          for(d=0; d<dh[mi][i]; d++){
   /* Variance of health expectancies */            newm=savm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **newm;            for (kk=1; kk<=cptcovage;kk++) {
   double **dnewm,**doldm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, j, nhstepm, hstepm, h;            }
   int k, cptcode;          
    double *xp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **gp, **gm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***gradg, ***trgradg;            savm=oldm;
   double ***p3mat;            oldm=newm;
   double age,agelim;          } /* end mult */
   int theta;        
           s1=s[mw[mi][i]][i];
    fprintf(ficresvij,"# Covariances of life expectancies\n");          s2=s[mw[mi+1][i]][i];
   fprintf(ficresvij,"# Age");          if( s2 > nlstate){ 
   for(i=1; i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
     for(j=1; j<=nlstate;j++)          }else{
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fprintf(ficresvij,"\n");          }
           ipmx +=1;
   xp=vector(1,npar);          sw += weight[i];
   dnewm=matrix(1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   doldm=matrix(1,nlstate,1,nlstate);  /*      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 */
   hstepm=1*YEARM; /* Every year of age */      } /* end of individual */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   agelim = AGESUP;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        for(mi=1; mi<= wav[i]-1; mi++){
     if (stepm >= YEARM) hstepm=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (j=1;j<=nlstate+ndeath;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gp=matrix(0,nhstepm,1,nlstate);            }
     gm=matrix(0,nhstepm,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for(theta=1; theta <=npar; theta++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (kk=1; kk<=cptcovage;kk++) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<= nlstate; j++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(h=0; h<=nhstepm; h++){            savm=oldm;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            oldm=newm;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          } /* end mult */
         }        
       }          s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ipmx +=1;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            sw += weight[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(j=1; j<= nlstate; j++){          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         for(h=0; h<=nhstepm; h++){        } /* end of wave */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      } /* end of individual */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<= nlstate; j++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(h=0; h<=nhstepm; h++){    return -l;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  
     } /* End theta */  /*************** log-likelihood *************/
   double funcone( double *x)
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  {
     /* Same as likeli but slower because of a lot of printf and if */
     for(h=0; h<=nhstepm; h++)    int i, ii, j, k, mi, d, kk;
       for(j=1; j<=nlstate;j++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         for(theta=1; theta <=npar; theta++)    double **out;
           trgradg[h][j][theta]=gradg[h][theta][j];    double lli; /* Individual log likelihood */
     double llt;
     for(i=1;i<=nlstate;i++)    int s1, s2;
       for(j=1;j<=nlstate;j++)    double bbh, survp;
         vareij[i][j][(int)age] =0.;    /*extern weight */
     for(h=0;h<=nhstepm;h++){    /* We are differentiating ll according to initial status */
       for(k=0;k<=nhstepm;k++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /*for(i=1;i<imx;i++) 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      printf(" %d\n",s[4][i]);
         for(i=1;i<=nlstate;i++)    */
           for(j=1;j<=nlstate;j++)    cov[1]=1.;
             vareij[i][j][(int)age] += doldm[i][j];  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     h=1;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (stepm >= YEARM) h=stepm/YEARM;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficresvij,"%.0f ",age );      for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1; i<=nlstate;i++)        for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<=nlstate;j++){          for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);        for(d=0; d<dh[mi][i]; d++){
     free_matrix(gm,0,nhstepm,1,nlstate);          newm=savm;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          for (kk=1; kk<=cptcovage;kk++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   } /* End age */          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(xp,1,npar);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(doldm,1,nlstate,1,npar);          savm=oldm;
   free_matrix(dnewm,1,nlstate,1,nlstate);          oldm=newm;
         } /* end mult */
 }        
         s1=s[mw[mi][i]][i];
 /************ Variance of prevlim ******************/        s2=s[mw[mi+1][i]][i];
 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)        bbh=(double)bh[mi][i]/(double)stepm; 
 {        /* bias is positive if real duration
   /* Variance of prevalence limit */         * is higher than the multiple of stepm and negative otherwise.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/         */
   double **newm;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   double **dnewm,**doldm;          lli=log(out[s1][s2] - savm[s1][s2]);
   int i, j, nhstepm, hstepm;        } else if (mle==1){
   int k, cptcode;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double *xp;        } else if(mle==2){
   double *gp, *gm;          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 */
   double **gradg, **trgradg;        } else if(mle==3){  /* exponential inter-extrapolation */
   double age,agelim;          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 */
   int theta;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
              lli=log(out[s1][s2]); /* Original formula */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   fprintf(ficresvpl,"# Age");          lli=log(out[s1][s2]); /* Original formula */
   for(i=1; i<=nlstate;i++)        } /* End of if */
       fprintf(ficresvpl," %1d-%1d",i,i);        ipmx +=1;
   fprintf(ficresvpl,"\n");        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   xp=vector(1,npar);  /*       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]); */
   dnewm=matrix(1,nlstate,1,npar);        if(globpr){
   doldm=matrix(1,nlstate,1,nlstate);          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     %10.6f %10.6f %10.6f ", \
   hstepm=1*YEARM; /* Every year of age */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   agelim = AGESUP;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            llt +=ll[k]*gipmx/gsw;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     if (stepm >= YEARM) hstepm=1;          }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          fprintf(ficresilk," %10.6f\n", -llt);
     gradg=matrix(1,npar,1,nlstate);        }
     gp=vector(1,nlstate);      } /* end of wave */
     gm=vector(1,nlstate);    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for(theta=1; theta <=npar; theta++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(i=1; i<=npar; i++){ /* Computes gradient */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    if(globpr==0){ /* First time we count the contributions and weights */
       }      gipmx=ipmx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      gsw=sw;
       for(i=1;i<=nlstate;i++)    }
         gp[i] = prlim[i][i];    return -l;
      }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*************** function likelione ***********/
       for(i=1;i<=nlstate;i++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         gm[i] = prlim[i][i];  {
     /* This routine should help understanding what is done with 
       for(i=1;i<=nlstate;i++)       the selection of individuals/waves and
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       to check the exact contribution to the likelihood.
     } /* End theta */       Plotting could be done.
      */
     trgradg =matrix(1,nlstate,1,npar);    int k;
   
     for(j=1; j<=nlstate;j++)    if(*globpri !=0){ /* Just counts and sums, no printings */
       for(theta=1; theta <=npar; theta++)      strcpy(fileresilk,"ilk"); 
         trgradg[j][theta]=gradg[theta][j];      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     for(i=1;i<=nlstate;i++)        printf("Problem with resultfile: %s\n", fileresilk);
       varpl[i][(int)age] =0.;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     for(i=1;i<=nlstate;i++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      /*  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(ficresvpl,"%.0f ",age );        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     for(i=1; i<=nlstate;i++)      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);    *fretone=(*funcone)(p);
     free_vector(gm,1,nlstate);    if(*globpri !=0){
     free_matrix(gradg,1,npar,1,nlstate);      fclose(ficresilk);
     free_matrix(trgradg,1,nlstate,1,npar);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   } /* End age */      fflush(fichtm); 
     } 
   free_vector(xp,1,npar);    return;
   free_matrix(doldm,1,nlstate,1,npar);  }
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   
 }  /*********** Maximum Likelihood Estimation ***************/
   
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
 /***********************************************/    int i,j, iter;
 /**************** Main Program *****************/    double **xi;
 /***********************************************/    double fret;
     double fretone; /* Only one call to likelihood */
 /*int main(int argc, char *argv[])*/    /*  char filerespow[FILENAMELENGTH];*/
 int main()    xi=matrix(1,npar,1,npar);
 {    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        xi[i][j]=(i==j ? 1.0 : 0.0);
   double agedeb, agefin,hf;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double agemin=1.e20, agemax=-1.e20;    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
   double fret;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double **xi,tmp,delta;      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double dum; /* Dummy variable */    }
   double ***p3mat;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   int *indx;    for (i=1;i<=nlstate;i++)
   char line[MAXLINE], linepar[MAXLINE];      for(j=1;j<=nlstate+ndeath;j++)
   char title[MAXLINE];        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    fprintf(ficrespow,"\n");
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];  
   char filerest[FILENAMELENGTH];    powell(p,xi,npar,ftol,&iter,&fret,func);
   char fileregp[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fclose(ficrespow);
   int firstobs=1, lastobs=10;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   int sdeb, sfin; /* Status at beginning and end */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int c,  h , cpt,l;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
    /**** Computes Hessian and covariance matrix ***/
   int hstepm, nhstepm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double bage, fage, age, agelim, agebase;  {
   double ftolpl=FTOL;    double  **a,**y,*x,pd;
   double **prlim;    double **hess;
   double *severity;    int i, j,jk;
   double ***param; /* Matrix of parameters */    int *indx;
   double  *p;  
   double **matcov; /* Matrix of covariance */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double ***delti3; /* Scale */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   double *delti; /* Scale */    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double ***eij, ***vareij;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double **varpl; /* Variances of prevalence limits by age */    double gompertz(double p[]);
   double *epj, vepp;    hess=matrix(1,npar,1,npar);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   char z[1]="c", occ;    for (i=1;i<=npar;i++){
 #include <sys/time.h>      printf("%d",i);fflush(stdout);
 #include <time.h>      fprintf(ficlog,"%d",i);fflush(ficlog);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];     
   /* long total_usecs;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   struct timeval start_time, end_time;      
        /*  printf(" %f ",p[i]);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
     
   printf("\nIMACH, Version 0.64b");    for (i=1;i<=npar;i++) {
   printf("\nEnter the parameter file name: ");      for (j=1;j<=npar;j++)  {
         if (j>i) { 
 #ifdef windows          printf(".%d%d",i,j);fflush(stdout);
   scanf("%s",pathtot);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   getcwd(pathcd, size);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   /*cygwin_split_path(pathtot,path,optionfile);          
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          hess[j][i]=hess[i][j];    
   /* cutv(path,optionfile,pathtot,'\\');*/          /*printf(" %lf ",hess[i][j]);*/
         }
 split(pathtot, path,optionfile);      }
   chdir(path);    }
   replace(pathc,path);    printf("\n");
 #endif    fprintf(ficlog,"\n");
 #ifdef unix  
   scanf("%s",optionfile);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 #endif    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
 /*-------- arguments in the command line --------*/    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
   strcpy(fileres,"r");    x=vector(1,npar);
   strcat(fileres, optionfile);    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
   /*---------arguments file --------*/      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);    for (j=1;j<=npar;j++) {
     goto end;      for (i=1;i<=npar;i++) x[i]=0;
   }      x[j]=1;
       lubksb(a,npar,indx,x);
   strcpy(filereso,"o");      for (i=1;i<=npar;i++){ 
   strcat(filereso,fileres);        matcov[i][j]=x[i];
   if((ficparo=fopen(filereso,"w"))==NULL) {      }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    }
   }  
     printf("\n#Hessian matrix#\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficlog,"\n#Hessian matrix#\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=npar;i++) { 
     ungetc(c,ficpar);      for (j=1;j<=npar;j++) { 
     fgets(line, MAXLINE, ficpar);        printf("%.3e ",hess[i][j]);
     puts(line);        fprintf(ficlog,"%.3e ",hess[i][j]);
     fputs(line,ficparo);      }
   }      printf("\n");
   ungetc(c,ficpar);      fprintf(ficlog,"\n");
     }
   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);    /* Recompute Inverse */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   covar=matrix(0,NCOVMAX,1,n);    ludcmp(a,npar,indx,&pd);
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    /*  printf("\n#Hessian matrix recomputed#\n");
   
   ncovmodel=2+cptcovn;    for (j=1;j<=npar;j++) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
   /* Read guess parameters */      lubksb(a,npar,indx,x);
   /* Reads comments: lines beginning with '#' */      for (i=1;i<=npar;i++){ 
   while((c=getc(ficpar))=='#' && c!= EOF){        y[i][j]=x[i];
     ungetc(c,ficpar);        printf("%.3e ",y[i][j]);
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"%.3e ",y[i][j]);
     puts(line);      }
     fputs(line,ficparo);      printf("\n");
   }      fprintf(ficlog,"\n");
   ungetc(c,ficpar);    }
      */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)    free_matrix(a,1,npar,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(y,1,npar,1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    free_vector(x,1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    free_ivector(indx,1,npar);
       printf("%1d%1d",i,j);    free_matrix(hess,1,npar,1,npar);
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);  }
         fprintf(ficparo," %lf",param[i][j][k]);  
       }  /*************** hessian matrix ****************/
       fscanf(ficpar,"\n");  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       printf("\n");  {
       fprintf(ficparo,"\n");    int i;
     }    int l=1, lmax=20;
      double k1,k2;
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    double p2[NPARMAX+1];
   p=param[1][1];    double res;
      double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   /* Reads comments: lines beginning with '#' */    double fx;
   while((c=getc(ficpar))=='#' && c!= EOF){    int k=0,kmax=10;
     ungetc(c,ficpar);    double l1;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    fx=func(x);
     fputs(line,ficparo);    for (i=1;i<=npar;i++) p2[i]=x[i];
   }    for(l=0 ; l <=lmax; l++){
   ungetc(c,ficpar);      l1=pow(10,l);
       delts=delt;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(k=1 ; k <kmax; k=k+1){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        delt = delta*(l1*k);
   for(i=1; i <=nlstate; i++){        p2[theta]=x[theta] +delt;
     for(j=1; j <=nlstate+ndeath-1; j++){        k1=func(p2)-fx;
       fscanf(ficpar,"%1d%1d",&i1,&j1);        p2[theta]=x[theta]-delt;
       printf("%1d%1d",i,j);        k2=func(p2)-fx;
       fprintf(ficparo,"%1d%1d",i1,j1);        /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(k=1; k<=ncovmodel;k++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         fscanf(ficpar,"%le",&delti3[i][j][k]);        
         printf(" %le",delti3[i][j][k]);  #ifdef DEBUG
         fprintf(ficparo," %le",delti3[i][j][k]);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fscanf(ficpar,"\n");  #endif
       printf("\n");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       fprintf(ficparo,"\n");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     }          k=kmax;
   }        }
   delti=delti3[1][1];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
            k=kmax; l=lmax*10.;
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     ungetc(c,ficpar);          delts=delt;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      }
     fputs(line,ficparo);    }
   }    delti[theta]=delts;
   ungetc(c,ficpar);    return res; 
      
   matcov=matrix(1,npar,1,npar);  }
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     printf("%s",str);  {
     fprintf(ficparo,"%s",str);    int i;
     for(j=1; j <=i; j++){    int l=1, l1, lmax=20;
       fscanf(ficpar," %le",&matcov[i][j]);    double k1,k2,k3,k4,res,fx;
       printf(" %.5le",matcov[i][j]);    double p2[NPARMAX+1];
       fprintf(ficparo," %.5le",matcov[i][j]);    int k;
     }  
     fscanf(ficpar,"\n");    fx=func(x);
     printf("\n");    for (k=1; k<=2; k++) {
     fprintf(ficparo,"\n");      for (i=1;i<=npar;i++) p2[i]=x[i];
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
   for(i=1; i <=npar; i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(j=i+1;j<=npar;j++)      k1=func(p2)-fx;
       matcov[i][j]=matcov[j][i];    
          p2[thetai]=x[thetai]+delti[thetai]/k;
   printf("\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     
     /*-------- data file ----------*/      p2[thetai]=x[thetai]-delti[thetai]/k;
     if((ficres =fopen(fileres,"w"))==NULL) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       printf("Problem with resultfile: %s\n", fileres);goto end;      k3=func(p2)-fx;
     }    
     fprintf(ficres,"#%s\n",version);      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if((fic=fopen(datafile,"r"))==NULL)    {      k4=func(p2)-fx;
       printf("Problem with datafile: %s\n", datafile);goto end;      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);
     n= lastobs;      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);
     severity = vector(1,maxwav);  #endif
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    return res;
     moisnais=vector(1,n);  }
     annais=vector(1,n);  
     moisdc=vector(1,n);  /************** Inverse of matrix **************/
     andc=vector(1,n);  void ludcmp(double **a, int n, int *indx, double *d) 
     agedc=vector(1,n);  { 
     cod=ivector(1,n);    int i,imax,j,k; 
     weight=vector(1,n);    double big,dum,sum,temp; 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double *vv; 
     mint=matrix(1,maxwav,1,n);   
     anint=matrix(1,maxwav,1,n);    vv=vector(1,n); 
     s=imatrix(1,maxwav+1,1,n);    *d=1.0; 
     adl=imatrix(1,maxwav+1,1,n);        for (i=1;i<=n;i++) { 
     tab=ivector(1,NCOVMAX);      big=0.0; 
     ncodemax=ivector(1,8);      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
     i=1;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     while (fgets(line, MAXLINE, fic) != NULL)    {      vv[i]=1.0/big; 
       if ((i >= firstobs) && (i <=lastobs)) {    } 
            for (j=1;j<=n;j++) { 
         for (j=maxwav;j>=1;j--){      for (i=1;i<j;i++) { 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        sum=a[i][j]; 
           strcpy(line,stra);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        a[i][j]=sum; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         }      big=0.0; 
              for (i=j;i<=n;i++) { 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        sum=a[i][j]; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        a[i][j]=sum; 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          imax=i; 
         for (j=ncov;j>=1;j--){        } 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      } 
         }      if (j != imax) { 
         num[i]=atol(stra);        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
         /*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]));*/          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
         i=i+1;        } 
       }        *d = -(*d); 
     }        vv[imax]=vv[j]; 
       } 
     /*scanf("%d",i);*/      indx[j]=imax; 
   imx=i-1; /* Number of individuals */      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   /* Calculation of the number of parameter from char model*/        dum=1.0/(a[j][j]); 
   Tvar=ivector(1,15);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   Tprod=ivector(1,15);      } 
   Tvaraff=ivector(1,15);    } 
   Tvard=imatrix(1,15,1,2);    free_vector(vv,1,n);  /* Doesn't work */
   Tage=ivector(1,15);        ;
      } 
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;  void lubksb(double **a, int n, int *indx, double b[]) 
     j=nbocc(model,'+');  { 
     j1=nbocc(model,'*');    int i,ii=0,ip,j; 
     cptcovn=j+1;    double sum; 
     cptcovprod=j1;   
        for (i=1;i<=n;i++) { 
          ip=indx[i]; 
     strcpy(modelsav,model);      sum=b[ip]; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      b[ip]=b[i]; 
       printf("Error. Non available option model=%s ",model);      if (ii) 
       goto end;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     }      else if (sum) ii=i; 
          b[i]=sum; 
     for(i=(j+1); i>=1;i--){    } 
       cutv(stra,strb,modelsav,'+');    for (i=n;i>=1;i--) { 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      sum=b[i]; 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       /*scanf("%d",i);*/      b[i]=sum/a[i][i]; 
       if (strchr(strb,'*')) {    } 
         cutv(strd,strc,strb,'*');  } 
         if (strcmp(strc,"age")==0) {  
           cptcovprod--;  /************ Frequencies ********************/
           cutv(strb,stre,strd,'V');  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[])
           Tvar[i]=atoi(stre);  {  /* Some frequencies */
           cptcovage++;    
             Tage[cptcovage]=i;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
             /*printf("stre=%s ", stre);*/    int first;
         }    double ***freq; /* Frequencies */
         else if (strcmp(strd,"age")==0) {    double *pp, **prop;
           cptcovprod--;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           cutv(strb,stre,strc,'V');    FILE *ficresp;
           Tvar[i]=atoi(stre);    char fileresp[FILENAMELENGTH];
           cptcovage++;    
           Tage[cptcovage]=i;    pp=vector(1,nlstate);
         }    prop=matrix(1,nlstate,iagemin,iagemax+3);
         else {    strcpy(fileresp,"p");
           cutv(strb,stre,strc,'V');    strcat(fileresp,fileres);
           Tvar[i]=ncov+k1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
           cutv(strb,strc,strd,'V');      printf("Problem with prevalence resultfile: %s\n", fileresp);
           Tprod[k1]=i;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           Tvard[k1][1]=atoi(strc);      exit(0);
           Tvard[k1][2]=atoi(stre);    }
           Tvar[cptcovn+k2]=Tvard[k1][1];    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    j1=0;
           for (k=1; k<=lastobs;k++)    
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    j=cptcoveff;
           k1++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           k2=k2+2;  
         }    first=1;
       }  
       else {    for(k1=1; k1<=j;k1++){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      for(i1=1; i1<=ncodemax[k1];i1++){
        /*  scanf("%d",i);*/        j1++;
       cutv(strd,strc,strb,'V');        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       Tvar[i]=atoi(strc);          scanf("%d", i);*/
       }        for (i=-5; i<=nlstate+ndeath; i++)  
       strcpy(modelsav,stra);            for (jk=-5; jk<=nlstate+ndeath; jk++)  
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            for(m=iagemin; m <= iagemax+3; m++)
         scanf("%d",i);*/              freq[i][jk][m]=0;
     }  
 }      for (i=1; i<=nlstate; i++)  
          for(m=iagemin; m <= iagemax+3; m++)
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          prop[i][m]=0;
   printf("cptcovprod=%d ", cptcovprod);        
   scanf("%d ",i);*/        dateintsum=0;
     fclose(fic);        k2cpt=0;
         for (i=1; i<=imx; i++) {
     /*  if(mle==1){*/          bool=1;
     if (weightopt != 1) { /* Maximisation without weights*/          if  (cptcovn>0) {
       for(i=1;i<=n;i++) weight[i]=1.0;            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     /*-calculation of age at interview from date of interview and age at death -*/                bool=0;
     agev=matrix(1,maxwav,1,imx);          }
              if (bool==1){
     for (i=1; i<=imx; i++)  {            for(m=firstpass; m<=lastpass; m++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              k2=anint[m][i]+(mint[m][i]/12.);
       for(m=1; (m<= maxwav); m++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         if(s[m][i] >0){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           if (s[m][i] == nlstate+1) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             if(agedc[i]>0)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
               if(moisdc[i]!=99 && andc[i]!=9999)                if (m<lastpass) {
               agev[m][i]=agedc[i];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             else {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               if (andc[i]!=9999){                }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                
               agev[m][i]=-1;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
               }                  dateintsum=dateintsum+k2;
             }                  k2cpt++;
           }                }
           else if(s[m][i] !=9){ /* Should no more exist */                /*}*/
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            }
             if(mint[m][i]==99 || anint[m][i]==9999)          }
               agev[m][i]=1;        }
             else if(agev[m][i] <agemin){         
               agemin=agev[m][i];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  fprintf(ficresp, "#Local time at start: %s", strstart);
             }        if  (cptcovn>0) {
             else if(agev[m][i] >agemax){          fprintf(ficresp, "\n#********** Variable "); 
               agemax=agev[m][i];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          fprintf(ficresp, "**********\n#");
             }        }
             /*agev[m][i]=anint[m][i]-annais[i];*/        for(i=1; i<=nlstate;i++) 
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           }        fprintf(ficresp, "\n");
           else { /* =9 */        
             agev[m][i]=1;        for(i=iagemin; i <= iagemax+3; i++){
             s[m][i]=-1;          if(i==iagemax+3){
           }            fprintf(ficlog,"Total");
         }          }else{
         else /*= 0 Unknown */            if(first==1){
           agev[m][i]=1;              first=0;
       }              printf("See log file for details...\n");
                }
     }            fprintf(ficlog,"Age %d", i);
     for (i=1; i<=imx; i++)  {          }
       for(m=1; (m<= maxwav); m++){          for(jk=1; jk <=nlstate ; jk++){
         if (s[m][i] > (nlstate+ndeath)) {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
           printf("Error: Wrong value in nlstate or ndeath\n");                pp[jk] += freq[jk][m][i]; 
           goto end;          }
         }          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_vector(severity,1,maxwav);              }
     free_imatrix(outcome,1,maxwav+1,1,n);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_vector(moisnais,1,n);            }else{
     free_vector(annais,1,n);              if(first==1)
     free_matrix(mint,1,maxwav,1,n);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_matrix(anint,1,maxwav,1,n);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_vector(moisdc,1,n);            }
     free_vector(andc,1,n);          }
   
              for(jk=1; jk <=nlstate ; jk++){
     wav=ivector(1,imx);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              pp[jk] += freq[jk][m][i];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          }       
              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     /* Concatenates waves */            pos += pp[jk];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            posprop += prop[jk][i];
           }
           for(jk=1; jk <=nlstate ; jk++){
       Tcode=ivector(1,100);            if(pos>=1.e-5){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              if(first==1)
       ncodemax[1]=1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  }else{
    codtab=imatrix(1,100,1,10);              if(first==1)
    h=0;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    m=pow(2,cptcoveff);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
              }
    for(k=1;k<=cptcoveff; k++){            if( i <= iagemax){
      for(i=1; i <=(m/pow(2,k));i++){              if(pos>=1.e-5){
        for(j=1; j <= ncodemax[k]; j++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
            h++;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
            if (h>m) h=1;codtab[h][k]=j;              }
          }              else
        }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
      }            }
    }          }
           
           for(jk=-1; jk <=nlstate+ndeath; jk++)
    /*for(i=1; i <=m ;i++){            for(m=-1; m <=nlstate+ndeath; m++)
      for(k=1; k <=cptcovn; k++){              if(freq[jk][m][i] !=0 ) {
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);              if(first==1)
      }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      printf("\n");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
    }              }
    scanf("%d",i);*/          if(i <= iagemax)
                fprintf(ficresp,"\n");
    /* Calculates basic frequencies. Computes observed prevalence at single age          if(first==1)
        and prints on file fileres'p'. */            printf("Others in log...\n");
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);          fprintf(ficlog,"\n");
         }
     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 */    dateintmean=dateintsum/k2cpt; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fclose(ficresp);
        free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     /* For Powell, parameters are in a vector p[] starting at p[1]    free_vector(pp,1,nlstate);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    /* End of Freq */
   }
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  /************ Prevalence ********************/
     }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
      {  
     /*--------- results files --------------*/    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);       in each health status at the date of interview (if between dateprev1 and dateprev2).
           We still use firstpass and lastpass as another selection.
    jk=1;    */
    fprintf(ficres,"# Parameters\n");   
    printf("# Parameters\n");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    for(i=1,jk=1; i <=nlstate; i++){    double ***freq; /* Frequencies */
      for(k=1; k <=(nlstate+ndeath); k++){    double *pp, **prop;
        if (k != i)    double pos,posprop; 
          {    double  y2; /* in fractional years */
            printf("%d%d ",i,k);    int iagemin, iagemax;
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    iagemin= (int) agemin;
              printf("%f ",p[jk]);    iagemax= (int) agemax;
              fprintf(ficres,"%f ",p[jk]);    /*pp=vector(1,nlstate);*/
              jk++;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
            }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
            printf("\n");    j1=0;
            fprintf(ficres,"\n");    
          }    j=cptcoveff;
      }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    }    
  if(mle==1){    for(k1=1; k1<=j;k1++){
     /* Computing hessian and covariance matrix */      for(i1=1; i1<=ncodemax[k1];i1++){
     ftolhess=ftol; /* Usually correct */        j1++;
     hesscov(matcov, p, npar, delti, ftolhess, func);        
  }        for (i=1; i<=nlstate; i++)  
     fprintf(ficres,"# Scales\n");          for(m=iagemin; m <= iagemax+3; m++)
     printf("# Scales\n");            prop[i][m]=0.0;
      for(i=1,jk=1; i <=nlstate; i++){       
       for(j=1; j <=nlstate+ndeath; j++){        for (i=1; i<=imx; i++) { /* Each individual */
         if (j!=i) {          bool=1;
           fprintf(ficres,"%1d%1d",i,j);          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]]) 
             printf(" %.5e",delti[jk]);                bool=0;
             fprintf(ficres," %.5e",delti[jk]);          } 
             jk++;          if (bool==1) { 
           }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           printf("\n");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           fprintf(ficres,"\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                    if (s[m][i]>0 && s[m][i]<=nlstate) { 
     k=1;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     fprintf(ficres,"# Covariance\n");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     printf("# Covariance\n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
     for(i=1;i<=npar;i++){                } 
       /*  if (k>nlstate) k=1;              }
       i1=(i-1)/(ncovmodel*nlstate)+1;            } /* end selection of waves */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          }
       printf("%s%d%d",alph[k],i1,tab[i]);*/        }
       fprintf(ficres,"%3d",i);        for(i=iagemin; i <= iagemax+3; i++){  
       printf("%3d",i);          
       for(j=1; j<=i;j++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         fprintf(ficres," %.5e",matcov[i][j]);            posprop += prop[jk][i]; 
         printf(" %.5e",matcov[i][j]);          } 
       }  
       fprintf(ficres,"\n");          for(jk=1; jk <=nlstate ; jk++){     
       printf("\n");            if( i <=  iagemax){ 
       k++;              if(posprop>=1.e-5){ 
     }                probs[i][jk][j1]= prop[jk][i]/posprop;
                  } 
     while((c=getc(ficpar))=='#' && c!= EOF){            } 
       ungetc(c,ficpar);          }/* end jk */ 
       fgets(line, MAXLINE, ficpar);        }/* end i */ 
       puts(line);      } /* end i1 */
       fputs(line,ficparo);    } /* end k1 */
     }    
     ungetc(c,ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      }  /* End of prevalence */
     if (fage <= 2) {  
       bage = agemin;  /************* Waves Concatenation ***************/
       fage = agemax;  
     }  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)
   {
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 /*------------ gnuplot -------------*/       and mw[mi+1][i]. dh depends on stepm.
 chdir(pathcd);       */
   if((ficgp=fopen("graph.plt","w"))==NULL) {  
     printf("Problem with file graph.gp");goto end;    int i, mi, m;
   }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 #ifdef windows       double sum=0., jmean=0.;*/
   fprintf(ficgp,"cd \"%s\" \n",pathc);    int first;
 #endif    int j, k=0,jk, ju, jl;
 m=pow(2,cptcoveff);    double sum=0.;
      first=0;
  /* 1eme*/    jmin=1e+5;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    jmax=-1;
    for (k1=1; k1<= m ; k1 ++) {    jmean=0.;
     for(i=1; i<=imx; i++){
 #ifdef windows      mi=0;
     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);      m=firstpass;
 #endif      while(s[m][i] <= nlstate){
 #ifdef unix        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          mw[++mi][i]=m;
 #endif        if(m >=lastpass)
           break;
 for (i=1; i<= nlstate ; i ++) {        else
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          m++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }/* end while */
 }      if (s[m][i] > nlstate){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        mi++;     /* Death is another wave */
     for (i=1; i<= nlstate ; i ++) {        /* if(mi==0)  never been interviewed correctly before death */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           /* Only death is a correct wave */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        mw[mi][i]=m;
 }      }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {      wav[i]=mi;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      if(mi==0){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        nbwarn++;
 }          if(first==0){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 #ifdef unix          first=1;
 fprintf(ficgp,"\nset ter gif small size 400,300");        }
 #endif        if(first==1){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
    }        }
   }      } /* end mi==0 */
   /*2 eme*/    } /* End individuals */
   
   for (k1=1; k1<= m ; k1 ++) {    for(i=1; i<=imx; i++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      for(mi=1; mi<wav[i];mi++){
            if (stepm <=0)
     for (i=1; i<= nlstate+1 ; i ++) {          dh[mi][i]=1;
       k=2*i;        else{
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       for (j=1; j<= nlstate+1 ; j ++) {            if (agedc[i] < 2*AGESUP) {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(j==0) j=1;  /* Survives at least one month after exam */
 }                else if(j<0){
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                nberr++;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                j=1; /* Temporary Dangerous patch */
       for (j=1; j<= nlstate+1 ; j ++) {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                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]);
         else fprintf(ficgp," \%%*lf (\%%*lf)");                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);
 }                }
       fprintf(ficgp,"\" t\"\" w l 0,");              k=k+1;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              if (j >= jmax){
       for (j=1; j<= nlstate+1 ; j ++) {                jmax=j;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                ijmax=i;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              }
 }                if (j <= jmin){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                jmin=j;
       else fprintf(ficgp,"\" t\"\" w l 0,");                ijmin=i;
     }              }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);              sum=sum+j;
   }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   /*3eme*/            }
           }
   for (k1=1; k1<= m ; k1 ++) {          else{
     for (cpt=1; cpt<= nlstate ; cpt ++) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       k=2+nlstate*(cpt-1);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {            k=k+1;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);            if (j >= jmax) {
       }              jmax=j;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              ijmax=i;
     }            }
   }            else if (j <= jmin){
                jmin=j;
   /* CV preval stat */              ijmin=i;
   for (k1=1; k1<= m ; k1 ++) {            }
     for (cpt=1; cpt<nlstate ; cpt ++) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       k=3;            /*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]);*/
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);            if(j<0){
       for (i=1; i< nlstate ; i ++)              nberr++;
         fprintf(ficgp,"+$%d",k+i+1);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              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]);
                  }
       l=3+(nlstate+ndeath)*cpt;            sum=sum+j;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          }
       for (i=1; i< nlstate ; i ++) {          jk= j/stepm;
         l=3+(nlstate+ndeath)*cpt;          jl= j -jk*stepm;
         fprintf(ficgp,"+$%d",l+i+1);          ju= j -(jk+1)*stepm;
       }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              if(jl==0){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              dh[mi][i]=jk;
     }              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
   /* proba elementaires */              dh[mi][i]=jk+1;
    for(i=1,jk=1; i <=nlstate; i++){              bh[mi][i]=ju;
     for(k=1; k <=(nlstate+ndeath); k++){            }
       if (k != i) {          }else{
         for(j=1; j <=ncovmodel; j++){            if(jl <= -ju){
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/              dh[mi][i]=jk;
           /*fprintf(ficgp,"%s",alph[1]);*/              bh[mi][i]=jl;       /* bias is positive if real duration
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                                   * is higher than the multiple of stepm and negative otherwise.
           jk++;                                   */
           fprintf(ficgp,"\n");            }
         }            else{
       }              dh[mi][i]=jk+1;
     }              bh[mi][i]=ju;
     }            }
             if(dh[mi][i]==0){
   for(jk=1; jk <=m; jk++) {              dh[mi][i]=1; /* At least one step */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);              bh[mi][i]=ju; /* At least one step */
    i=1;              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
    for(k2=1; k2<=nlstate; k2++) {            }
      k3=i;          } /* end if mle */
      for(k=1; k<=(nlstate+ndeath); k++) {        }
        if (k != k2){      } /* end wave */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    }
 ij=1;    jmean=sum/k;
         for(j=3; j <=ncovmodel; j++) {    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);   }
             ij++;  
           }  /*********** Tricode ****************************/
           else  void tricode(int *Tvar, int **nbcode, int imx)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  {
         }    
           fprintf(ficgp,")/(1");    int Ndum[20],ij=1, k, j, i, maxncov=19;
            int cptcode=0;
         for(k1=1; k1 <=nlstate; k1++){      cptcoveff=0; 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);   
 ij=1;    for (k=0; k<maxncov; k++) Ndum[k]=0;
           for(j=3; j <=ncovmodel; j++){    for (k=1; k<=7; k++) ncodemax[k]=0;
           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]]]);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
             ij++;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           }                                 modality*/ 
           else        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        Ndum[ij]++; /*store the modality */
           }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           fprintf(ficgp,")");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         }                                         Tvar[j]. If V=sex and male is 0 and 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                                         female is 1, then  cptcode=1.*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      }
         i=i+ncovmodel;  
        }      for (i=0; i<=cptcode; i++) {
      }        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(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
   }      ij=1; 
          for (i=1; i<=ncodemax[j]; i++) {
   fclose(ficgp);        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
 chdir(path);            nbcode[Tvar[j]][ij]=k; 
     free_matrix(agev,1,maxwav,1,imx);            /* 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; */
     free_ivector(wav,1,imx);            
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            ij++;
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          }
              if (ij > ncodemax[j]) break; 
     free_imatrix(s,1,maxwav+1,1,n);        }  
          } 
        }  
     free_ivector(num,1,n);  
     free_vector(agedc,1,n);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     free_vector(weight,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/   for (i=1; i<=ncovmodel-2; i++) { 
     fclose(ficparo);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     fclose(ficres);     ij=Tvar[i];
     /*  }*/     Ndum[ij]++;
       }
    /*________fin mle=1_________*/  
       ij=1;
    for (i=1; i<= maxncov; i++) {
       if((Ndum[i]!=0) && (i<=ncovcol)){
     /* No more information from the sample is required now */       Tvaraff[ij]=i; /*For printing */
   /* Reads comments: lines beginning with '#' */       ij++;
   while((c=getc(ficpar))=='#' && c!= EOF){     }
     ungetc(c,ficpar);   }
     fgets(line, MAXLINE, ficpar);   
     puts(line);   cptcoveff=ij-1; /*Number of simple covariates*/
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  /*********** Health Expectancies ****************/
    
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  {
 /*--------- index.htm --------*/    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   strcpy(optionfilehtm,optionfile);    double age, agelim, hf;
   strcat(optionfilehtm,".htm");    double ***p3mat,***varhe;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    double **dnewm,**doldm;
     printf("Problem with %s \n",optionfilehtm);goto end;    double *xp;
   }    double **gp, **gm;
     double ***gradg, ***trgradg;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">    int theta;
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  
 Total number of observations=%d <br>    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    xp=vector(1,npar);
 <hr  size=\"2\" color=\"#EC5E5E\">    dnewm=matrix(1,nlstate*nlstate,1,npar);
 <li>Outputs files<br><br>\n    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    fprintf(ficreseij,"# Local time at start: %s", strstart);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    fprintf(ficreseij,"# Health expectancies\n");
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    fprintf(ficreseij,"# Age");
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for(i=1; i<=nlstate;i++)
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      for(j=1; j<=nlstate;j++)
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        fprintf(ficreseij," %1d-%1d (SE)",i,j);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    fprintf(ficreseij,"\n");
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
     if(estepm < stepm){
  fprintf(fichtm," <li>Graphs</li><p>");      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
  m=cptcoveff;    else  hstepm=estepm;   
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
  j1=0;     * if stepm=24 months pijx are given only every 2 years and by summing them
  for(k1=1; k1<=m;k1++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
    for(i1=1; i1<=ncodemax[k1];i1++){     * progression in between and thus overestimating or underestimating according
        j1++;     * to the curvature of the survival function. If, for the same date, we 
        if (cptcovn > 0) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");     * to compare the new estimate of Life expectancy with the same linear 
          for (cpt=1; cpt<=cptcoveff;cpt++)     * hypothesis. A more precise result, taking into account a more precise
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);     * curvature will be obtained if estepm is as small as stepm. */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }    /* For example we decided to compute the life expectancy with the smallest unit */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);           nhstepm is the number of hstepm from age to agelim 
        for(cpt=1; cpt<nlstate;cpt++){       nstepm is the number of stepm from age to agelin. 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>       Look at hpijx to understand the reason of that which relies in memory size
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       and note for a fixed period like estepm months */
        }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(cpt=1; cpt<=nlstate;cpt++) {       survival function given by stepm (the optimization length). Unfortunately it
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       means that if the survival funtion is printed only each two years of age and if
 interval) in state (%d): v%s%d%d.gif <br>       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);         results. So we changed our mind and took the option of the best precision.
      }    */
      for(cpt=1; cpt<=nlstate;cpt++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    agelim=AGESUP;
      }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      /* nhstepm age range expressed in number of stepm */
 health expectancies in states (1) and (2): e%s%d.gif<br>      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 fprintf(fichtm,"\n</body>");      /* if (stepm >= YEARM) hstepm=1;*/
    }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fclose(fichtm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       gp=matrix(0,nhstepm,1,nlstate*nlstate);
   /*--------------- Prevalence limit --------------*/      gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
   strcpy(filerespl,"pl");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   strcat(filerespl,fileres);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;   
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");      /* Computing  Variances of health expectancies */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");       for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ 
   prlim=matrix(1,nlstate,1,nlstate);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        cptj=0;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1; j<= nlstate; j++){
   k=0;          for(i=1; i<=nlstate; i++){
   agebase=agemin;            cptj=cptj+1;
   agelim=agemax;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   ftolpl=1.e-10;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   i1=cptcoveff;            }
   if (cptcovn < 1){i1=1;}          }
         }
   for(cptcov=1;cptcov<=i1;cptcov++){       
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       
         k=k+1;        for(i=1; i<=npar; i++) 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficrespl,"\n#******");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         for(j=1;j<=cptcoveff;j++)        
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        cptj=0;
         fprintf(ficrespl,"******\n");        for(j=1; j<= nlstate; j++){
                  for(i=1;i<=nlstate;i++){
         for (age=agebase; age<=agelim; age++){            cptj=cptj+1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           fprintf(ficrespl," %.5f", prlim[i][i]);            }
           fprintf(ficrespl,"\n");          }
         }        }
       }        for(j=1; j<= nlstate*nlstate; j++)
     }          for(h=0; h<=nhstepm-1; h++){
   fclose(ficrespl);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   /*------------- h Pij x at various ages ------------*/          }
         } 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);     
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /* End theta */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   printf("Computing pij: result on file '%s' \n", filerespij);  
         for(h=0; h<=nhstepm-1; h++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=1; j<=nlstate*nlstate;j++)
   if (stepm<=24) stepsize=2;          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   agelim=AGESUP;       
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       for(i=1;i<=nlstate*nlstate;i++)
          for(j=1;j<=nlstate*nlstate;j++)
   k=0;          varhe[i][j][(int)age] =0.;
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       printf("%d|",(int)age);fflush(stdout);
       k=k+1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         fprintf(ficrespij,"\n#****** ");       for(h=0;h<=nhstepm-1;h++){
         for(j=1;j<=cptcoveff;j++)        for(k=0;k<=nhstepm-1;k++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         fprintf(ficrespij,"******\n");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
                  for(i=1;i<=nlstate*nlstate;i++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            for(j=1;j<=nlstate*nlstate;j++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           oldm=oldms;savm=savms;      /* Computing expectancies */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(i=1; i<=nlstate;i++)
           fprintf(ficrespij,"# Age");        for(j=1; j<=nlstate;j++)
           for(i=1; i<=nlstate;i++)          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             for(j=1; j<=nlstate+ndeath;j++)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               fprintf(ficrespij," %1d-%1d",i,j);            
           fprintf(ficrespij,"\n");  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          }
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)      fprintf(ficreseij,"%3.0f",age );
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      cptj=0;
             fprintf(ficrespij,"\n");      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          cptj++;
           fprintf(ficrespij,"\n");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         }        }
     }      fprintf(ficreseij,"\n");
   }     
       free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   fclose(ficrespij);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   /*---------- Health expectancies and variances ------------*/      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(filerest,"t");    }
   strcat(filerest,fileres);    printf("\n");
   if((ficrest=fopen(filerest,"w"))==NULL) {    fprintf(ficlog,"\n");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }    free_vector(xp,1,npar);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    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);
   strcpy(filerese,"e");  }
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {  /************ Variance ******************/
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  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[])
   }  {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
  strcpy(fileresv,"v");    /* double **newm;*/
   strcat(fileresv,fileres);    double **dnewm,**doldm;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    double **dnewmp,**doldmp;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    int i, j, nhstepm, hstepm, h, nstepm ;
   }    int k, cptcode;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double *xp;
     double **gp, **gm;  /* for var eij */
   k=0;    double ***gradg, ***trgradg; /*for var eij */
   for(cptcov=1;cptcov<=i1;cptcov++){    double **gradgp, **trgradgp; /* for var p point j */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double *gpp, *gmp; /* for var p point j */
       k=k+1;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       fprintf(ficrest,"\n#****** ");    double ***p3mat;
       for(j=1;j<=cptcoveff;j++)    double age,agelim, hf;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***mobaverage;
       fprintf(ficrest,"******\n");    int theta;
     char digit[4];
       fprintf(ficreseij,"\n#****** ");    char digitp[25];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    char fileresprobmorprev[FILENAMELENGTH];
       fprintf(ficreseij,"******\n");  
     if(popbased==1){
       fprintf(ficresvij,"\n#****** ");      if(mobilav!=0)
       for(j=1;j<=cptcoveff;j++)        strcpy(digitp,"-populbased-mobilav-");
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      else strcpy(digitp,"-populbased-nomobil-");
       fprintf(ficresvij,"******\n");    }
     else 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      strcpy(digitp,"-stablbased-");
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      if (mobilav!=0) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       oldm=oldms;savm=savms;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
              printf(" Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    }
       fprintf(ficrest,"\n");  
            strcpy(fileresprobmorprev,"prmorprev"); 
       hf=1;    sprintf(digit,"%-d",ij);
       if (stepm >= YEARM) hf=stepm/YEARM;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       epj=vector(1,nlstate+1);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       for(age=bage; age <=fage ;age++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    strcat(fileresprobmorprev,fileres);
         fprintf(ficrest," %.0f",age);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    }
           }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           epj[nlstate+1] +=epj[j];   
         }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
           for(j=1;j <=nlstate;j++)    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
             vepp += vareij[i][j][(int)age];    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         for(j=1;j <=nlstate;j++){      fprintf(ficresprobmorprev," p.%-d SE",j);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      for(i=1; i<=nlstate;i++)
         }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         fprintf(ficrest,"\n");    }  
       }    fprintf(ficresprobmorprev,"\n");
     }    fprintf(ficgp,"\n# Routine varevsij");
   }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
            fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
  fclose(ficreseij);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  fclose(ficresvij);  /*   } */
   fclose(ficrest);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fclose(ficpar);   fprintf(ficresvij, "#Local time at start: %s", strstart);
   free_vector(epj,1,nlstate+1);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   /*  scanf("%d ",i); */    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   /*------- Variance limit prevalence------*/        for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
 strcpy(fileresvpl,"vpl");    fprintf(ficresvij,"\n");
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    xp=vector(1,npar);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    dnewm=matrix(1,nlstate,1,npar);
     exit(0);    doldm=matrix(1,nlstate,1,nlstate);
   }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
  k=0;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  for(cptcov=1;cptcov<=i1;cptcov++){    gpp=vector(nlstate+1,nlstate+ndeath);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    gmp=vector(nlstate+1,nlstate+ndeath);
      k=k+1;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      fprintf(ficresvpl,"\n#****** ");    
      for(j=1;j<=cptcoveff;j++)    if(estepm < stepm){
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf ("Problem %d lower than %d\n",estepm, stepm);
      fprintf(ficresvpl,"******\n");    }
          else  hstepm=estepm;   
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    /* For example we decided to compute the life expectancy with the smallest unit */
      oldm=oldms;savm=savms;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       nhstepm is the number of hstepm from age to agelim 
    }       nstepm is the number of stepm from age to agelin. 
  }       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   fclose(ficresvpl);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   /*---------- End : free ----------------*/       means that if the survival funtion is printed every two years of age and if
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       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.
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
   free_matrix(matcov,1,npar,1,npar);      gm=matrix(0,nhstepm,1,nlstate);
   free_vector(delti,1,npar);  
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   printf("End of Imach\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        }
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /* 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);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/        if (popbased==1) {
           if(mobilav ==0){
  end:            for(i=1; i<=nlstate;i++)
 #ifdef windows              prlim[i][i]=probs[(int)age][i][ij];
  chdir(pathcd);          }else{ /* mobilav */ 
 #endif            for(i=1; i<=nlstate;i++)
  /*system("wgnuplot graph.plt");*/              prlim[i][i]=mobaverage[(int)age][i][ij];
  /*system("../gp37mgw/wgnuplot graph.plt");*/          }
  /*system("cd ../gp37mgw");*/        }
  system("..\\gp37mgw\\wgnuplot graph.plt");    
         for(j=1; j<= nlstate; j++){
 #ifdef windows          for(h=0; h<=nhstepm; h++){
   while (z[0] != 'q') {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     chdir(pathcd);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          }
     scanf("%s",z);        }
     if (z[0] == 'c') system("./imach");        /* This for computing probability of death (h=1 means
     else if (z[0] == 'e') {           computed over hstepm matrices product = hstepm*stepm months) 
       chdir(path);           as a weighted average of prlim.
       system(optionfilehtm);        */
     }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     else if (z[0] == 'q') exit(0);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
 #endif        }    
 }        /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficresprob, "#Local time at start: %s", strstart);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# 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_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       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 */
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%swgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.11  
changed lines
  Added in v.1.111

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