Diff for /imach/src/imach.c between versions 1.30 and 1.103

version 1.30, 2002/03/08 16:17:18 version 1.103, 2005/09/30 15:54:49
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.103  2005/09/30 15:54:49  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.102  2004/09/15 17:31:30  brouard
   first survey ("cross") where individuals from different ages are    Add the possibility to read data file including tab characters.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.101  2004/09/15 10:38:38  brouard
   second wave of interviews ("longitudinal") which measure each change    Fix on curr_time
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.100  2004/07/12 18:29:06  brouard
   model. More health states you consider, more time is necessary to reach the    Add version for Mac OS X. Just define UNIX in Makefile
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.99  2004/06/05 08:57:40  brouard
   probabibility to be observed in state j at the second wave    *** empty log message ***
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.98  2004/05/16 15:05:56  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    New version 0.97 . First attempt to estimate force of mortality
   complex model than "constant and age", you should modify the program    directly from the data i.e. without the need of knowing the health
   where the markup *Covariates have to be included here again* invites    state at each age, but using a Gompertz model: log u =a + b*age .
   you to do it.  More covariates you add, slower the    This is the basic analysis of mortality and should be done before any
   convergence.    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
   The advantage of this computer programme, compared to a simple    from other sources like vital statistic data.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    The same imach parameter file can be used but the option for mle should be -3.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    The output is very simple: only an estimate of the intercept and of
   split into an exact number (nh*stepm) of unobserved intermediate    the slope with 95% confident intervals.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Current limitations:
   matrix is simply the matrix product of nh*stepm elementary matrices    A) Even if you enter covariates, i.e. with the
   and the contribution of each individual to the likelihood is simply    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   hPijx.    B) There is no computation of Life Expectancy nor Life Table.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.97  2004/02/20 13:25:42  lievre
   of the life expectancies. It also computes the prevalence limits.    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.96  2003/07/15 15:38:55  brouard
   This software have been partly granted by Euro-REVES, a concerted action    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   from the European Union.    rewritten within the same printf. Workaround: many printfs.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.95  2003/07/08 07:54:34  brouard
   can be accessed at http://euroreves.ined.fr/imach .    * imach.c (Repository):
   **********************************************************************/    (Repository): Using imachwizard code to output a more meaningful covariance
      matrix (cov(a12,c31) instead of numbers.
 #include <math.h>  
 #include <stdio.h>    Revision 1.94  2003/06/27 13:00:02  brouard
 #include <stdlib.h>    Just cleaning
 #include <unistd.h>  
     Revision 1.93  2003/06/25 16:33:55  brouard
 #define MAXLINE 256    (Module): On windows (cygwin) function asctime_r doesn't
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    exist so I changed back to asctime which exists.
 #define FILENAMELENGTH 80    (Module): Version 0.96b
 /*#define DEBUG*/  
 #define windows    Revision 1.92  2003/06/25 16:30:45  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): On windows (cygwin) function asctime_r doesn't
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    exist so I changed back to asctime which exists.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.91  2003/06/25 15:30:29  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 #define NINTERVMAX 8    helps to forecast when convergence will be reached. Elapsed time
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    is stamped in powell.  We created a new html file for the graphs
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    concerning matrix of covariance. It has extension -cov.htm.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.90  2003/06/24 12:34:15  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Some bugs corrected for windows. Also, when
 #define AGESUP 130    mle=-1 a template is output in file "or"mypar.txt with the design
 #define AGEBASE 40    of the covariance matrix to be input.
   
     Revision 1.89  2003/06/24 12:30:52  brouard
 int erreur; /* Error number */    (Module): Some bugs corrected for windows. Also, when
 int nvar;    mle=-1 a template is output in file "or"mypar.txt with the design
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    of the covariance matrix to be input.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.88  2003/06/23 17:54:56  brouard
 int ndeath=1; /* Number of dead states */    * 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.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.86  2003/06/17 20:04:08  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Change position of html and gnuplot routines and added
 int mle, weightopt;    routine fileappend.
 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 1.85  2003/06/17 13:12:43  brouard
 double jmean; /* Mean space between 2 waves */    * imach.c (Repository): Check when date of death was earlier that
 double **oldm, **newm, **savm; /* Working pointers to matrices */    current date of interview. It may happen when the death was just
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    prior to the death. In this case, dh was negative and likelihood
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    was wrong (infinity). We still send an "Error" but patch by
 FILE *ficgp,*ficresprob,*ficpop;    assuming that the date of death was just one stepm after the
 FILE *ficreseij;    interview.
   char filerese[FILENAMELENGTH];    (Repository): Because some people have very long ID (first column)
  FILE  *ficresvij;    we changed int to long in num[] and we added a new lvector for
   char fileresv[FILENAMELENGTH];    memory allocation. But we also truncated to 8 characters (left
  FILE  *ficresvpl;    truncation)
   char fileresvpl[FILENAMELENGTH];    (Repository): No more line truncation errors.
   
 #define NR_END 1    Revision 1.84  2003/06/13 21:44:43  brouard
 #define FREE_ARG char*    * imach.c (Repository): Replace "freqsummary" at a correct
 #define FTOL 1.0e-10    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 #define NRANSI    parcimony.
 #define ITMAX 200    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 #define TOL 2.0e-4    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.82  2003/06/05 15:57:20  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Add log in  imach.c and  fullversion number is now printed.
   
 #define GOLD 1.618034  */
 #define GLIMIT 100.0  /*
 #define TINY 1.0e-20     Interpolated Markov Chain
   
 static double maxarg1,maxarg2;    Short summary of the programme:
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    This program computes Healthy Life Expectancies from
      cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    first survey ("cross") where individuals from different ages are
 #define rint(a) floor(a+0.5)    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 static double sqrarg;    second wave of interviews ("longitudinal") which measure each change
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (if any) in individual health status.  Health expectancies are
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 int imx;    Maximum Likelihood of the parameters involved in the model.  The
 int stepm;    simplest model is the multinomial logistic model where pij is the
 /* Stepm, step in month: minimum step interpolation*/    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 int m,nb;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    'age' is age and 'sex' is a covariate. If you want to have a more
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    complex model than "constant and age", you should modify the program
 double **pmmij, ***probs, ***mobaverage;    where the markup *Covariates have to be included here again* invites
 double dateintmean=0;    you to do it.  More covariates you add, slower the
     convergence.
 double *weight;  
 int **s; /* Status */    The advantage of this computer programme, compared to a simple
 double *agedc, **covar, idx;    multinomial logistic model, is clear when the delay between waves is not
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    account using an interpolation or extrapolation.  
 double ftolhess; /* Tolerance for computing hessian */  
     hPijx is the probability to be observed in state i at age x+h
 /**************** split *************************/    conditional to the observed state i at age x. The delay 'h' can be
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    split into an exact number (nh*stepm) of unobserved intermediate
 {    states. This elementary transition (by month, quarter,
    char *s;                             /* pointer */    semester or year) is modelled as a multinomial logistic.  The hPx
    int  l1, l2;                         /* length counters */    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
    l1 = strlen( path );                 /* length of path */    hPijx.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Also this programme outputs the covariance matrix of the parameters but also
    s = strrchr( path, '\\' );           /* find last / */    of the life expectancies. It also computes the stable prevalence. 
 #else    
    s = strrchr( path, '/' );            /* find last / */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #endif             Institut national d'études démographiques, Paris.
    if ( s == NULL ) {                   /* no directory, so use current */    This software have been partly granted by Euro-REVES, a concerted action
 #if     defined(__bsd__)                /* get current working directory */    from the European Union.
       extern char       *getwd( );    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
       if ( getwd( dirc ) == NULL ) {    can be accessed at http://euroreves.ined.fr/imach .
 #else  
       extern char       *getcwd( );    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    
 #endif    **********************************************************************/
          return( GLOCK_ERROR_GETCWD );  /*
       }    main
       strcpy( name, path );             /* we've got it */    read parameterfile
    } else {                             /* strip direcotry from path */    read datafile
       s++;                              /* after this, the filename */    concatwav
       l2 = strlen( s );                 /* length of filename */    freqsummary
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    if (mle >= 1)
       strcpy( name, s );                /* save file name */      mlikeli
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    print results files
       dirc[l1-l2] = 0;                  /* add zero */    if mle==1 
    }       computes hessian
    l1 = strlen( dirc );                 /* length of directory */    read end of parameter file: agemin, agemax, bage, fage, estepm
 #ifdef windows        begin-prev-date,...
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    open gnuplot file
 #else    open html file
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    stable prevalence
 #endif     for age prevalim()
    s = strrchr( name, '.' );            /* find last / */    h Pij x
    s++;    variance of p varprob
    strcpy(ext,s);                       /* save extension */    forecasting if prevfcast==1 prevforecast call prevalence()
    l1= strlen( name);    health expectancies
    l2= strlen( s)+1;    Variance-covariance of DFLE
    strncpy( finame, name, l1-l2);    prevalence()
    finame[l1-l2]= 0;     movingaverage()
    return( 0 );                         /* we're done */    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
     Variance of stable prevalence
 /******************************************/   end
   */
 void replace(char *s, char*t)  
 {  
   int i;  
   int lg=20;   
   i=0;  #include <math.h>
   lg=strlen(t);  #include <stdio.h>
   for(i=0; i<= lg; i++) {  #include <stdlib.h>
     (s[i] = t[i]);  #include <unistd.h>
     if (t[i]== '\\') s[i]='/';  
   }  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 int nbocc(char *s, char occ)  
 {  /* #include <libintl.h> */
   int i,j=0;  /* #define _(String) gettext (String) */
   int lg=20;  
   i=0;  #define MAXLINE 256
   lg=strlen(s);  #define GNUPLOTPROGRAM "gnuplot"
   for(i=0; i<= lg; i++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   if  (s[i] == occ ) j++;  #define FILENAMELENGTH 132
   }  /*#define DEBUG*/
   return j;  /*#define windows*/
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 void cutv(char *u,char *v, char*t, char occ)  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   int i,lg,j,p=0;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  #define NINTERVMAX 8
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
   lg=strlen(t);  #define MAXN 20000
   for(j=0; j<p; j++) {  #define YEARM 12. /* Number of months per year */
     (u[j] = t[j]);  #define AGESUP 130
   }  #define AGEBASE 40
      u[p]='\0';  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
    for(j=0; j<= lg; j++) {  #define DIRSEPARATOR '/'
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define ODIRSEPARATOR '\\'
   }  #else
 }  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 /********************** nrerror ********************/  #endif
   
 void nrerror(char error_text[])  /* $Id$ */
 {  /* $State$ */
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
   exit(1);  char fullversion[]="$Revision$ $Date$"; 
 }  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 /*********************** vector *******************/  int nvar;
 double *vector(int nl, int nh)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 {  int npar=NPARMAX;
   double *v;  int nlstate=2; /* Number of live states */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int ndeath=1; /* Number of dead states */
   if (!v) nrerror("allocation failure in vector");  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   return v-nl+NR_END;  int popbased=0;
 }  
   int *wav; /* Number of waves for this individuual 0 is possible */
 /************************ free vector ******************/  int maxwav; /* Maxim number of waves */
 void free_vector(double*v, int nl, int nh)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   free((FREE_ARG)(v+nl-NR_END));                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /************************ivector *******************************/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int *ivector(long nl,long nh)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   int *v;  double jmean; /* Mean space between 2 waves */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  double **oldm, **newm, **savm; /* Working pointers to matrices */
   if (!v) nrerror("allocation failure in ivector");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   return v-nl+NR_END;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 }  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
 /******************free ivector **************************/  double fretone; /* Only one call to likelihood */
 void free_ivector(int *v, long nl, long nh)  long ipmx; /* Number of contributions */
 {  double sw; /* Sum of weights */
   free((FREE_ARG)(v+nl-NR_END));  char filerespow[FILENAMELENGTH];
 }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 /******************* imatrix *******************************/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  FILE *ficresprobmorprev;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  FILE *fichtm, *fichtmcov; /* Html File */
 {  FILE *ficreseij;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  char filerese[FILENAMELENGTH];
   int **m;  FILE  *ficresvij;
    char fileresv[FILENAMELENGTH];
   /* allocate pointers to rows */  FILE  *ficresvpl;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  char fileresvpl[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  char title[MAXLINE];
   m += NR_END;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   m -= nrl;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
    char command[FILENAMELENGTH];
   /* allocate rows and set pointers to them */  int  outcmd=0;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  char filelog[FILENAMELENGTH]; /* Log file */
    char filerest[FILENAMELENGTH];
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  char fileregp[FILENAMELENGTH];
    char popfile[FILENAMELENGTH];
   /* return pointer to array of pointers to rows */  
   return m;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /****************** free_imatrix *************************/  struct timezone tzp;
 void free_imatrix(m,nrl,nrh,ncl,nch)  extern int gettimeofday();
       int **m;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       long nch,ncl,nrh,nrl;  long time_value;
      /* free an int matrix allocated by imatrix() */  extern long time();
 {  char strcurr[80], strfor[80];
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  #define NR_END 1
 }  #define FREE_ARG char*
   #define FTOL 1.0e-10
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define NRANSI 
 {  #define ITMAX 200 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  #define TOL 2.0e-4 
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define CGOLD 0.3819660 
   if (!m) nrerror("allocation failure 1 in matrix()");  #define ZEPS 1.0e-10 
   m += NR_END;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   m -= nrl;  
   #define GOLD 1.618034 
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define GLIMIT 100.0 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define TINY 1.0e-20 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   return m;    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   free((FREE_ARG)(m+nrl-NR_END));  int agegomp= AGEGOMP;
 }  
   int imx; 
 /******************* ma3x *******************************/  int stepm=1;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /* Stepm, step in month: minimum step interpolation*/
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int estepm;
   double ***m;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int m,nb;
   if (!m) nrerror("allocation failure 1 in matrix()");  long *num;
   m += NR_END;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   m -= nrl;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  double *ageexmed,*agecens;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double dateintmean=0;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  double *weight;
   int **s; /* Status */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   m[nrl][ncl] += NR_END;  double ftolhess; /* Tolerance for computing hessian */
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  /**************** split *************************/
     m[nrl][j]=m[nrl][j-1]+nlay;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    {
   for (i=nrl+1; i<=nrh; i++) {    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     for (j=ncl+1; j<=nch; j++)    */ 
       m[i][j]=m[i][j-1]+nlay;    char  *ss;                            /* pointer */
   }    int   l1, l2;                         /* length counters */
   return m;  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /*************************free ma3x ************************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if ( ss == NULL ) {                   /* no directory, so use current */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      /* get current working directory */
   free((FREE_ARG)(m+nrl-NR_END));      /*    extern  char* getcwd ( char *buf , int len);*/
 }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 /***************** f1dim *************************/      }
 extern int ncom;      strcpy( name, path );               /* we've got it */
 extern double *pcom,*xicom;    } else {                              /* strip direcotry from path */
 extern double (*nrfunc)(double []);      ss++;                               /* after this, the filename */
        l2 = strlen( ss );                  /* length of filename */
 double f1dim(double x)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   int j;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double f;      dirc[l1-l2] = 0;                    /* add zero */
   double *xt;    }
      l1 = strlen( dirc );                  /* length of directory */
   xt=vector(1,ncom);    /*#ifdef windows
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   f=(*nrfunc)(xt);  #else
   free_vector(xt,1,ncom);    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   return f;  #endif
 }    */
     ss = strrchr( name, '.' );            /* find last / */
 /*****************brent *************************/    if (ss >0){
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)      ss++;
 {      strcpy(ext,ss);                     /* save extension */
   int iter;      l1= strlen( name);
   double a,b,d,etemp;      l2= strlen(ss)+1;
   double fu,fv,fw,fx;      strncpy( finame, name, l1-l2);
   double ftemp;      finame[l1-l2]= 0;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    }
   double e=0.0;    return( 0 );                          /* we're done */
    }
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  /******************************************/
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  void replace_back_to_slash(char *s, char*t)
     xm=0.5*(a+b);  {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    int i;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    int lg=0;
     printf(".");fflush(stdout);    i=0;
 #ifdef DEBUG    lg=strlen(t);
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    for(i=0; i<= lg; i++) {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      (s[i] = t[i]);
 #endif      if (t[i]== '\\') s[i]='/';
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    }
       *xmin=x;  }
       return fx;  
     }  int nbocc(char *s, char occ)
     ftemp=fu;  {
     if (fabs(e) > tol1) {    int i,j=0;
       r=(x-w)*(fx-fv);    int lg=20;
       q=(x-v)*(fx-fw);    i=0;
       p=(x-v)*q-(x-w)*r;    lg=strlen(s);
       q=2.0*(q-r);    for(i=0; i<= lg; i++) {
       if (q > 0.0) p = -p;    if  (s[i] == occ ) j++;
       q=fabs(q);    }
       etemp=e;    return j;
       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));  void cutv(char *u,char *v, char*t, char occ)
       else {  {
         d=p/q;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         u=x+d;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
         if (u-a < tol2 || b-u < tol2)       gives u="abcedf" and v="ghi2j" */
           d=SIGN(tol1,xm-x);    int i,lg,j,p=0;
       }    i=0;
     } else {    for(j=0; j<=strlen(t)-1; j++) {
       d=CGOLD*(e=(x >= xm ? a-x : b-x));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }    }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    lg=strlen(t);
     if (fu <= fx) {    for(j=0; j<p; j++) {
       if (u >= x) a=x; else b=x;      (u[j] = t[j]);
       SHFT(v,w,x,u)    }
         SHFT(fv,fw,fx,fu)       u[p]='\0';
         } else {  
           if (u < x) a=u; else b=u;     for(j=0; j<= lg; j++) {
           if (fu <= fw || w == x) {      if (j>=(p+1))(v[j-p-1] = t[j]);
             v=w;    }
             w=u;  }
             fv=fw;  
             fw=fu;  /********************** nrerror ********************/
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  void nrerror(char error_text[])
             fv=fu;  {
           }    fprintf(stderr,"ERREUR ...\n");
         }    fprintf(stderr,"%s\n",error_text);
   }    exit(EXIT_FAILURE);
   nrerror("Too many iterations in brent");  }
   *xmin=x;  /*********************** vector *******************/
   return fx;  double *vector(int nl, int nh)
 }  {
     double *v;
 /****************** mnbrak ***********************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    return v-nl+NR_END;
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  /************************ free vector ******************/
   double fu;  void free_vector(double*v, int nl, int nh)
    {
   *fa=(*func)(*ax);    free((FREE_ARG)(v+nl-NR_END));
   *fb=(*func)(*bx);  }
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  /************************ivector *******************************/
       SHFT(dum,*fb,*fa,dum)  int *ivector(long nl,long nh)
       }  {
   *cx=(*bx)+GOLD*(*bx-*ax);    int *v;
   *fc=(*func)(*cx);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   while (*fb > *fc) {    if (!v) nrerror("allocation failure in ivector");
     r=(*bx-*ax)*(*fb-*fc);    return v-nl+NR_END;
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /******************free ivector **************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  void free_ivector(int *v, long nl, long nh)
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    free((FREE_ARG)(v+nl-NR_END));
     } else if ((*cx-u)*(u-ulim) > 0.0) {  }
       fu=(*func)(u);  
       if (fu < *fc) {  /************************lvector *******************************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  long *lvector(long nl,long nh)
           SHFT(*fb,*fc,fu,(*func)(u))  {
           }    long *v;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       u=ulim;    if (!v) nrerror("allocation failure in ivector");
       fu=(*func)(u);    return v-nl+NR_END;
     } else {  }
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  /******************free lvector **************************/
     }  void free_lvector(long *v, long nl, long nh)
     SHFT(*ax,*bx,*cx,u)  {
       SHFT(*fa,*fb,*fc,fu)    free((FREE_ARG)(v+nl-NR_END));
       }  }
 }  
   /******************* imatrix *******************************/
 /*************** linmin ************************/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 int ncom;  { 
 double *pcom,*xicom;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 double (*nrfunc)(double []);    int **m; 
      
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    /* allocate pointers to rows */ 
 {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double brent(double ax, double bx, double cx,    if (!m) nrerror("allocation failure 1 in matrix()"); 
                double (*f)(double), double tol, double *xmin);    m += NR_END; 
   double f1dim(double x);    m -= nrl; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    
               double *fc, double (*func)(double));    
   int j;    /* allocate rows and set pointers to them */ 
   double xx,xmin,bx,ax;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double fx,fb,fa;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
      m[nrl] += NR_END; 
   ncom=n;    m[nrl] -= ncl; 
   pcom=vector(1,n);    
   xicom=vector(1,n);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   nrfunc=func;    
   for (j=1;j<=n;j++) {    /* return pointer to array of pointers to rows */ 
     pcom[j]=p[j];    return m; 
     xicom[j]=xi[j];  } 
   }  
   ax=0.0;  /****************** free_imatrix *************************/
   xx=1.0;  void free_imatrix(m,nrl,nrh,ncl,nch)
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);        int **m;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        long nch,ncl,nrh,nrl; 
 #ifdef DEBUG       /* free an int matrix allocated by imatrix() */ 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  { 
 #endif    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for (j=1;j<=n;j++) {    free((FREE_ARG) (m+nrl-NR_END)); 
     xi[j] *= xmin;  } 
     p[j] += xi[j];  
   }  /******************* matrix *******************************/
   free_vector(xicom,1,n);  double **matrix(long nrl, long nrh, long ncl, long nch)
   free_vector(pcom,1,n);  {
 }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
             double (*func)(double []))    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   void linmin(double p[], double xi[], int n, double *fret,    m -= nrl;
               double (*func)(double []));  
   int i,ibig,j;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double del,t,*pt,*ptt,*xit;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double fp,fptt;    m[nrl] += NR_END;
   double *xits;    m[nrl] -= ncl;
   pt=vector(1,n);  
   ptt=vector(1,n);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   xit=vector(1,n);    return m;
   xits=vector(1,n);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   *fret=(*func)(p);     */
   for (j=1;j<=n;j++) pt[j]=p[j];  }
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /*************************free matrix ************************/
     ibig=0;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     del=0.0;  {
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for (i=1;i<=n;i++)    free((FREE_ARG)(m+nrl-NR_END));
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  /******************* ma3x *******************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       fptt=(*fret);  {
 #ifdef DEBUG    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       printf("fret=%lf \n",*fret);    double ***m;
 #endif  
       printf("%d",i);fflush(stdout);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       linmin(p,xit,n,fret,func);    if (!m) nrerror("allocation failure 1 in matrix()");
       if (fabs(fptt-(*fret)) > del) {    m += NR_END;
         del=fabs(fptt-(*fret));    m -= nrl;
         ibig=i;  
       }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       printf("%d %.12e",i,(*fret));    m[nrl] += NR_END;
       for (j=1;j<=n;j++) {    m[nrl] -= ncl;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
       for(j=1;j<=n;j++)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         printf(" p=%.12e",p[j]);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       printf("\n");    m[nrl][ncl] += NR_END;
 #endif    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      m[nrl][j]=m[nrl][j-1]+nlay;
 #ifdef DEBUG    
       int k[2],l;    for (i=nrl+1; i<=nrh; i++) {
       k[0]=1;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       k[1]=-1;      for (j=ncl+1; j<=nch; j++) 
       printf("Max: %.12e",(*func)(p));        m[i][j]=m[i][j-1]+nlay;
       for (j=1;j<=n;j++)    }
         printf(" %.12e",p[j]);    return m; 
       printf("\n");    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       for(l=0;l<=1;l++) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         for (j=1;j<=n;j++) {    */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  }
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  /*************************free ma3x ************************/
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       }  {
 #endif    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
       free_vector(xit,1,n);  }
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  /*************** function subdirf ***********/
       free_vector(pt,1,n);  char *subdirf(char fileres[])
       return;  {
     }    /* Caution optionfilefiname is hidden */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    strcpy(tmpout,optionfilefiname);
     for (j=1;j<=n;j++) {    strcat(tmpout,"/"); /* Add to the right */
       ptt[j]=2.0*p[j]-pt[j];    strcat(tmpout,fileres);
       xit[j]=p[j]-pt[j];    return tmpout;
       pt[j]=p[j];  }
     }  
     fptt=(*func)(ptt);  /*************** function subdirf2 ***********/
     if (fptt < fp) {  char *subdirf2(char fileres[], char *preop)
       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);    /* Caution optionfilefiname is hidden */
         for (j=1;j<=n;j++) {    strcpy(tmpout,optionfilefiname);
           xi[j][ibig]=xi[j][n];    strcat(tmpout,"/");
           xi[j][n]=xit[j];    strcat(tmpout,preop);
         }    strcat(tmpout,fileres);
 #ifdef DEBUG    return tmpout;
         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++)  
           printf(" %.12e",xit[j]);  /*************** function subdirf3 ***********/
         printf("\n");  char *subdirf3(char fileres[], char *preop, char *preop2)
 #endif  {
       }    
     }    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/");
     strcat(tmpout,preop);
 /**** Prevalence limit ****************/    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    return tmpout;
 {  }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /***************** f1dim *************************/
   extern int ncom; 
   int i, ii,j,k;  extern double *pcom,*xicom;
   double min, max, maxmin, maxmax,sumnew=0.;  extern double (*nrfunc)(double []); 
   double **matprod2();   
   double **out, cov[NCOVMAX], **pmij();  double f1dim(double x) 
   double **newm;  { 
   double agefin, delaymax=50 ; /* Max number of years to converge */    int j; 
     double f;
   for (ii=1;ii<=nlstate+ndeath;ii++)    double *xt; 
     for (j=1;j<=nlstate+ndeath;j++){   
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
    cov[1]=1.;    free_vector(xt,1,ncom); 
      return f; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  } 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  /*****************brent *************************/
     /* Covariates have to be included here again */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
      cov[2]=agefin;  { 
      int iter; 
       for (k=1; k<=cptcovn;k++) {    double a,b,d,etemp;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double fu,fv,fw,fx;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    double ftemp;
       }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (k=1; k<=cptcovage;k++)    double e=0.0; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];   
       for (k=1; k<=cptcovprod;k++)    a=(ax < cx ? ax : cx); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    fw=fv=fx=(*f)(x); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     savm=oldm;      printf(".");fflush(stdout);
     oldm=newm;      fprintf(ficlog,".");fflush(ficlog);
     maxmax=0.;  #ifdef DEBUG
     for(j=1;j<=nlstate;j++){      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);
       min=1.;      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);
       max=0.;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for(i=1; i<=nlstate; i++) {  #endif
         sumnew=0;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        *xmin=x; 
         prlim[i][j]= newm[i][j]/(1-sumnew);        return fx; 
         max=FMAX(max,prlim[i][j]);      } 
         min=FMIN(min,prlim[i][j]);      ftemp=fu;
       }      if (fabs(e) > tol1) { 
       maxmin=max-min;        r=(x-w)*(fx-fv); 
       maxmax=FMAX(maxmax,maxmin);        q=(x-v)*(fx-fw); 
     }        p=(x-v)*q-(x-w)*r; 
     if(maxmax < ftolpl){        q=2.0*(q-r); 
       return prlim;        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
   }        etemp=e; 
 }        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 /*************** transition probabilities ***************/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )          d=p/q; 
 {          u=x+d; 
   double s1, s2;          if (u-a < tol2 || b-u < tol2) 
   /*double t34;*/            d=SIGN(tol1,xm-x); 
   int i,j,j1, nc, ii, jj;        } 
       } else { 
     for(i=1; i<= nlstate; i++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(j=1; j<i;j++){      } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         /*s2 += param[i][j][nc]*cov[nc];*/      fu=(*f)(u); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if (fu <= fx) { 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        if (u >= x) a=x; else b=x; 
       }        SHFT(v,w,x,u) 
       ps[i][j]=s2;          SHFT(fv,fw,fx,fu) 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          } else { 
     }            if (u < x) a=u; else b=u; 
     for(j=i+1; j<=nlstate+ndeath;j++){            if (fu <= fw || w == x) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){              v=w; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];              w=u; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/              fv=fw; 
       }              fw=fu; 
       ps[i][j]=s2;            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
   }              fv=fu; 
     /*ps[3][2]=1;*/            } 
           } 
   for(i=1; i<= nlstate; i++){    } 
      s1=0;    nrerror("Too many iterations in brent"); 
     for(j=1; j<i; j++)    *xmin=x; 
       s1+=exp(ps[i][j]);    return fx; 
     for(j=i+1; j<=nlstate+ndeath; j++)  } 
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  /****************** mnbrak ***********************/
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for(j=i+1; j<=nlstate+ndeath; j++)              double (*func)(double)) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    double ulim,u,r,q, dum;
   } /* end i */    double fu; 
    
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    *fa=(*func)(*ax); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    *fb=(*func)(*bx); 
       ps[ii][jj]=0;    if (*fb > *fa) { 
       ps[ii][ii]=1;      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
   }        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    while (*fb > *fc) { 
     for(jj=1; jj<= nlstate+ndeath; jj++){      r=(*bx-*ax)*(*fb-*fc); 
      printf("%lf ",ps[ii][jj]);      q=(*bx-*cx)*(*fb-*fa); 
    }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     printf("\n ");        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     printf("\n ");printf("%lf ",cov[2]);*/      if ((*bx-u)*(u-*cx) > 0.0) { 
 /*        fu=(*func)(u); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   goto end;*/        fu=(*func)(u); 
     return ps;        if (fu < *fc) { 
 }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 /**************** Product of 2 matrices ******************/            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        u=ulim; 
 {        fu=(*func)(u); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      } else { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        u=(*cx)+GOLD*(*cx-*bx); 
   /* in, b, out are matrice of pointers which should have been initialized        fu=(*func)(u); 
      before: only the contents of out is modified. The function returns      } 
      a pointer to pointers identical to out */      SHFT(*ax,*bx,*cx,u) 
   long i, j, k;        SHFT(*fa,*fb,*fc,fu) 
   for(i=nrl; i<= nrh; i++)        } 
     for(k=ncolol; k<=ncoloh; k++)  } 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /*************** linmin ************************/
   
   return out;  int ncom; 
 }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
    
 /************* Higher Matrix Product ***************/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    double brent(double ax, double bx, double cx, 
 {                 double (*f)(double), double tol, double *xmin); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    double f1dim(double x); 
      duration (i.e. until    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.                double *fc, double (*func)(double)); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    int j; 
      (typically every 2 years instead of every month which is too big).    double xx,xmin,bx,ax; 
      Model is determined by parameters x and covariates have to be    double fx,fb,fa;
      included manually here.   
     ncom=n; 
      */    pcom=vector(1,n); 
     xicom=vector(1,n); 
   int i, j, d, h, k;    nrfunc=func; 
   double **out, cov[NCOVMAX];    for (j=1;j<=n;j++) { 
   double **newm;      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   /* Hstepm could be zero and should return the unit matrix */    } 
   for (i=1;i<=nlstate+ndeath;i++)    ax=0.0; 
     for (j=1;j<=nlstate+ndeath;j++){    xx=1.0; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for(h=1; h <=nhstepm; h++){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(d=1; d <=hstepm; d++){  #endif
       newm=savm;    for (j=1;j<=n;j++) { 
       /* Covariates have to be included here again */      xi[j] *= xmin; 
       cov[1]=1.;      p[j] += xi[j]; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free_vector(xicom,1,n); 
       for (k=1; k<=cptcovage;k++)    free_vector(pcom,1,n); 
         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]]];  char *asc_diff_time(long time_sec, char ascdiff[])
   {
     long sec_left, days, hours, minutes;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    days = (time_sec) / (60*60*24);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    sec_left = (time_sec) % (60*60*24);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    hours = (sec_left) / (60*60) ;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    sec_left = (sec_left) %(60*60);
       savm=oldm;    minutes = (sec_left) /60;
       oldm=newm;    sec_left = (sec_left) % (60);
     }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for(i=1; i<=nlstate+ndeath; i++)    return ascdiff;
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /*************** powell ************************/
          */  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       }              double (*func)(double [])) 
   } /* end h */  { 
   return po;    void linmin(double p[], double xi[], int n, double *fret, 
 }                double (*func)(double [])); 
     int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 /*************** log-likelihood *************/    double fp,fptt;
 double func( double *x)    double *xits;
 {    int niterf, itmp;
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    pt=vector(1,n); 
   double **out;    ptt=vector(1,n); 
   double sw; /* Sum of weights */    xit=vector(1,n); 
   double lli; /* Individual log likelihood */    xits=vector(1,n); 
   long ipmx;    *fret=(*func)(p); 
   /*extern weight */    for (j=1;j<=n;j++) pt[j]=p[j]; 
   /* We are differentiating ll according to initial status */    for (*iter=1;;++(*iter)) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      fp=(*fret); 
   /*for(i=1;i<imx;i++)      ibig=0; 
     printf(" %d\n",s[4][i]);      del=0.0; 
   */      last_time=curr_time;
   cov[1]=1.;      (void) gettimeofday(&curr_time,&tzp);
       printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   for(k=1; k<=nlstate; k++) ll[k]=0.;      /*    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);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      */
     for(mi=1; mi<= wav[i]-1; mi++){     for (i=1;i<=n;i++) {
       for (ii=1;ii<=nlstate+ndeath;ii++)        printf(" %d %.12f",i, p[i]);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fprintf(ficlog," %d %.12lf",i, p[i]);
       for(d=0; d<dh[mi][i]; d++){        fprintf(ficrespow," %.12lf", p[i]);
         newm=savm;      }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      printf("\n");
         for (kk=1; kk<=cptcovage;kk++) {      fprintf(ficlog,"\n");
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      fprintf(ficrespow,"\n");fflush(ficrespow);
         }      if(*iter <=3){
                tm = *localtime(&curr_time.tv_sec);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        strcpy(strcurr,asctime(&tm));
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*       asctime_r(&tm,strcurr); */
         savm=oldm;        forecast_time=curr_time; 
         oldm=newm;        itmp = strlen(strcurr);
                if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                  strcurr[itmp-1]='\0';
       } /* end mult */        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
              fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        for(niterf=10;niterf<=30;niterf+=10){
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       ipmx +=1;          tmf = *localtime(&forecast_time.tv_sec);
       sw += weight[i];  /*      asctime_r(&tmf,strfor); */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          strcpy(strfor,asctime(&tmf));
     } /* end of wave */          itmp = strlen(strfor);
   } /* end of individual */          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          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("l1=%f l2=%f ",ll[1],ll[2]); */          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        }
   return -l;      }
 }      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
 /*********** Maximum Likelihood Estimation ***************/  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        fprintf(ficlog,"fret=%lf \n",*fret);
 {  #endif
   int i,j, iter;        printf("%d",i);fflush(stdout);
   double **xi,*delti;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double fret;        linmin(p,xit,n,fret,func); 
   xi=matrix(1,npar,1,npar);        if (fabs(fptt-(*fret)) > del) { 
   for (i=1;i<=npar;i++)          del=fabs(fptt-(*fret)); 
     for (j=1;j<=npar;j++)          ibig=i; 
       xi[i][j]=(i==j ? 1.0 : 0.0);        } 
   printf("Powell\n");  #ifdef DEBUG
   powell(p,xi,npar,ftol,&iter,&fret,func);        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        for (j=1;j<=n;j++) {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          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]);
         }
 /**** Computes Hessian and covariance matrix ***/        for(j=1;j<=n;j++) {
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          printf(" p=%.12e",p[j]);
 {          fprintf(ficlog," p=%.12e",p[j]);
   double  **a,**y,*x,pd;        }
   double **hess;        printf("\n");
   int i, j,jk;        fprintf(ficlog,"\n");
   int *indx;  #endif
       } 
   double hessii(double p[], double delta, int theta, double delti[]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double hessij(double p[], double delti[], int i, int j);  #ifdef DEBUG
   void lubksb(double **a, int npar, int *indx, double b[]) ;        int k[2],l;
   void ludcmp(double **a, int npar, int *indx, double *d) ;        k[0]=1;
         k[1]=-1;
   hess=matrix(1,npar,1,npar);        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   printf("\nCalculation of the hessian matrix. Wait...\n");        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++){          printf(" %.12e",p[j]);
     printf("%d",i);fflush(stdout);          fprintf(ficlog," %.12e",p[j]);
     hess[i][i]=hessii(p,ftolhess,i,delti);        }
     /*printf(" %f ",p[i]);*/        printf("\n");
     /*printf(" %lf ",hess[i][i]);*/        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
            for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for (j=1;j<=npar;j++)  {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       if (j>i) {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         printf(".%d%d",i,j);fflush(stdout);          }
         hess[i][j]=hessij(p,delti,i,j);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         hess[j][i]=hess[i][j];              fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         /*printf(" %lf ",hess[i][j]);*/        }
       }  #endif
     }  
   }  
   printf("\n");        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
   a=matrix(1,npar,1,npar);        return; 
   y=matrix(1,npar,1,npar);      } 
   x=vector(1,npar);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   indx=ivector(1,npar);      for (j=1;j<=n;j++) { 
   for (i=1;i<=npar;i++)        ptt[j]=2.0*p[j]-pt[j]; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        xit[j]=p[j]-pt[j]; 
   ludcmp(a,npar,indx,&pd);        pt[j]=p[j]; 
       } 
   for (j=1;j<=npar;j++) {      fptt=(*func)(ptt); 
     for (i=1;i<=npar;i++) x[i]=0;      if (fptt < fp) { 
     x[j]=1;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     lubksb(a,npar,indx,x);        if (t < 0.0) { 
     for (i=1;i<=npar;i++){          linmin(p,xit,n,fret,func); 
       matcov[i][j]=x[i];          for (j=1;j<=n;j++) { 
     }            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
           }
   printf("\n#Hessian matrix#\n");  #ifdef DEBUG
   for (i=1;i<=npar;i++) {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (j=1;j<=npar;j++) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       printf("%.3e ",hess[i][j]);          for(j=1;j<=n;j++){
     }            printf(" %.12e",xit[j]);
     printf("\n");            fprintf(ficlog," %.12e",xit[j]);
   }          }
           printf("\n");
   /* Recompute Inverse */          fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        }
   ludcmp(a,npar,indx,&pd);      } 
     } 
   /*  printf("\n#Hessian matrix recomputed#\n");  } 
   
   for (j=1;j<=npar;j++) {  /**** Prevalence limit (stable prevalence)  ****************/
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       y[i][j]=x[i];       matrix by transitions matrix until convergence is reached */
       printf("%.3e ",y[i][j]);  
     }    int i, ii,j,k;
     printf("\n");    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
   */    double **out, cov[NCOVMAX], **pmij();
     double **newm;
   free_matrix(a,1,npar,1,npar);    double agefin, delaymax=50 ; /* Max number of years to converge */
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);    for (ii=1;ii<=nlstate+ndeath;ii++)
   free_ivector(indx,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   free_matrix(hess,1,npar,1,npar);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   
 }     cov[1]=1.;
    
 /*************** hessian matrix ****************/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 double hessii( double x[], double delta, int theta, double delti[])    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {      newm=savm;
   int i;      /* Covariates have to be included here again */
   int l=1, lmax=20;       cov[2]=agefin;
   double k1,k2;    
   double p2[NPARMAX+1];        for (k=1; k<=cptcovn;k++) {
   double res;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          /*      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]]);*/
   double fx;        }
   int k=0,kmax=10;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double l1;        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]]];
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for(l=0 ; l <=lmax; l++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     l1=pow(10,l);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     delts=delt;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);      savm=oldm;
       p2[theta]=x[theta] +delt;      oldm=newm;
       k1=func(p2)-fx;      maxmax=0.;
       p2[theta]=x[theta]-delt;      for(j=1;j<=nlstate;j++){
       k2=func(p2)-fx;        min=1.;
       /*res= (k1-2.0*fx+k2)/delt/delt; */        max=0.;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        for(i=1; i<=nlstate; i++) {
                sumnew=0;
 #ifdef DEBUG          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+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);          prlim[i][j]= newm[i][j]/(1-sumnew);
 #endif          max=FMAX(max,prlim[i][j]);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          min=FMIN(min,prlim[i][j]);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        }
         k=kmax;        maxmin=max-min;
       }        maxmax=FMAX(maxmax,maxmin);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      }
         k=kmax; l=lmax*10.;      if(maxmax < ftolpl){
       }        return prlim;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      }
         delts=delt;    }
       }  }
     }  
   }  /*************** transition probabilities ***************/ 
   delti[theta]=delts;  
   return res;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    {
 }    double s1, s2;
     /*double t34;*/
 double hessij( double x[], double delti[], int thetai,int thetaj)    int i,j,j1, nc, ii, jj;
 {  
   int i;      for(i=1; i<= nlstate; i++){
   int l=1, l1, lmax=20;        for(j=1; j<i;j++){
   double k1,k2,k3,k4,res,fx;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double p2[NPARMAX+1];            /*s2 += param[i][j][nc]*cov[nc];*/
   int k;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   fx=func(x);          }
   for (k=1; k<=2; k++) {          ps[i][j]=s2;
     for (i=1;i<=npar;i++) p2[i]=x[i];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(j=i+1; j<=nlstate+ndeath;j++){
     k1=func(p2)-fx;          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];
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          }
     k2=func(p2)-fx;          ps[i][j]=s2;
          }
     p2[thetai]=x[thetai]-delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      /*ps[3][2]=1;*/
     k3=func(p2)-fx;      
        for(i=1; i<= nlstate; i++){
     p2[thetai]=x[thetai]-delti[thetai]/k;        s1=0;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(j=1; j<i; j++)
     k4=func(p2)-fx;          s1+=exp(ps[i][j]);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        for(j=i+1; j<=nlstate+ndeath; j++)
 #ifdef DEBUG          s1+=exp(ps[i][j]);
     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);        ps[i][i]=1./(s1+1.);
 #endif        for(j=1; j<i; j++)
   }          ps[i][j]= exp(ps[i][j])*ps[i][i];
   return res;        for(j=i+1; j<=nlstate+ndeath; j++)
 }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 /************** Inverse of matrix **************/      } /* end i */
 void ludcmp(double **a, int n, int *indx, double *d)      
 {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   int i,imax,j,k;        for(jj=1; jj<= nlstate+ndeath; jj++){
   double big,dum,sum,temp;          ps[ii][jj]=0;
   double *vv;          ps[ii][ii]=1;
          }
   vv=vector(1,n);      }
   *d=1.0;      
   for (i=1;i<=n;i++) {  
     big=0.0;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     for (j=1;j<=n;j++)  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*         printf("ddd %lf ",ps[ii][jj]); */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  /*       } */
     vv[i]=1.0/big;  /*       printf("\n "); */
   }  /*        } */
   for (j=1;j<=n;j++) {  /*        printf("\n ");printf("%lf ",cov[2]); */
     for (i=1;i<j;i++) {         /*
       sum=a[i][j];        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        goto end;*/
       a[i][j]=sum;      return ps;
     }  }
     big=0.0;  
     for (i=j;i<=n;i++) {  /**************** Product of 2 matrices ******************/
       sum=a[i][j];  
       for (k=1;k<j;k++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         sum -= a[i][k]*a[k][j];  {
       a[i][j]=sum;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       if ( (dum=vv[i]*fabs(sum)) >= big) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         big=dum;    /* in, b, out are matrice of pointers which should have been initialized 
         imax=i;       before: only the contents of out is modified. The function returns
       }       a pointer to pointers identical to out */
     }    long i, j, k;
     if (j != imax) {    for(i=nrl; i<= nrh; i++)
       for (k=1;k<=n;k++) {      for(k=ncolol; k<=ncoloh; k++)
         dum=a[imax][k];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         a[imax][k]=a[j][k];          out[i][k] +=in[i][j]*b[j][k];
         a[j][k]=dum;  
       }    return out;
       *d = -(*d);  }
       vv[imax]=vv[j];  
     }  
     indx[j]=imax;  /************* Higher Matrix Product ***************/
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       dum=1.0/(a[j][j]);  {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    /* Computes the transition matrix starting at age 'age' over 
     }       'nhstepm*hstepm*stepm' months (i.e. until
   }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   free_vector(vv,1,n);  /* Doesn't work */       nhstepm*hstepm matrices. 
 ;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 }       (typically every 2 years instead of every month which is too big 
        for the memory).
 void lubksb(double **a, int n, int *indx, double b[])       Model is determined by parameters x and covariates have to be 
 {       included manually here. 
   int i,ii=0,ip,j;  
   double sum;       */
    
   for (i=1;i<=n;i++) {    int i, j, d, h, k;
     ip=indx[i];    double **out, cov[NCOVMAX];
     sum=b[ip];    double **newm;
     b[ip]=b[i];  
     if (ii)    /* Hstepm could be zero and should return the unit matrix */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    for (i=1;i<=nlstate+ndeath;i++)
     else if (sum) ii=i;      for (j=1;j<=nlstate+ndeath;j++){
     b[i]=sum;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   }        po[i][j][0]=(i==j ? 1.0 : 0.0);
   for (i=n;i>=1;i--) {      }
     sum=b[i];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    for(h=1; h <=nhstepm; h++){
     b[i]=sum/a[i][i];      for(d=1; d <=hstepm; d++){
   }        newm=savm;
 }        /* Covariates have to be included here again */
         cov[1]=1.;
 /************ Frequencies ********************/        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {  /* Some frequencies */        for (k=1; k<=cptcovage;k++)
            cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        for (k=1; k<=cptcovprod;k++)
   double ***freq; /* Frequencies */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   char fileresp[FILENAMELENGTH];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   pp=vector(1,nlstate);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        savm=oldm;
   strcpy(fileresp,"p");        oldm=newm;
   strcat(fileresp,fileres);      }
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for(i=1; i<=nlstate+ndeath; i++)
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(j=1;j<=nlstate+ndeath;j++) {
     exit(0);          po[i][j][h]=newm[i][j];
   }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           */
   j1=0;        }
     } /* end h */
   j=cptcoveff;    return po;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
   
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  /*************** log-likelihood *************/
        j1++;  double func( double *x)
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  {
          scanf("%d", i);*/    int i, ii, j, k, mi, d, kk;
         for (i=-1; i<=nlstate+ndeath; i++)      double l, ll[NLSTATEMAX], cov[NCOVMAX];
          for (jk=-1; jk<=nlstate+ndeath; jk++)      double **out;
            for(m=agemin; m <= agemax+3; m++)    double sw; /* Sum of weights */
              freq[i][jk][m]=0;    double lli; /* Individual log likelihood */
     int s1, s2;
         dateintsum=0;    double bbh, survp;
         k2cpt=0;    long ipmx;
        for (i=1; i<=imx; i++) {    /*extern weight */
          bool=1;    /* We are differentiating ll according to initial status */
          if  (cptcovn>0) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
            for (z1=1; z1<=cptcoveff; z1++)    /*for(i=1;i<imx;i++) 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      printf(" %d\n",s[4][i]);
                bool=0;    */
          }    cov[1]=1.;
          if (bool==1) {  
            for(m=firstpass; m<=lastpass; m++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
              k2=anint[m][i]+(mint[m][i]/12.);  
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    if(mle==1){
                if(agev[m][i]==0) agev[m][i]=agemax+1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                if(agev[m][i]==1) agev[m][i]=agemax+2;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for(mi=1; mi<= wav[i]-1; mi++){
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            for (j=1;j<=nlstate+ndeath;j++){
                  dateintsum=dateintsum+k2;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                  k2cpt++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }            }
           for(d=0; d<dh[mi][i]; d++){
              }            newm=savm;
            }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          }            for (kk=1; kk<=cptcovage;kk++) {
        }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                    }
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if  (cptcovn>0) {            savm=oldm;
          fprintf(ficresp, "\n#********** Variable ");            oldm=newm;
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          } /* end mult */
        fprintf(ficresp, "**********\n#");        
         }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
        for(i=1; i<=nlstate;i++)          /* But now since version 0.9 we anticipate for bias at large stepm.
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
        fprintf(ficresp, "\n");           * (in months) between two waves is not a multiple of stepm, we rounded to 
                   * the nearest (and in case of equal distance, to the lowest) interval but now
   for(i=(int)agemin; i <= (int)agemax+3; i++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if(i==(int)agemax+3)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       printf("Total");           * 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
       printf("Age %d", i);           * -stepm/2 to stepm/2 .
     for(jk=1; jk <=nlstate ; jk++){           * For stepm=1 the results are the same as for previous versions of Imach.
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * For stepm > 1 the results are less biased than in previous versions. 
         pp[jk] += freq[jk][m][i];           */
     }          s1=s[mw[mi][i]][i];
     for(jk=1; jk <=nlstate ; jk++){          s2=s[mw[mi+1][i]][i];
       for(m=-1, pos=0; m <=0 ; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
         pos += freq[jk][m][i];          /* bias bh is positive if real duration
       if(pp[jk]>=1.e-10)           * is higher than the multiple of stepm and negative otherwise.
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);           */
       else          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          if( s2 > nlstate){ 
     }            /* i.e. if s2 is a death state and if the date of death is known then the contribution
                to the likelihood is the probability to die between last step unit time and current 
      for(jk=1; jk <=nlstate ; jk++){               step unit time, which is also equal to probability to die before dh 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)               minus probability to die before dh-stepm . 
         pp[jk] += freq[jk][m][i];               In version up to 0.92 likelihood was computed
      }          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
     for(jk=1,pos=0; jk <=nlstate ; jk++)          and not the date of a change in health state. The former idea was
       pos += pp[jk];          to consider that at each interview the state was recorded
     for(jk=1; jk <=nlstate ; jk++){          (healthy, disable or death) and IMaCh was corrected; but when we
       if(pos>=1.e-5)          introduced the exact date of death then we should have modified
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          the contribution of an exact death to the likelihood. This new
       else          contribution is smaller and very dependent of the step unit
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          stepm. It is no more the probability to die between last interview
       if( i <= (int) agemax){          and month of death but the probability to survive from last
         if(pos>=1.e-5){          interview up to one month before death multiplied by the
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          probability to die within a month. Thanks to Chris
           probs[i][jk][j1]= pp[jk]/pos;          Jackson for correcting this bug.  Former versions increased
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          mortality artificially. The bad side is that we add another loop
         }          which slows down the processing. The difference can be up to 10%
       else          lower mortality.
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            */
       }            lli=log(out[s1][s2] - savm[s1][s2]);
     }          }else{
     for(jk=-1; jk <=nlstate+ndeath; jk++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(m=-1; m <=nlstate+ndeath; m++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          } 
     if(i <= (int) agemax)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       fprintf(ficresp,"\n");          /*if(lli ==000.0)*/
     printf("\n");          /*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;
   dateintmean=dateintsum/k2cpt;        } /* end of wave */
        } /* end of individual */
   fclose(ficresp);    }  else if(mle==2){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_vector(pp,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   /* End of Freq */          for (ii=1;ii<=nlstate+ndeath;ii++)
 }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Prevalence ********************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            }
 {  /* Some frequencies */          for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***freq; /* Frequencies */            for (kk=1; kk<=cptcovage;kk++) {
   double *pp;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double pos, k2;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   pp=vector(1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            savm=oldm;
              oldm=newm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } /* end mult */
   j1=0;        
            s1=s[mw[mi][i]][i];
   j=cptcoveff;          s2=s[mw[mi+1][i]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          bbh=(double)bh[mi][i]/(double)stepm; 
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
  for(k1=1; k1<=j;k1++){          ipmx +=1;
     for(i1=1; i1<=ncodemax[k1];i1++){          sw += weight[i];
       j1++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
       for (i=-1; i<=nlstate+ndeath; i++)        } /* end of individual */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      }  else if(mle==3){  /* exponential inter-extrapolation */
           for(m=agemin; m <= agemax+3; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             freq[i][jk][m]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
       for (i=1; i<=imx; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         bool=1;            for (j=1;j<=nlstate+ndeath;j++){
         if  (cptcovn>0) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for (z1=1; z1<=cptcoveff; z1++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
               bool=0;          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
         if (bool==1) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=firstpass; m<=lastpass; m++){            for (kk=1; kk<=cptcovage;kk++) {
             k2=anint[m][i]+(mint[m][i]/12.);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            }
               if(agev[m][i]==0) agev[m][i]=agemax+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               if(agev[m][i]==1) agev[m][i]=agemax+2;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            savm=oldm;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            oldm=newm;
             }          } /* end mult */
           }        
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
         for(i=(int)agemin; i <= (int)agemax+3; i++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(jk=1; jk <=nlstate ; jk++){          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          ipmx +=1;
               pp[jk] += freq[jk][m][i];          sw += weight[i];
           }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
             for(m=-1, pos=0; m <=0 ; m++)      } /* end of individual */
             pos += freq[jk][m][i];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(jk=1; jk <=nlstate ; jk++){        for(mi=1; mi<= wav[i]-1; mi++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          for (ii=1;ii<=nlstate+ndeath;ii++)
              pp[jk] += freq[jk][m][i];            for (j=1;j<=nlstate+ndeath;j++){
          }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                        savm[ii][j]=(ii==j ? 1.0 : 0.0);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            }
           for(d=0; d<dh[mi][i]; d++){
          for(jk=1; jk <=nlstate ; jk++){                      newm=savm;
            if( i <= (int) agemax){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              if(pos>=1.e-5){            for (kk=1; kk<=cptcovage;kk++) {
                probs[i][jk][j1]= pp[jk]/pos;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }            }
            }          
          }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                   1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
     }            oldm=newm;
   }          } /* end mult */
          
            s1=s[mw[mi][i]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          s2=s[mw[mi+1][i]][i];
   free_vector(pp,1,nlstate);          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
 }  /* End of Freq */          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 /************* Waves Concatenation ***************/          }
           ipmx +=1;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  /*      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]); */
      Death is a valid wave (if date is known).        } /* end of wave */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      } /* end of individual */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
      and mw[mi+1][i]. dh depends on stepm.      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   int i, mi, m;          for (ii=1;ii<=nlstate+ndeath;ii++)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            for (j=1;j<=nlstate+ndeath;j++){
      double sum=0., jmean=0.;*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int j, k=0,jk, ju, jl;            }
   double sum=0.;          for(d=0; d<dh[mi][i]; d++){
   jmin=1e+5;            newm=savm;
   jmax=-1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   jmean=0.;            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=imx; i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     mi=0;            }
     m=firstpass;          
     while(s[m][i] <= nlstate){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(s[m][i]>=1)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         mw[++mi][i]=m;            savm=oldm;
       if(m >=lastpass)            oldm=newm;
         break;          } /* end mult */
       else        
         m++;          s1=s[mw[mi][i]][i];
     }/* end while */          s2=s[mw[mi+1][i]][i];
     if (s[m][i] > nlstate){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       mi++;     /* Death is another wave */          ipmx +=1;
       /* if(mi==0)  never been interviewed correctly before death */          sw += weight[i];
          /* Only death is a correct wave */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       mw[mi][i]=m;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     }        } /* end of wave */
       } /* end of individual */
     wav[i]=mi;    } /* End of if */
     if(mi==0)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
   for(i=1; i<=imx; i++){  }
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  /*************** log-likelihood *************/
         dh[mi][i]=1;  double funcone( double *x)
       else{  {
         if (s[mw[mi+1][i]][i] > nlstate) {    /* Same as likeli but slower because of a lot of printf and if */
           if (agedc[i] < 2*AGESUP) {    int i, ii, j, k, mi, d, kk;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           if(j==0) j=1;  /* Survives at least one month after exam */    double **out;
           k=k+1;    double lli; /* Individual log likelihood */
           if (j >= jmax) jmax=j;    double llt;
           if (j <= jmin) jmin=j;    int s1, s2;
           sum=sum+j;    double bbh, survp;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    /*extern weight */
           }    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         else{    /*for(i=1;i<imx;i++) 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      printf(" %d\n",s[4][i]);
           k=k+1;    */
           if (j >= jmax) jmax=j;    cov[1]=1.;
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    for(k=1; k<=nlstate; k++) ll[k]=0.;
           sum=sum+j;  
         }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         jk= j/stepm;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         jl= j -jk*stepm;      for(mi=1; mi<= wav[i]-1; mi++){
         ju= j -(jk+1)*stepm;        for (ii=1;ii<=nlstate+ndeath;ii++)
         if(jl <= -ju)          for (j=1;j<=nlstate+ndeath;j++){
           dh[mi][i]=jk;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         else            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=jk+1;          }
         if(dh[mi][i]==0)        for(d=0; d<dh[mi][i]; d++){
           dh[mi][i]=1; /* At least one step */          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];
   jmean=sum/k;          }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*********** Tricode ****************************/          savm=oldm;
 void tricode(int *Tvar, int **nbcode, int imx)          oldm=newm;
 {        } /* end mult */
   int Ndum[20],ij=1, k, j, i;        
   int cptcode=0;        s1=s[mw[mi][i]][i];
   cptcoveff=0;        s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm; 
   for (k=0; k<19; k++) Ndum[k]=0;        /* bias is positive if real duration
   for (k=1; k<=7; k++) ncodemax[k]=0;         * is higher than the multiple of stepm and negative otherwise.
          */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     for (i=1; i<=imx; i++) {          lli=log(out[s1][s2] - savm[s1][s2]);
       ij=(int)(covar[Tvar[j]][i]);        } else if (mle==1){
       Ndum[ij]++;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        } else if(mle==2){
       if (ij > cptcode) cptcode=ij;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     }        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for (i=0; i<=cptcode; i++) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       if(Ndum[i]!=0) ncodemax[j]++;          lli=log(out[s1][s2]); /* Original formula */
     }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     ij=1;          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
         ipmx +=1;
     for (i=1; i<=ncodemax[j]; i++) {        sw += weight[i];
       for (k=0; k<=19; k++) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if (Ndum[k] != 0) {  /*       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]); */
           nbcode[Tvar[j]][ij]=k;        if(globpr){
           ij++;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
         if (ij > ncodemax[j]) break;                  num[i],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,llt=0.,l=0.; k<=nlstate; k++){
   }              llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
  for (k=0; k<19; k++) Ndum[k]=0;          }
           fprintf(ficresilk," %10.6f\n", -llt);
  for (i=1; i<=ncovmodel-2; i++) {        }
       ij=Tvar[i];      } /* end of wave */
       Ndum[ij]++;    } /* end of individual */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  ij=1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  for (i=1; i<=10; i++) {    if(globpr==0){ /* First time we count the contributions and weights */
    if((Ndum[i]!=0) && (i<=ncov)){      gipmx=ipmx;
      Tvaraff[ij]=i;      gsw=sw;
      ij++;    }
    }    return -l;
  }  }
    
     cptcoveff=ij-1;  
 }  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 /*********** Health Expectancies ****************/  {
     /* This routine should help understanding what is done with 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)       the selection of individuals/waves and
 {       to check the exact contribution to the likelihood.
   /* Health expectancies */       Plotting could be done.
   int i, j, nhstepm, hstepm, h;     */
   double age, agelim,hf;    int k;
   double ***p3mat;  
      if(*globpri !=0){ /* Just counts and sums, no printings */
   fprintf(ficreseij,"# Health expectancies\n");      strcpy(fileresilk,"ilk"); 
   fprintf(ficreseij,"# Age");      strcat(fileresilk,fileres);
   for(i=1; i<=nlstate;i++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     for(j=1; j<=nlstate;j++)        printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficreseij," %1d-%1d",i,j);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   fprintf(ficreseij,"\n");      }
       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");
   hstepm=1*YEARM; /*  Every j years of age (in month) */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      /*  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++) 
   agelim=AGESUP;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     /* nhstepm age range expressed in number of stepm */    }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */    *fretone=(*funcone)(p);
     /*if (stepm >= YEARM) hstepm=1;*/    if(*globpri !=0){
 hstepm=1;      fclose(ficresilk);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fflush(fichtm); 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    } 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    return;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    }
 hf=stepm/YEARM;  
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/  
     for(i=1; i<=nlstate;i++)  /*********** Maximum Likelihood Estimation ***************/
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;  {
         }    int i,j, iter;
        double **xi;
     /* hf=1;    double fret;
        if (stepm >= YEARM) hf=stepm/YEARM;*/    double fretone; /* Only one call to likelihood */
 hf=stepm/YEARM;    /*  char filerespow[FILENAMELENGTH];*/
      xi=matrix(1,npar,1,npar);
     fprintf(ficreseij,"%3.0f",age );    for (i=1;i<=npar;i++)
     for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++)
       for(j=1; j<=nlstate;j++){        xi[i][j]=(i==j ? 1.0 : 0.0);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       }    strcpy(filerespow,"pow"); 
     fprintf(ficreseij,"\n");    strcat(filerespow,fileres);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
 /************ Variance ******************/    fprintf(ficrespow,"# Powell\n# iter -2*LL");
 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 (i=1;i<=nlstate;i++)
 {      for(j=1;j<=nlstate+ndeath;j++)
   /* Variance of health expectancies */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficrespow,"\n");
   double **newm;  
   double **dnewm,**doldm;    powell(p,xi,npar,ftol,&iter,&fret,func);
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;    fclose(ficrespow);
   double *xp;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   double **gp, **gm;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double ***gradg, ***trgradg;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double ***p3mat;  
   double age,agelim;  }
   int theta;  
   /**** Computes Hessian and covariance matrix ***/
    fprintf(ficresvij,"# Covariances of life expectancies\n");  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   fprintf(ficresvij,"# Age");  {
   for(i=1; i<=nlstate;i++)    double  **a,**y,*x,pd;
     for(j=1; j<=nlstate;j++)    double **hess;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int i, j,jk;
   fprintf(ficresvij,"\n");    int *indx;
   
   xp=vector(1,npar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   dnewm=matrix(1,nlstate,1,npar);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   doldm=matrix(1,nlstate,1,nlstate);    void lubksb(double **a, int npar, int *indx, double b[]) ;
      void ludcmp(double **a, int npar, int *indx, double *d) ;
   hstepm=1*YEARM; /* Every year of age */    double gompertz(double p[]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    hess=matrix(1,npar,1,npar);
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    printf("\nCalculation of the hessian matrix. Wait...\n");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     if (stepm >= YEARM) hstepm=1;    for (i=1;i<=npar;i++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      printf("%d",i);fflush(stdout);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficlog,"%d",i);fflush(ficlog);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);     
     gp=matrix(0,nhstepm,1,nlstate);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     gm=matrix(0,nhstepm,1,nlstate);      
       /*  printf(" %f ",p[i]);
     for(theta=1; theta <=npar; theta++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       for(i=1; i<=npar; i++){ /* Computes gradient */    }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    
       }    for (i=1;i<=npar;i++) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (j=1;j<=npar;j++)  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
       if (popbased==1) {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for(i=1; i<=nlstate;i++)          hess[i][j]=hessij(p,delti,i,j,func,npar);
           prlim[i][i]=probs[(int)age][i][ij];          
       }          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
       for(j=1; j<= nlstate; j++){        }
         for(h=0; h<=nhstepm; h++){      }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    printf("\n");
         }    fprintf(ficlog,"\n");
       }  
        printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(i=1; i<=npar; i++) /* Computes gradient */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      a=matrix(1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    y=matrix(1,npar,1,npar);
      x=vector(1,npar);
       if (popbased==1) {    indx=ivector(1,npar);
         for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++)
           prlim[i][i]=probs[(int)age][i][ij];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
   
       for(j=1; j<= nlstate; j++){    for (j=1;j<=npar;j++) {
         for(h=0; h<=nhstepm; h++){      for (i=1;i<=npar;i++) x[i]=0;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      x[j]=1;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
       }        matcov[i][j]=x[i];
       }
       for(j=1; j<= nlstate; j++)    }
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
     } /* End theta */    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
     for(h=0; h<=nhstepm; h++)      }
       for(j=1; j<=nlstate;j++)      printf("\n");
         for(theta=1; theta <=npar; theta++)      fprintf(ficlog,"\n");
           trgradg[h][j][theta]=gradg[h][theta][j];    }
   
     for(i=1;i<=nlstate;i++)    /* Recompute Inverse */
       for(j=1;j<=nlstate;j++)    for (i=1;i<=npar;i++)
         vareij[i][j][(int)age] =0.;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     for(h=0;h<=nhstepm;h++){    ludcmp(a,npar,indx,&pd);
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /*  printf("\n#Hessian matrix recomputed#\n");
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)    for (j=1;j<=npar;j++) {
           for(j=1;j<=nlstate;j++)      for (i=1;i<=npar;i++) x[i]=0;
             vareij[i][j][(int)age] += doldm[i][j];      x[j]=1;
       }      lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
     h=1;        y[i][j]=x[i];
     if (stepm >= YEARM) h=stepm/YEARM;        printf("%.3e ",y[i][j]);
     fprintf(ficresvij,"%.0f ",age );        fprintf(ficlog,"%.3e ",y[i][j]);
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++){      printf("\n");
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      fprintf(ficlog,"\n");
       }    }
     fprintf(ficresvij,"\n");    */
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    free_matrix(a,1,npar,1,npar);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    free_matrix(y,1,npar,1,npar);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    free_vector(x,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ivector(indx,1,npar);
   } /* End age */    free_matrix(hess,1,npar,1,npar);
    
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  }
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   /*************** hessian matrix ****************/
 }  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
 /************ Variance of prevlim ******************/    int 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)    int l=1, lmax=20;
 {    double k1,k2;
   /* Variance of prevalence limit */    double p2[NPARMAX+1];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double res;
   double **newm;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double **dnewm,**doldm;    double fx;
   int i, j, nhstepm, hstepm;    int k=0,kmax=10;
   int k, cptcode;    double l1;
   double *xp;  
   double *gp, *gm;    fx=func(x);
   double **gradg, **trgradg;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double age,agelim;    for(l=0 ; l <=lmax; l++){
   int theta;      l1=pow(10,l);
          delts=delt;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for(k=1 ; k <kmax; k=k+1){
   fprintf(ficresvpl,"# Age");        delt = delta*(l1*k);
   for(i=1; i<=nlstate;i++)        p2[theta]=x[theta] +delt;
       fprintf(ficresvpl," %1d-%1d",i,i);        k1=func(p2)-fx;
   fprintf(ficresvpl,"\n");        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
   xp=vector(1,npar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   dnewm=matrix(1,nlstate,1,npar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   doldm=matrix(1,nlstate,1,nlstate);        
    #ifdef DEBUG
   hstepm=1*YEARM; /* Every year of age */        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);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        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);
   agelim = AGESUP;  #endif
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     if (stepm >= YEARM) hstepm=1;          k=kmax;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        }
     gradg=matrix(1,npar,1,nlstate);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     gp=vector(1,nlstate);          k=kmax; l=lmax*10.;
     gm=vector(1,nlstate);        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     for(theta=1; theta <=npar; theta++){          delts=delt;
       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);    delti[theta]=delts;
       for(i=1;i<=nlstate;i++)    return res; 
         gp[i] = prlim[i][i];    
      }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    int i;
         gm[i] = prlim[i][i];    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
       for(i=1;i<=nlstate;i++)    double p2[NPARMAX+1];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int k;
     } /* End theta */  
     fx=func(x);
     trgradg =matrix(1,nlstate,1,npar);    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
     for(j=1; j<=nlstate;j++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(theta=1; theta <=npar; theta++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         trgradg[j][theta]=gradg[theta][j];      k1=func(p2)-fx;
     
     for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       varpl[i][(int)age] =0.;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      k2=func(p2)-fx;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    
     for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     fprintf(ficresvpl,"%.0f ",age );    
     for(i=1; i<=nlstate;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     fprintf(ficresvpl,"\n");      k4=func(p2)-fx;
     free_vector(gp,1,nlstate);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     free_vector(gm,1,nlstate);  #ifdef DEBUG
     free_matrix(gradg,1,npar,1,nlstate);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     free_matrix(trgradg,1,nlstate,1,npar);      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);
   } /* End age */  #endif
     }
   free_vector(xp,1,npar);    return res;
   free_matrix(doldm,1,nlstate,1,npar);  }
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   /************** Inverse of matrix **************/
 }  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
 /************ Variance of one-step probabilities  ******************/    int i,imax,j,k; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double big,dum,sum,temp; 
 {    double *vv; 
   int i, j;   
   int k=0, cptcode;    vv=vector(1,n); 
   double **dnewm,**doldm;    *d=1.0; 
   double *xp;    for (i=1;i<=n;i++) { 
   double *gp, *gm;      big=0.0; 
   double **gradg, **trgradg;      for (j=1;j<=n;j++) 
   double age,agelim, cov[NCOVMAX];        if ((temp=fabs(a[i][j])) > big) big=temp; 
   int theta;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   char fileresprob[FILENAMELENGTH];      vv[i]=1.0/big; 
     } 
   strcpy(fileresprob,"prob");    for (j=1;j<=n;j++) { 
   strcat(fileresprob,fileres);      for (i=1;i<j;i++) { 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        sum=a[i][j]; 
     printf("Problem with resultfile: %s\n", fileresprob);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   }        a[i][j]=sum; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      } 
        big=0.0; 
       for (i=j;i<=n;i++) { 
   xp=vector(1,npar);        sum=a[i][j]; 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for (k=1;k<j;k++) 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
   cov[1]=1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   for (age=bage; age<=fage; age ++){          big=dum; 
     cov[2]=age;          imax=i; 
     gradg=matrix(1,npar,1,9);        } 
     trgradg=matrix(1,9,1,npar);      } 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      if (j != imax) { 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        for (k=1;k<=n;k++) { 
              dum=a[imax][k]; 
     for(theta=1; theta <=npar; theta++){          a[imax][k]=a[j][k]; 
       for(i=1; i<=npar; i++)          a[j][k]=dum; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } 
              *d = -(*d); 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        vv[imax]=vv[j]; 
          } 
       k=0;      indx[j]=imax; 
       for(i=1; i<= (nlstate+ndeath); i++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
         for(j=1; j<=(nlstate+ndeath);j++){      if (j != n) { 
            k=k+1;        dum=1.0/(a[j][j]); 
           gp[k]=pmmij[i][j];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         }      } 
       }    } 
     free_vector(vv,1,n);  /* Doesn't work */
       for(i=1; i<=npar; i++)  ;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  } 
      
   void lubksb(double **a, int n, int *indx, double b[]) 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  { 
       k=0;    int i,ii=0,ip,j; 
       for(i=1; i<=(nlstate+ndeath); i++){    double sum; 
         for(j=1; j<=(nlstate+ndeath);j++){   
           k=k+1;    for (i=1;i<=n;i++) { 
           gm[k]=pmmij[i][j];      ip=indx[i]; 
         }      sum=b[ip]; 
       }      b[ip]=b[i]; 
            if (ii) 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        else if (sum) ii=i; 
     }      b[i]=sum; 
     } 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    for (i=n;i>=1;i--) { 
       for(theta=1; theta <=npar; theta++)      sum=b[i]; 
       trgradg[j][theta]=gradg[theta][j];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        b[i]=sum/a[i][i]; 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    } 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  } 
   
      pmij(pmmij,cov,ncovmodel,x,nlstate);  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
      k=0;  {  /* Some frequencies */
      for(i=1; i<=(nlstate+ndeath); i++){    
        for(j=1; j<=(nlstate+ndeath);j++){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
          k=k+1;    int first;
          gm[k]=pmmij[i][j];    double ***freq; /* Frequencies */
         }    double *pp, **prop;
      }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
          FILE *ficresp;
      /*printf("\n%d ",(int)age);    char fileresp[FILENAMELENGTH];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    
            pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    strcpy(fileresp,"p");
      }*/    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
   fprintf(ficresprob,"\n%d ",(int)age);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      exit(0);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   }    j1=0;
     
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    j=cptcoveff;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    first=1;
 }  
  free_vector(xp,1,npar);    for(k1=1; k1<=j;k1++){
 fclose(ficresprob);      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
 }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
 /******************* Printing html file ***********/        for (i=-1; i<=nlstate+ndeath; i++)  
 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 optionfile[],char optionfilehtm[],char rfileres[] ){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   int jj1, k1, i1, cpt;            for(m=iagemin; m <= iagemax+3; m++)
   FILE *fichtm;              freq[i][jk][m]=0;
   /*char optionfilehtm[FILENAMELENGTH];*/  
       for (i=1; i<=nlstate; i++)  
   strcpy(optionfilehtm,optionfile);        for(m=iagemin; m <= iagemax+3; m++)
   strcat(optionfilehtm,".htm");          prop[i][m]=0;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        
     printf("Problem with %s \n",optionfilehtm), exit(0);        dateintsum=0;
   }        k2cpt=0;
         for (i=1; i<=imx; i++) {
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">          bool=1;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
 Total number of observations=%d <br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>                bool=0;
 <hr  size=\"2\" color=\"#EC5E5E\">          }
 <li>Outputs files<br><br>\n          if (bool==1){
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            for(m=firstpass; m<=lastpass; m++){
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>              k2=anint[m][i]+(mint[m][i]/12.);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                if (m<lastpass) {
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>                }
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>                
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                    dateintsum=dateintsum+k2;
 fprintf(fichtm," <li>Graphs</li><p>");                  k2cpt++;
                 }
  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++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        jj1++;  
        if (cptcovn > 0) {        if  (cptcovn>0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          fprintf(ficresp, "\n#********** Variable "); 
          for (cpt=1; cpt<=cptcoveff;cpt++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          fprintf(ficresp, "**********\n#");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        }
        }        for(i=1; i<=nlstate;i++) 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            fprintf(ficresp, "\n");
        for(cpt=1; cpt<nlstate;cpt++){        
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        for(i=iagemin; i <= iagemax+3; i++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          if(i==iagemax+3){
        }            fprintf(ficlog,"Total");
     for(cpt=1; cpt<=nlstate;cpt++) {          }else{
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            if(first==1){
 interval) in state (%d): v%s%d%d.gif <br>              first=0;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                printf("See log file for details...\n");
      }            }
      for(cpt=1; cpt<=nlstate;cpt++) {            fprintf(ficlog,"Age %d", i);
         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,jj1,strtok(optionfile, "."),cpt,jj1);          for(jk=1; jk <=nlstate ; jk++){
      }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              pp[jk] += freq[jk][m][i]; 
 health expectancies in states (1) and (2): e%s%d.gif<br>          }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for(jk=1; jk <=nlstate ; jk++){
 fprintf(fichtm,"\n</body>");            for(m=-1, pos=0; m <=0 ; m++)
    }              pos += freq[jk][m][i];
    }            if(pp[jk]>=1.e-10){
 fclose(fichtm);              if(first==1){
 }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
 /******************* Gnuplot file **************/              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){            }else{
               if(first==1)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   strcpy(optionfilegnuplot,optionfilefiname);            }
   strcat(optionfilegnuplot,".plt");          }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
 #ifdef windows          }       
     fprintf(ficgp,"cd \"%s\" \n",pathc);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 #endif            pos += pp[jk];
 m=pow(2,cptcoveff);            posprop += prop[jk][i];
            }
  /* 1eme*/          for(jk=1; jk <=nlstate ; jk++){
   for (cpt=1; cpt<= nlstate ; cpt ++) {            if(pos>=1.e-5){
    for (k1=1; k1<= m ; k1 ++) {              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 #ifdef windows              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     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);            }else{
 #endif              if(first==1)
 #ifdef unix                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #endif            }
             if( i <= iagemax){
 for (i=1; i<= nlstate ; i ++) {              if(pos>=1.e-5){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   else fprintf(ficgp," \%%*lf (\%%*lf)");                /*probs[i][jk][j1]= pp[jk]/pos;*/
 }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              }
     for (i=1; i<= nlstate ; i ++) {              else
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }          }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          
      for (i=1; i<= nlstate ; i ++) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1; m <=nlstate+ndeath; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(freq[jk][m][i] !=0 ) {
 }                if(first==1)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 #ifdef unix                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 fprintf(ficgp,"\nset ter gif small size 400,300");              }
 #endif          if(i <= iagemax)
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            fprintf(ficresp,"\n");
    }          if(first==1)
   }            printf("Others in log...\n");
   /*2 eme*/          fprintf(ficlog,"\n");
         }
   for (k1=1; k1<= m ; k1 ++) {      }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    }
        dateintmean=dateintsum/k2cpt; 
     for (i=1; i<= nlstate+1 ; i ++) {   
       k=2*i;    fclose(ficresp);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
       for (j=1; j<= nlstate+1 ; j ++) {    free_vector(pp,1,nlstate);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* End of Freq */
 }    }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  /************ Prevalence ********************/
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       for (j=1; j<= nlstate+1 ; j ++) {  {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         else fprintf(ficgp," \%%*lf (\%%*lf)");       in each health status at the date of interview (if between dateprev1 and dateprev2).
 }         We still use firstpass and lastpass as another selection.
       fprintf(ficgp,"\" t\"\" w l 0,");    */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);   
       for (j=1; j<= nlstate+1 ; j ++) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***freq; /* Frequencies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *pp, **prop;
 }      double pos,posprop; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    double  y2; /* in fractional years */
       else fprintf(ficgp,"\" t\"\" w l 0,");    int iagemin, iagemax;
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    iagemin= (int) agemin;
   }    iagemax= (int) agemax;
      /*pp=vector(1,nlstate);*/
   /*3eme*/    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   for (k1=1; k1<= m ; k1 ++) {    j1=0;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    
       k=2+nlstate*(cpt-1);    j=cptcoveff;
       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);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for (i=1; i< nlstate ; i ++) {    
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    for(k1=1; k1<=j;k1++){
       }      for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        j1++;
     }        
     }        for (i=1; i<=nlstate; i++)  
            for(m=iagemin; m <= iagemax+3; m++)
   /* CV preval stat */            prop[i][m]=0.0;
     for (k1=1; k1<= m ; k1 ++) {       
     for (cpt=1; cpt<nlstate ; cpt ++) {        for (i=1; i<=imx; i++) { /* Each individual */
       k=3;          bool=1;
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
       for (i=1; i< nlstate ; i ++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         fprintf(ficgp,"+$%d",k+i+1);                bool=0;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          } 
                if (bool==1) { 
       l=3+(nlstate+ndeath)*cpt;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       for (i=1; i< nlstate ; i ++) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         l=3+(nlstate+ndeath)*cpt;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fprintf(ficgp,"+$%d",l+i+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); 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                  /*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]]);*/
     }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                    prop[s[m][i]][iagemax+3] += weight[i]; 
                  } 
   /* proba elementaires */              }
    for(i=1,jk=1; i <=nlstate; i++){            } /* end selection of waves */
     for(k=1; k <=(nlstate+ndeath); k++){          }
       if (k != i) {        }
         for(j=1; j <=ncovmodel; j++){        for(i=iagemin; i <= iagemax+3; i++){  
                  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           jk++;            posprop += prop[jk][i]; 
           fprintf(ficgp,"\n");          } 
         }  
       }          for(jk=1; jk <=nlstate ; jk++){     
     }            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
     for(jk=1; jk <=m; jk++) {              } 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);            } 
    i=1;          }/* end jk */ 
    for(k2=1; k2<=nlstate; k2++) {        }/* end i */ 
      k3=i;      } /* end i1 */
      for(k=1; k<=(nlstate+ndeath); k++) {    } /* end k1 */
        if (k != k2){    
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 ij=1;    /*free_vector(pp,1,nlstate);*/
         for(j=3; j <=ncovmodel; j++) {    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  }  /* End of prevalence */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  /************* Waves Concatenation ***************/
           }  
           else  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(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  {
         }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           fprintf(ficgp,")/(1");       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
         for(k1=1; k1 <=nlstate; k1++){         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);       and mw[mi+1][i]. dh depends on stepm.
 ij=1;       */
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    int i, mi, m;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             ij++;       double sum=0., jmean=0.;*/
           }    int first;
           else    int j, k=0,jk, ju, jl;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double sum=0.;
           }    first=0;
           fprintf(ficgp,")");    jmin=1e+5;
         }    jmax=-1;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    jmean=0.;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    for(i=1; i<=imx; i++){
         i=i+ncovmodel;      mi=0;
        }      m=firstpass;
      }      while(s[m][i] <= nlstate){
    }        if(s[m][i]>=1)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          mw[++mi][i]=m;
    }        if(m >=lastpass)
              break;
   fclose(ficgp);        else
 }  /* end gnuplot */          m++;
       }/* end while */
       if (s[m][i] > nlstate){
 /*************** Moving average **************/        mi++;     /* Death is another wave */
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
   int i, cpt, cptcod;        mw[mi][i]=m;
     for (agedeb=agemin; agedeb<=fage; agedeb++)      }
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      wav[i]=mi;
           mobaverage[(int)agedeb][i][cptcod]=0.;      if(mi==0){
            nbwarn++;
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){        if(first==0){
       for (i=1; i<=nlstate;i++){          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          first=1;
           for (cpt=0;cpt<=4;cpt++){        }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        if(first==1){
           }          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }
         }      } /* end mi==0 */
       }    } /* End individuals */
     }  
        for(i=1; i<=imx; i++){
 }      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
           dh[mi][i]=1;
 /************** Forecasting ******************/        else{
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   int *popage;              if(j==0) j=1;  /* Survives at least one month after exam */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              else if(j<0){
   double *popeffectif,*popcount;                nberr++;
   double ***p3mat;                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]);
   char fileresf[FILENAMELENGTH];                j=1; /* Temporary Dangerous patch */
                 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.\n  You MUST fix the contradiction between dates.\n",stepm);
  agelim=AGESUP;                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]);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                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.\n  You MUST fix the contradiction between dates.\n",stepm);
               }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              k=k+1;
                if (j >= jmax) jmax=j;
                if (j <= jmin) jmin=j;
   strcpy(fileresf,"f");              sum=sum+j;
   strcat(fileresf,fileres);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   if((ficresf=fopen(fileresf,"w"))==NULL) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     printf("Problem with forecast resultfile: %s\n", fileresf);            }
   }          }
   printf("Computing forecasting: result on file '%s' \n", fileresf);          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
   if (mobilav==1) {            if (j >= jmax) jmax=j;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            else if (j <= jmin)jmin=j;
     movingaverage(agedeb, fage, agemin, mobaverage);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
   stepsize=(int) (stepm+YEARM-1)/YEARM;              nberr++;
   if (stepm<=12) stepsize=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(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]);
   agelim=AGESUP;            }
              sum=sum+j;
   hstepm=1;          }
   hstepm=hstepm/stepm;          jk= j/stepm;
   yp1=modf(dateintmean,&yp);          jl= j -jk*stepm;
   anprojmean=yp;          ju= j -(jk+1)*stepm;
   yp2=modf((yp1*12),&yp);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   mprojmean=yp;            if(jl==0){
   yp1=modf((yp2*30.5),&yp);              dh[mi][i]=jk;
   jprojmean=yp;              bh[mi][i]=0;
   if(jprojmean==0) jprojmean=1;            }else{ /* We want a negative bias in order to only have interpolation ie
   if(mprojmean==0) jprojmean=1;                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              bh[mi][i]=ju;
              }
   for(cptcov=1;cptcov<=i2;cptcov++){          }else{
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            if(jl <= -ju){
       k=k+1;              dh[mi][i]=jk;
       fprintf(ficresf,"\n#******");              bh[mi][i]=jl;       /* bias is positive if real duration
       for(j=1;j<=cptcoveff;j++) {                                   * is higher than the multiple of stepm and negative otherwise.
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                   */
       }            }
       fprintf(ficresf,"******\n");            else{
       fprintf(ficresf,"# StartingAge FinalAge");              dh[mi][i]=jk+1;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);              bh[mi][i]=ju;
                  }
                  if(dh[mi][i]==0){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              dh[mi][i]=1; /* At least one step */
         fprintf(ficresf,"\n");              bh[mi][i]=ju; /* At least one step */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                /*  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 (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){          } /* end if mle */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }
           nhstepm = nhstepm/hstepm;      } /* end wave */
              }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    jmean=sum/k;
           oldm=oldms;savm=savms;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           }
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  /*********** Tricode ****************************/
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  void tricode(int *Tvar, int **nbcode, int imx)
             }  {
             for(j=1; j<=nlstate+ndeath;j++) {    
               kk1=0.;kk2=0;    int Ndum[20],ij=1, k, j, i, maxncov=19;
               for(i=1; i<=nlstate;i++) {                  int cptcode=0;
                 if (mobilav==1)    cptcoveff=0; 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];   
                 else {    for (k=0; k<maxncov; k++) Ndum[k]=0;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    for (k=1; k<=7; k++) ncodemax[k]=0;
                 }  
                    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
               }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
               if (h==(int)(calagedate+12*cpt)){                                 modality*/ 
                 fprintf(ficresf," %.3f", kk1);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                                Ndum[ij]++; /*store the modality */
               }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           }                                         Tvar[j]. If V=sex and male is 0 and 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                         female is 1, then  cptcode=1.*/
         }      }
       }  
     }      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 */
              }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
       ij=1; 
   fclose(ficresf);      for (i=1; i<=ncodemax[j]; i++) {
 }        for (k=0; k<= maxncov; k++) {
 /************** Forecasting ******************/          if (Ndum[k] != 0) {
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){            nbcode[Tvar[j]][ij]=k; 
              /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            
   int *popage;            ij++;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }
   double *popeffectif,*popcount;          if (ij > ncodemax[j]) break; 
   double ***p3mat,***tabpop,***tabpopprev;        }  
   char filerespop[FILENAMELENGTH];      } 
     }  
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;   for (i=1; i<=ncovmodel-2; i++) { 
       /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     ij=Tvar[i];
       Ndum[ij]++;
     }
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);   ij=1;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {   for (i=1; i<= maxncov; i++) {
     printf("Problem with forecast resultfile: %s\n", filerespop);     if((Ndum[i]!=0) && (i<=ncovcol)){
   }       Tvaraff[ij]=i; /*For printing */
   printf("Computing forecasting: result on file '%s' \n", filerespop);       ij++;
      }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;   }
    
   if (mobilav==1) {   cptcoveff=ij-1; /*Number of simple covariates*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
     movingaverage(agedeb, fage, agemin, mobaverage);  
   }  /*********** Health Expectancies ****************/
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  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 )
   if (stepm<=12) stepsize=1;  
    {
   agelim=AGESUP;    /* Health expectancies */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   hstepm=1;    double age, agelim, hf;
   hstepm=hstepm/stepm;    double ***p3mat,***varhe;
      double **dnewm,**doldm;
   if (popforecast==1) {    double *xp;
     if((ficpop=fopen(popfile,"r"))==NULL) {    double **gp, **gm;
       printf("Problem with population file : %s\n",popfile);exit(0);    double ***gradg, ***trgradg;
     }    int theta;
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     popcount=vector(0,AGESUP);    xp=vector(1,npar);
        dnewm=matrix(1,nlstate*nlstate,1,npar);
     i=1;      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    
        fprintf(ficreseij,"# Health expectancies\n");
     imx=i;    fprintf(ficreseij,"# Age");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficreseij,"\n");
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;    if(estepm < stepm){
       fprintf(ficrespop,"\n#******");      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(j=1;j<=cptcoveff;j++) {    }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    else  hstepm=estepm;   
       }    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficrespop,"******\n");     * This is mainly to measure the difference between two models: for example
       fprintf(ficrespop,"# Age");     * if stepm=24 months pijx are given only every 2 years and by summing them
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       if (popforecast==1)  fprintf(ficrespop," [Population]");     * progression in between and thus overestimating or underestimating according
           * to the curvature of the survival function. If, for the same date, we 
       for (cpt=0; cpt<=0;cpt++) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);       * to compare the new estimate of Life expectancy with the same linear 
             * hypothesis. A more precise result, taking into account a more precise
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){     * curvature will be obtained if estepm is as small as stepm. */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    /* For example we decided to compute the life expectancy with the smallest unit */
              /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       nhstepm is the number of hstepm from age to agelim 
           oldm=oldms;savm=savms;       nstepm is the number of stepm from age to agelin. 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         Look at hpijx to understand the reason of that which relies in memory size
               and note for a fixed period like estepm months */
           for (h=0; h<=nhstepm; h++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             if (h==(int) (calagedate+YEARM*cpt)) {       survival function given by stepm (the optimization length). Unfortunately it
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       means that if the survival funtion is printed only each two years of age and if
             }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             for(j=1; j<=nlstate+ndeath;j++) {       results. So we changed our mind and took the option of the best precision.
               kk1=0.;kk2=0;    */
               for(i=1; i<=nlstate;i++) {                  hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    agelim=AGESUP;
                 else {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      /* nhstepm age range expressed in number of stepm */
                 }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
               }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
               if (h==(int)(calagedate+12*cpt)){      /* if (stepm >= YEARM) hstepm=1;*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                   /*fprintf(ficrespop," %.3f", kk1);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
               }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
             }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
             for(i=1; i<=nlstate;i++){  
               kk1=0.;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 for(j=1; j<=nlstate;j++){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
                 }   
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      /* Computing  Variances of health expectancies */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  
           }       for(theta=1; theta <=npar; theta++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1; i<=npar; i++){ 
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   /******/    
         cptj=0;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        for(j=1; j<= nlstate; j++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            for(i=1; i<=nlstate; i++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){            cptj=cptj+1;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           nhstepm = nhstepm/hstepm;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                      }
           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) (calagedate+YEARM*cpt)) {        for(i=1; i<=npar; i++) 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             for(j=1; j<=nlstate+ndeath;j++) {        
               kk1=0.;kk2=0;        cptj=0;
               for(i=1; i<=nlstate;i++) {                      for(j=1; j<= nlstate; j++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              for(i=1;i<=nlstate;i++){
               }            cptj=cptj+1;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
             }  
           }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }          }
       }        }
    }        for(j=1; j<= nlstate*nlstate; j++)
   }          for(h=0; h<=nhstepm-1; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
        } 
   if (popforecast==1) {     
     free_ivector(popage,0,AGESUP);  /* End theta */
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       for(h=0; h<=nhstepm-1; h++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<=nlstate*nlstate;j++)
   fclose(ficrespop);          for(theta=1; theta <=npar; theta++)
 }            trgradg[h][j][theta]=gradg[h][theta][j];
        
 /***********************************************/  
 /**************** Main Program *****************/       for(i=1;i<=nlstate*nlstate;i++)
 /***********************************************/        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
 int main(int argc, char *argv[])  
 {       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       for(h=0;h<=nhstepm-1;h++){
   double agedeb, agefin,hf;        for(k=0;k<=nhstepm-1;k++){
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   double fret;          for(i=1;i<=nlstate*nlstate;i++)
   double **xi,tmp,delta;            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   double dum; /* Dummy variable */        }
   double ***p3mat;      }
   int *indx;      /* Computing expectancies */
   char line[MAXLINE], linepar[MAXLINE];      for(i=1; i<=nlstate;i++)
   char title[MAXLINE];        for(j=1; j<=nlstate;j++)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
              
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  /* 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]);*/
   
   char filerest[FILENAMELENGTH];          }
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];      fprintf(ficreseij,"%3.0f",age );
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      cptj=0;
   int firstobs=1, lastobs=10;      for(i=1; i<=nlstate;i++)
   int sdeb, sfin; /* Status at beginning and end */        for(j=1; j<=nlstate;j++){
   int c,  h , cpt,l;          cptj++;
   int ju,jl, mi;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      fprintf(ficreseij,"\n");
   int mobilav=0,popforecast=0;     
   int hstepm, nhstepm;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   double bage, fage, age, agelim, agebase;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   double ftolpl=FTOL;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double **prlim;    }
   double *severity;    printf("\n");
   double ***param; /* Matrix of parameters */    fprintf(ficlog,"\n");
   double  *p;  
   double **matcov; /* Matrix of covariance */    free_vector(xp,1,npar);
   double ***delti3; /* Scale */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   double *delti; /* Scale */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   double ***eij, ***vareij;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   double **varpl; /* Variances of prevalence limits by age */  }
   double *epj, vepp;  
   double kk1, kk2;  /************ Variance ******************/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  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)
    {
     /* Variance of health expectancies */
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
   char z[1]="c", occ;    int i, j, nhstepm, hstepm, h, nstepm ;
 #include <sys/time.h>    int k, cptcode;
 #include <time.h>    double *xp;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double **gp, **gm;  /* for var eij */
      double ***gradg, ***trgradg; /*for var eij */
   /* long total_usecs;    double **gradgp, **trgradgp; /* for var p point j */
   struct timeval start_time, end_time;    double *gpp, *gmp; /* for var p point j */
      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
   printf("\n%s",version);    int theta;
   if(argc <=1){    char digit[4];
     printf("\nEnter the parameter file name: ");    char digitp[25];
     scanf("%s",pathtot);  
   }    char fileresprobmorprev[FILENAMELENGTH];
   else{  
     strcpy(pathtot,argv[1]);    if(popbased==1){
   }      if(mobilav!=0)
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        strcpy(digitp,"-populbased-mobilav-");
   /*cygwin_split_path(pathtot,path,optionfile);      else strcpy(digitp,"-populbased-nomobil-");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    }
   /* cutv(path,optionfile,pathtot,'\\');*/    else 
       strcpy(digitp,"-stablbased-");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    if (mobilav!=0) {
   chdir(path);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   replace(pathc,path);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 /*-------- arguments in the command line --------*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   strcpy(fileres,"r");    }
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   /*---------arguments file --------*/    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     printf("Problem with optionfile %s\n",optionfile);    strcat(fileresprobmorprev,fileres);
     goto end;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   strcpy(filereso,"o");    }
   strcat(filereso,fileres);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if((ficparo=fopen(filereso,"w"))==NULL) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /* Reads comments: lines beginning with '#' */      fprintf(ficresprobmorprev," p.%-d SE",j);
   while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     fgets(line, MAXLINE, ficpar);    }  
     puts(line);    fprintf(ficresprobmorprev,"\n");
     fputs(line,ficparo);    fprintf(ficgp,"\n# Routine varevsij");
   }    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");
   ungetc(c,ficpar);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
   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);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   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);  
   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);    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");
 while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresvij,"# Age");
     ungetc(c,ficpar);    for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);      for(j=1; j<=nlstate;j++)
     puts(line);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     fputs(line,ficparo);    fprintf(ficresvij,"\n");
   }  
   ungetc(c,ficpar);    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
   covar=matrix(0,NCOVMAX,1,n);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   cptcovn=0;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   ncovmodel=2+cptcovn;    gpp=vector(nlstate+1,nlstate+ndeath);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   /* Read guess parameters */    
   /* Reads comments: lines beginning with '#' */    if(estepm < stepm){
   while((c=getc(ficpar))=='#' && c!= EOF){      printf ("Problem %d lower than %d\n",estepm, stepm);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    else  hstepm=estepm;   
     puts(line);    /* For example we decided to compute the life expectancy with the smallest unit */
     fputs(line,ficparo);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   }       nhstepm is the number of hstepm from age to agelim 
   ungetc(c,ficpar);       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       and note for a fixed period like k years */
     for(i=1; i <=nlstate; i++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(j=1; j <=nlstate+ndeath-1; j++){       survival function given by stepm (the optimization length). Unfortunately it
       fscanf(ficpar,"%1d%1d",&i1,&j1);       means that if the survival funtion is printed every two years of age and if
       fprintf(ficparo,"%1d%1d",i1,j1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("%1d%1d",i,j);       results. So we changed our mind and took the option of the best precision.
       for(k=1; k<=ncovmodel;k++){    */
         fscanf(ficpar," %lf",&param[i][j][k]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         printf(" %lf",param[i][j][k]);    agelim = AGESUP;
         fprintf(ficparo," %lf",param[i][j][k]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       fscanf(ficpar,"\n");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       printf("\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo,"\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     }      gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
   
   p=param[1][1];      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   /* Reads comments: lines beginning with '#' */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fgets(line, MAXLINE, ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     puts(line);  
     fputs(line,ficparo);        if (popbased==1) {
   }          if(mobilav ==0){
   ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          }else{ /* mobilav */ 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            for(i=1; i<=nlstate;i++)
   for(i=1; i <=nlstate; i++){              prlim[i][i]=mobaverage[(int)age][i][ij];
     for(j=1; j <=nlstate+ndeath-1; j++){          }
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }
       printf("%1d%1d",i,j);    
       fprintf(ficparo,"%1d%1d",i1,j1);        for(j=1; j<= nlstate; j++){
       for(k=1; k<=ncovmodel;k++){          for(h=0; h<=nhstepm; h++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         printf(" %le",delti3[i][j][k]);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         fprintf(ficparo," %le",delti3[i][j][k]);          }
       }        }
       fscanf(ficpar,"\n");        /* This for computing probability of death (h=1 means
       printf("\n");           computed over hstepm matrices product = hstepm*stepm months) 
       fprintf(ficparo,"\n");           as a weighted average of prlim.
     }        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   delti=delti3[1][1];          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   /* Reads comments: lines beginning with '#' */        }    
   while((c=getc(ficpar))=='#' && c!= EOF){        /* end probability of death */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     puts(line);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fputs(line,ficparo);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   ungetc(c,ficpar);   
          if (popbased==1) {
   matcov=matrix(1,npar,1,npar);          if(mobilav ==0){
   for(i=1; i <=npar; i++){            for(i=1; i<=nlstate;i++)
     fscanf(ficpar,"%s",&str);              prlim[i][i]=probs[(int)age][i][ij];
     printf("%s",str);          }else{ /* mobilav */ 
     fprintf(ficparo,"%s",str);            for(i=1; i<=nlstate;i++)
     for(j=1; j <=i; j++){              prlim[i][i]=mobaverage[(int)age][i][ij];
       fscanf(ficpar," %le",&matcov[i][j]);          }
       printf(" %.5le",matcov[i][j]);        }
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }        for(j=1; j<= nlstate; j++){
     fscanf(ficpar,"\n");          for(h=0; h<=nhstepm; h++){
     printf("\n");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     fprintf(ficparo,"\n");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   for(i=1; i <=npar; i++)        }
     for(j=i+1;j<=npar;j++)        /* This for computing probability of death (h=1 means
       matcov[i][j]=matcov[j][i];           computed over hstepm matrices product = hstepm*stepm months) 
               as a weighted average of prlim.
   printf("\n");        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
     /*-------- Rewriting paramater file ----------*/           gmp[j] += prlim[i][i]*p3mat[i][j][1];
      strcpy(rfileres,"r");    /* "Rparameterfile */        }    
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        /* end probability of death */
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        for(j=1; j<= nlstate; j++) /* vareij */
     if((ficres =fopen(rfileres,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     }          }
     fprintf(ficres,"#%s\n",version);  
            for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     /*-------- data file ----------*/          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     if((fic=fopen(datafile,"r"))==NULL)    {        }
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }      } /* End theta */
   
     n= lastobs;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);      for(h=0; h<=nhstepm; h++) /* veij */
     num=ivector(1,n);        for(j=1; j<=nlstate;j++)
     moisnais=vector(1,n);          for(theta=1; theta <=npar; theta++)
     annais=vector(1,n);            trgradg[h][j][theta]=gradg[h][theta][j];
     moisdc=vector(1,n);  
     andc=vector(1,n);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     agedc=vector(1,n);        for(theta=1; theta <=npar; theta++)
     cod=ivector(1,n);          trgradgp[j][theta]=gradgp[theta][j];
     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);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     anint=matrix(1,maxwav,1,n);      for(i=1;i<=nlstate;i++)
     s=imatrix(1,maxwav+1,1,n);        for(j=1;j<=nlstate;j++)
     adl=imatrix(1,maxwav+1,1,n);              vareij[i][j][(int)age] =0.;
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
     i=1;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     while (fgets(line, MAXLINE, fic) != NULL)    {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       if ((i >= firstobs) && (i <=lastobs)) {          for(i=1;i<=nlstate;i++)
                    for(j=1;j<=nlstate;j++)
         for (j=maxwav;j>=1;j--){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        }
           strcpy(line,stra);      }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      /* 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);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      /* end ppptj */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         for (j=ncov;j>=1;j--){   
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      if (popbased==1) {
         }        if(mobilav ==0){
         num[i]=atol(stra);          for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        }else{ /* mobilav */ 
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         i=i+1;        }
       }      }
     }               
     /* printf("ii=%d", ij);      /* This for computing probability of death (h=1 means
        scanf("%d",i);*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   imx=i-1; /* Number of individuals */         as a weighted average of prlim.
       */
   /* for (i=1; i<=imx; i++){      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      }    
     }      /* end probability of death */
   
     for (i=1; i<=imx; i++)      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   /* Calculation of the number of parameter from char model*/        for(i=1; i<=nlstate;i++){
   Tvar=ivector(1,15);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   Tprod=ivector(1,15);        }
   Tvaraff=ivector(1,15);      } 
   Tvard=imatrix(1,15,1,2);      fprintf(ficresprobmorprev,"\n");
   Tage=ivector(1,15);        
          fprintf(ficresvij,"%.0f ",age );
   if (strlen(model) >1){      for(i=1; i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;        for(j=1; j<=nlstate;j++){
     j=nbocc(model,'+');          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     j1=nbocc(model,'*');        }
     cptcovn=j+1;      fprintf(ficresvij,"\n");
     cptcovprod=j1;      free_matrix(gp,0,nhstepm,1,nlstate);
          free_matrix(gm,0,nhstepm,1,nlstate);
          free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     strcpy(modelsav,model);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("Error. Non available option model=%s ",model);    } /* End age */
       goto end;    free_vector(gpp,nlstate+1,nlstate+ndeath);
     }    free_vector(gmp,nlstate+1,nlstate+ndeath);
        free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     for(i=(j+1); i>=1;i--){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       cutv(stra,strb,modelsav,'+');    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       /*scanf("%d",i);*/  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       if (strchr(strb,'*')) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         cutv(strd,strc,strb,'*');  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         if (strcmp(strc,"age")==0) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           cptcovprod--;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
           cutv(strb,stre,strd,'V');    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
           Tvar[i]=atoi(stre);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           cptcovage++;    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);
             Tage[cptcovage]=i;    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
             /*printf("stre=%s ", stre);*/  */
         }  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         else if (strcmp(strd,"age")==0) {    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    free_vector(xp,1,npar);
           Tvar[i]=atoi(stre);    free_matrix(doldm,1,nlstate,1,nlstate);
           cptcovage++;    free_matrix(dnewm,1,nlstate,1,npar);
           Tage[cptcovage]=i;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         else {    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           cutv(strb,stre,strc,'V');    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           Tvar[i]=ncov+k1;    fclose(ficresprobmorprev);
           cutv(strb,strc,strd,'V');    fflush(ficgp);
           Tprod[k1]=i;    fflush(fichtm); 
           Tvard[k1][1]=atoi(strc);  }  /* end varevsij */
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];  /************ Variance of prevlim ******************/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  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)
           for (k=1; k<=lastobs;k++)  {
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    /* Variance of prevalence limit */
           k1++;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           k2=k2+2;    double **newm;
         }    double **dnewm,**doldm;
       }    int i, j, nhstepm, hstepm;
       else {    int k, cptcode;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double *xp;
        /*  scanf("%d",i);*/    double *gp, *gm;
       cutv(strd,strc,strb,'V');    double **gradg, **trgradg;
       Tvar[i]=atoi(strc);    double age,agelim;
       }    int theta;
       strcpy(modelsav,stra);       
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         scanf("%d",i);*/    fprintf(ficresvpl,"# Age");
     }    for(i=1; i<=nlstate;i++)
 }        fprintf(ficresvpl," %1d-%1d",i,i);
      fprintf(ficresvpl,"\n");
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);    xp=vector(1,npar);
   scanf("%d ",i);*/    dnewm=matrix(1,nlstate,1,npar);
     fclose(fic);    doldm=matrix(1,nlstate,1,nlstate);
     
     /*  if(mle==1){*/    hstepm=1*YEARM; /* Every year of age */
     if (weightopt != 1) { /* Maximisation without weights*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       for(i=1;i<=n;i++) weight[i]=1.0;    agelim = AGESUP;
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /*-calculation of age at interview from date of interview and age at death -*/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     agev=matrix(1,maxwav,1,imx);      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
    for (i=1; i<=imx; i++)      gradg=matrix(1,npar,1,nlstate);
      for(m=2; (m<= maxwav); m++)      gp=vector(1,nlstate);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      gm=vector(1,nlstate);
          anint[m][i]=9999;  
          s[m][i]=-1;      for(theta=1; theta <=npar; theta++){
        }        for(i=1; i<=npar; i++){ /* Computes gradient */
              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for (i=1; i<=imx; i++)  {        }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for(m=1; (m<= maxwav); m++){        for(i=1;i<=nlstate;i++)
         if(s[m][i] >0){          gp[i] = prlim[i][i];
           if (s[m][i] == nlstate+1) {      
             if(agedc[i]>0)        for(i=1; i<=npar; i++) /* Computes gradient */
               if(moisdc[i]!=99 && andc[i]!=9999)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               agev[m][i]=agedc[i];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             else {        for(i=1;i<=nlstate;i++)
               if (andc[i]!=9999){          gm[i] = prlim[i][i];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;        for(i=1;i<=nlstate;i++)
               }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
             }      } /* End theta */
           }  
           else if(s[m][i] !=9){ /* Should no more exist */      trgradg =matrix(1,nlstate,1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)      for(j=1; j<=nlstate;j++)
               agev[m][i]=1;        for(theta=1; theta <=npar; theta++)
             else if(agev[m][i] <agemin){          trgradg[j][theta]=gradg[theta][j];
               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);*/      for(i=1;i<=nlstate;i++)
             }        varpl[i][(int)age] =0.;
             else if(agev[m][i] >agemax){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
               agemax=agev[m][i];      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      for(i=1;i<=nlstate;i++)
             }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/      fprintf(ficresvpl,"%.0f ",age );
           }      for(i=1; i<=nlstate;i++)
           else { /* =9 */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             agev[m][i]=1;      fprintf(ficresvpl,"\n");
             s[m][i]=-1;      free_vector(gp,1,nlstate);
           }      free_vector(gm,1,nlstate);
         }      free_matrix(gradg,1,npar,1,nlstate);
         else /*= 0 Unknown */      free_matrix(trgradg,1,nlstate,1,npar);
           agev[m][i]=1;    } /* End age */
       }  
        free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,npar);
     for (i=1; i<=imx; i++)  {    free_matrix(dnewm,1,nlstate,1,nlstate);
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {  }
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;  /************ 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)
       }  {
     }    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    int k=0,l, cptcode;
     int first=1, first1;
     free_vector(severity,1,maxwav);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     free_imatrix(outcome,1,maxwav+1,1,n);    double **dnewm,**doldm;
     free_vector(moisnais,1,n);    double *xp;
     free_vector(annais,1,n);    double *gp, *gm;
     /* free_matrix(mint,1,maxwav,1,n);    double **gradg, **trgradg;
        free_matrix(anint,1,maxwav,1,n);*/    double **mu;
     free_vector(moisdc,1,n);    double age,agelim, cov[NCOVMAX];
     free_vector(andc,1,n);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
        char fileresprob[FILENAMELENGTH];
     wav=ivector(1,imx);    char fileresprobcov[FILENAMELENGTH];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    char fileresprobcor[FILENAMELENGTH];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
        double ***varpij;
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       Tcode=ivector(1,100);      printf("Problem with resultfile: %s\n", fileresprob);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       ncodemax[1]=1;    }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    strcpy(fileresprobcov,"probcov"); 
          strcat(fileresprobcov,fileres);
    codtab=imatrix(1,100,1,10);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
    h=0;      printf("Problem with resultfile: %s\n", fileresprobcov);
    m=pow(2,cptcoveff);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
    for(k=1;k<=cptcoveff; k++){    strcpy(fileresprobcor,"probcor"); 
      for(i=1; i <=(m/pow(2,k));i++){    strcat(fileresprobcor,fileres);
        for(j=1; j <= ncodemax[k]; j++){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      printf("Problem with resultfile: %s\n", fileresprobcor);
            h++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
            if (h>m) h=1;codtab[h][k]=j;    }
          }    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);
    /*for(i=1; i <=m ;i++){    
      for(k=1; k <=cptcovn; k++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    fprintf(ficresprob,"# Age");
      }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      printf("\n");    fprintf(ficresprobcov,"# Age");
    }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
    scanf("%d",i);*/    fprintf(ficresprobcov,"# Age");
      
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */    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);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   /* fprintf(ficresprob,"\n");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov,"\n");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresprobcor,"\n");
         */
     /* For Powell, parameters are in a vector p[] starting at p[1]   xp=vector(1,npar);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     if(mle==1){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    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");
     /*--------- results files --------------*/    fprintf(fichtm,"\n");
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);  
      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\
    jk=1;    file %s<br>\n",optionfilehtmcov);
    fprintf(ficres,"# Parameters\n");    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
    printf("# Parameters\n");  and drawn. It helps understanding how is the covariance between two incidences.\
    for(i=1,jk=1; i <=nlstate; i++){   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      for(k=1; k <=(nlstate+ndeath); k++){    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. \
        if (k != i)  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 \
            printf("%d%d ",i,k);  standard deviations wide on each axis. <br>\
            fprintf(ficres,"%1d%1d ",i,k);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
            for(j=1; j <=ncovmodel; j++){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
              printf("%f ",p[jk]);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
              fprintf(ficres,"%f ",p[jk]);  
              jk++;    cov[1]=1;
            }    tj=cptcoveff;
            printf("\n");    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
            fprintf(ficres,"\n");    j1=0;
          }    for(t=1; t<=tj;t++){
      }      for(i1=1; i1<=ncodemax[t];i1++){ 
    }        j1++;
  if(mle==1){        if  (cptcovn>0) {
     /* Computing hessian and covariance matrix */          fprintf(ficresprob, "\n#********** Variable "); 
     ftolhess=ftol; /* Usually correct */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     hesscov(matcov, p, npar, delti, ftolhess, func);          fprintf(ficresprob, "**********\n#\n");
  }          fprintf(ficresprobcov, "\n#********** Variable "); 
     fprintf(ficres,"# Scales\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("# Scales\n");          fprintf(ficresprobcov, "**********\n#\n");
      for(i=1,jk=1; i <=nlstate; i++){          
       for(j=1; j <=nlstate+ndeath; j++){          fprintf(ficgp, "\n#********** Variable "); 
         if (j!=i) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficres,"%1d%1d",i,j);          fprintf(ficgp, "**********\n#\n");
           printf("%1d%1d",i,j);          
           for(k=1; k<=ncovmodel;k++){          
             printf(" %.5e",delti[jk]);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
             fprintf(ficres," %.5e",delti[jk]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             jk++;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           }          
           printf("\n");          fprintf(ficresprobcor, "\n#********** Variable ");    
           fprintf(ficres,"\n");          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 ++){ 
     k=1;          cov[2]=age;
     fprintf(ficres,"# Covariance\n");          for (k=1; k<=cptcovn;k++) {
     printf("# Covariance\n");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     for(i=1;i<=npar;i++){          }
       /*  if (k>nlstate) k=1;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       i1=(i-1)/(ncovmodel*nlstate)+1;          for (k=1; k<=cptcovprod;k++)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       printf("%s%d%d",alph[k],i1,tab[i]);*/          
       fprintf(ficres,"%3d",i);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       printf("%3d",i);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       for(j=1; j<=i;j++){          gp=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(ficres," %.5e",matcov[i][j]);          gm=vector(1,(nlstate)*(nlstate+ndeath));
         printf(" %.5e",matcov[i][j]);      
       }          for(theta=1; theta <=npar; theta++){
       fprintf(ficres,"\n");            for(i=1; i<=npar; i++)
       printf("\n");              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       k++;            
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                
     while((c=getc(ficpar))=='#' && c!= EOF){            k=0;
       ungetc(c,ficpar);            for(i=1; i<= (nlstate); i++){
       fgets(line, MAXLINE, ficpar);              for(j=1; j<=(nlstate+ndeath);j++){
       puts(line);                k=k+1;
       fputs(line,ficparo);                gp[k]=pmmij[i][j];
     }              }
     ungetc(c,ficpar);            }
              
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);            for(i=1; i<=npar; i++)
                  xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     if (fage <= 2) {      
       bage = agemin;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fage = agemaxpar;            k=0;
     }            for(i=1; i<=(nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                k=k+1;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);                gm[k]=pmmij[i][j];
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);              }
              }
     while((c=getc(ficpar))=='#' && c!= EOF){       
     ungetc(c,ficpar);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     fgets(line, MAXLINE, ficpar);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     puts(line);          }
     fputs(line,ficparo);  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   ungetc(c,ficpar);            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   while((c=getc(ficpar))=='#' && c!= EOF){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     ungetc(c,ficpar);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     fgets(line, MAXLINE, ficpar);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     puts(line);  
     fputs(line,ficparo);          pmij(pmmij,cov,ncovmodel,x,nlstate);
   }          
   ungetc(c,ficpar);          k=0;
            for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              k=k+1;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              mu[k][(int) age]=pmmij[i][j];
             }
   fscanf(ficpar,"pop_based=%d\n",&popbased);          }
   fprintf(ficparo,"pop_based=%d\n",popbased);            for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   fprintf(ficres,"pop_based=%d\n",popbased);              for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                varpij[i][j][(int)age] = doldm[i][j];
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          /*printf("\n%d ",(int)age);
     fgets(line, MAXLINE, ficpar);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     puts(line);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fputs(line,ficparo);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   }            }*/
   ungetc(c,ficpar);  
           fprintf(ficresprob,"\n%d ",(int)age);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          fprintf(ficresprobcov,"\n%d ",(int)age);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficresprobcor,"\n%d ",(int)age);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
 while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     ungetc(c,ficpar);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     fgets(line, MAXLINE, ficpar);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     puts(line);          }
     fputs(line,ficparo);          i=0;
   }          for (k=1; k<=(nlstate);k++){
   ungetc(c,ficpar);            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
 /*------------ gnuplot -------------*/            }
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          }/* end of loop for state */
          } /* end of loop for age */
 /*------------ free_vector  -------------*/  
  chdir(path);        /* Confidence intervalle of pij  */
          /*
  free_ivector(wav,1,imx);          fprintf(ficgp,"\nset noparametric;unset label");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
  free_ivector(num,1,n);          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);
  free_vector(agedc,1,n);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
  fclose(ficparo);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
  fclose(ficres);        */
   
 /*--------- index.htm --------*/        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);        for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
              if(l2==k2) continue;
   /*--------------- Prevalence limit --------------*/            j=(k2-1)*(nlstate+ndeath)+l2;
              for (k1=1; k1<=(nlstate);k1++){
   strcpy(filerespl,"pl");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   strcat(filerespl,fileres);                if(l1==k1) continue;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                i=(k1-1)*(nlstate+ndeath)+l1;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                if(i<=j) continue;
   }                for (age=bage; age<=fage; age ++){ 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                  if ((int)age %5==0){
   fprintf(ficrespl,"#Prevalence limit\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   fprintf(ficrespl,"#Age ");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   fprintf(ficrespl,"\n");                    mu1=mu[i][(int) age]/stepm*YEARM ;
                      mu2=mu[j][(int) age]/stepm*YEARM;
   prlim=matrix(1,nlstate,1,nlstate);                    c12=cv12/sqrt(v1*v2);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* Computing eigen value of matrix of covariance */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    /* Eigen vectors */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   k=0;                    /*v21=sqrt(1.-v11*v11); *//* error */
   agebase=agemin;                    v21=(lc1-v1)/cv12*v11;
   agelim=agemaxpar;                    v12=-v21;
   ftolpl=1.e-10;                    v22=v11;
   i1=cptcoveff;                    tnalp=v21/v11;
   if (cptcovn < 1){i1=1;}                    if(first1==1){
                       first1=0;
   for(cptcov=1;cptcov<=i1;cptcov++){                      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);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    }
         k=k+1;                    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("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                    /*printf(fignu*/
         fprintf(ficrespl,"\n#******");                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         for(j=1;j<=cptcoveff;j++)                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    if(first==1){
         fprintf(ficrespl,"******\n");                      first=0;
                              fprintf(ficgp,"\nset parametric;unset label");
         for (age=agebase; age<=agelim; age++){                      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);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(ficrespl,"%.0f",age );                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           for(i=1; i<=nlstate;i++)   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
           fprintf(ficrespl," %.5f", prlim[i][i]);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
           fprintf(ficrespl,"\n");                              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);
   fclose(ficrespl);                      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);
   /*------------- h Pij x at various ages ------------*/                      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",\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                    }else{
   }                      first=0;
   printf("Computing pij: result on file '%s' \n", filerespij);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   stepsize=(int) (stepm+YEARM-1)/YEARM;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   /*if (stepm<=24) stepsize=2;*/                      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),\
   agelim=AGESUP;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   hstepm=stepsize*YEARM; /* Every year of age */                    }/* if first */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                  } /* age mod 5 */
                  } /* end loop age */
   k=0;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   for(cptcov=1;cptcov<=i1;cptcov++){                first=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              } /*l12 */
       k=k+1;            } /* k12 */
         fprintf(ficrespij,"\n#****** ");          } /*l1 */
         for(j=1;j<=cptcoveff;j++)        }/* k1 */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } /* loop covariates */
         fprintf(ficrespij,"******\n");    }
            free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_vector(xp,1,npar);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fclose(ficresprob);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficresprobcov);
           oldm=oldms;savm=savms;    fclose(ficresprobcor);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fflush(ficgp);
           fprintf(ficrespij,"# Age");    fflush(fichtmcov);
           for(i=1; i<=nlstate;i++)  }
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");  /******************* Printing html file ***********/
           for (h=0; h<=nhstepm; h++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                    int lastpass, int stepm, int weightopt, char model[],\
             for(i=1; i<=nlstate;i++)                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
               for(j=1; j<=nlstate+ndeath;j++)                    int popforecast, int estepm ,\
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    double jprev1, double mprev1,double anprev1, \
             fprintf(ficrespij,"\n");                    double jprev2, double mprev2,double anprev2){
           }    int jj1, k1, i1, cpt;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</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 ",
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
   fclose(ficrespij);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
   /*---------- Forecasting ------------------*/   - Life expectancies by age and initial health status (estepm=%2d months): \
   if((stepm == 1) && (model==".")){     <a href=\"%s\">%s</a> <br>\n</li>",
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
     free_matrix(mint,1,maxwav,1,n);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);}   m=cptcoveff;
   else{   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     erreur=108;  
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);   jj1=0;
   }   for(k1=1; k1<=m;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
   /*---------- Health expectancies and variances ------------*/       if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   strcpy(filerest,"t");         for (cpt=1; cpt<=cptcoveff;cpt++) 
   strcat(filerest,fileres);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   if((ficrest=fopen(filerest,"w"))==NULL) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;       }
   }       /* Pij */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       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 */
   strcpy(filerese,"e");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   strcat(filerese,fileres);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   if((ficreseij=fopen(filerese,"w"))==NULL) {  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);         /* Stable prevalence in each health state */
   }         for(cpt=1; cpt<nlstate;cpt++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);           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);
  strcpy(fileresv,"v");         }
   strcat(fileresv,fileres);       for(cpt=1; cpt<=nlstate;cpt++) {
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   }       }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     } /* end i1 */
    }/* End k1 */
   k=0;   fprintf(fichtm,"</ul>");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;   fprintf(fichtm,"\
       fprintf(ficrest,"\n#****** ");  \n<br><li><h4> Result files (second order: variances)</h4>\n\
       for(j=1;j<=cptcoveff;j++)   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       fprintf(ficreseij,"\n#****** ");   fprintf(fichtm,"\
       for(j=1;j<=cptcoveff;j++)   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
       fprintf(ficreseij,"******\n");  
    fprintf(fichtm,"\
       fprintf(ficresvij,"\n#****** ");   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       for(j=1;j<=cptcoveff;j++)           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   fprintf(fichtm,"\
       fprintf(ficresvij,"******\n");   - 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"));
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   fprintf(fichtm,"\
       oldm=oldms;savm=savms;   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);             subdirf2(fileres,"t"),subdirf2(fileres,"t"));
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   fprintf(fichtm,"\
       oldm=oldms;savm=savms;   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
      
   /*  if(popforecast==1) fprintf(fichtm,"\n */
    /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  /*      <br>",fileres,fileres,fileres,fileres); */
       fprintf(ficrest,"\n");  /*  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); */
       hf=1;   fflush(fichtm);
       if (stepm >= YEARM) hf=stepm/YEARM;   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){   m=cptcoveff;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)   jj1=0;
             prlim[i][i]=probs[(int)age][i][k];   for(k1=1; k1<=m;k1++){
         }     for(i1=1; i1<=ncodemax[k1];i1++){
               jj1++;
         fprintf(ficrest," %.0f",age);       if (cptcovn > 0) {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {         for (cpt=1; cpt<=cptcoveff;cpt++) 
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           epj[nlstate+1] +=epj[j];       }
         }       for(cpt=1; cpt<=nlstate;cpt++) {
         for(i=1, vepp=0.;i <=nlstate;i++)         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
           for(j=1;j <=nlstate;j++)  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
             vepp += vareij[i][j][(int)age];  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));       }
         for(j=1;j <=nlstate;j++){       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  health expectancies in states (1) and (2): %s%d.png<br>\
         }  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
         fprintf(ficrest,"\n");     } /* end i1 */
       }   }/* End k1 */
     }   fprintf(fichtm,"</ul>");
   }   fflush(fichtm);
   }
   fclose(ficreseij);  
   fclose(ficresvij);  /******************* Gnuplot file **************/
   fclose(ficrest);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    char dirfileres[132],optfileres[132];
      int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   /*------- Variance limit prevalence------*/      int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   strcpy(fileresvpl,"vpl");  /*     printf("Problem with file %s",optionfilegnuplot); */
   strcat(fileresvpl,fileres);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  /*   } */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);    /*#ifdef windows */
   }    fprintf(ficgp,"cd \"%s\" \n",pathc);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      /*#endif */
     m=pow(2,cptcoveff);
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    strcpy(dirfileres,optionfilefiname);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcpy(optfileres,"vpl");
       k=k+1;   /* 1eme*/
       fprintf(ficresvpl,"\n#****** ");    for (cpt=1; cpt<= nlstate ; cpt ++) {
       for(j=1;j<=cptcoveff;j++)     for (k1=1; k1<= m ; k1 ++) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
       fprintf(ficresvpl,"******\n");       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
             fprintf(ficgp,"set xlabel \"Age\" \n\
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  set ylabel \"Probability\" \n\
       oldm=oldms;savm=savms;  set ter png small\n\
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  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 ++) {
   fclose(ficresvpl);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*---------- End : free ----------------*/       }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       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 ++) {
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
         fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       for (i=1; i<= nlstate ; i ++) {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       }  
         fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
   free_matrix(matcov,1,npar,1,npar);     }
   free_vector(delti,1,npar);    }
   free_matrix(agev,1,maxwav,1,imx);    /*2 eme*/
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    
     for (k1=1; k1<= m ; k1 ++) { 
   if(erreur >0)      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     printf("End of Imach with error %d\n",erreur);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   else   printf("End of Imach\n");      
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      for (i=1; i<= nlstate+1 ; i ++) {
          k=2*i;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for (j=1; j<= nlstate+1 ; j ++) {
   /*------ End -----------*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
  end:        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
 #ifdef windows        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   /* chdir(pathcd);*/        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
 #endif        for (j=1; j<= nlstate+1 ; j ++) {
  /*system("wgnuplot graph.plt");*/          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  /*system("../gp37mgw/wgnuplot graph.plt");*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
  /*system("cd ../gp37mgw");*/        }   
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        fprintf(ficgp,"\" t\"\" w l 0,");
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
  strcat(plotcmd," ");        for (j=1; j<= nlstate+1 ; j ++) {
  strcat(plotcmd,optionfilegnuplot);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
  system(plotcmd);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
 #ifdef windows        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   while (z[0] != 'q') {        else fprintf(ficgp,"\" t\"\" w l 0,");
     chdir(path);      }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    }
     scanf("%s",z);    
     if (z[0] == 'c') system("./imach");    /*3eme*/
     else if (z[0] == 'e') {    
       chdir(path);    for (k1=1; k1<= m ; k1 ++) { 
       system(optionfilehtm);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     }        k=2+nlstate*(2*cpt-2);
     else if (z[0] == 'q') exit(0);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   }        fprintf(ficgp,"set ter png small\n\
 #endif  set size 0.65,0.65\n\
 }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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) {
           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){
     int i;
   
     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>");
     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 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];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     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;
     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],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,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;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); 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;
       }
     }
     /* 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 parameter 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){
           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);
   
     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 (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    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;
           
           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]=0.1; p[2]=0.1;
       /*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]));
       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);
     } /* 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,"#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,"#****** 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);
   
       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);  
    
           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);
           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);
           }
   
    
           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);
           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\nLocaltime 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);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" 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.1.30  
changed lines
  Added in v.1.103


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