Diff for /imach/src/imach.c between versions 1.15 and 1.94

version 1.15, 2002/02/20 17:08:52 version 1.94, 2003/06/27 13:00:02
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.94  2003/06/27 13:00:02  brouard
   individuals from different ages are interviewed on their health status    Just cleaning
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.93  2003/06/25 16:33:55  brouard
   Health expectancies are computed from the transistions observed between    (Module): On windows (cygwin) function asctime_r doesn't
   waves and are computed for each degree of severity of disability (number    exist so I changed back to asctime which exists.
   of life states). More degrees you consider, more time is necessary to    (Module): Version 0.96b
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.92  2003/06/25 16:30:45  brouard
   the probabibility to be observed in state j at the second wave conditional    (Module): On windows (cygwin) function asctime_r doesn't
   to be observed in state i at the first wave. Therefore the model is:    exist so I changed back to asctime which exists.
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.91  2003/06/25 15:30:29  brouard
   age", you should modify the program where the markup    * imach.c (Repository): Duplicated warning errors corrected.
     *Covariates have to be included here again* invites you to do it.    (Repository): Elapsed time after each iteration is now output. It
   More covariates you add, less is the speed of the convergence.    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
   The advantage that this computer programme claims, comes from that if the    concerning matrix of covariance. It has extension -cov.htm.
   delay between waves is not identical for each individual, or if some  
   individual missed an interview, the information is not rounded or lost, but    Revision 1.90  2003/06/24 12:34:15  brouard
   taken into account using an interpolation or extrapolation.    (Module): Some bugs corrected for windows. Also, when
   hPijx is the probability to be    mle=-1 a template is output in file "or"mypar.txt with the design
   observed in state i at age x+h conditional to the observed state i at age    of the covariance matrix to be input.
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.89  2003/06/24 12:30:52  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    (Module): Some bugs corrected for windows. Also, when
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    mle=-1 a template is output in file "or"mypar.txt with the design
   and the contribution of each individual to the likelihood is simply hPijx.    of the covariance matrix to be input.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.88  2003/06/23 17:54:56  brouard
   of the life expectancies. It also computes the prevalence limits.    * 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.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.87  2003/06/18 12:26:01  brouard
            Institut national d'études démographiques, Paris.    Version 0.96
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.86  2003/06/17 20:04:08  brouard
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Change position of html and gnuplot routines and added
   software can be distributed freely for non commercial use. Latest version    routine fileappend.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.85  2003/06/17 13:12:43  brouard
      * imach.c (Repository): Check when date of death was earlier that
 #include <math.h>    current date of interview. It may happen when the death was just
 #include <stdio.h>    prior to the death. In this case, dh was negative and likelihood
 #include <stdlib.h>    was wrong (infinity). We still send an "Error" but patch by
 #include <unistd.h>    assuming that the date of death was just one stepm after the
     interview.
 #define MAXLINE 256    (Repository): Because some people have very long ID (first column)
 #define FILENAMELENGTH 80    we changed int to long in num[] and we added a new lvector for
 /*#define DEBUG*/    memory allocation. But we also truncated to 8 characters (left
 #define windows    truncation)
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Repository): No more line truncation errors.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.84  2003/06/13 21:44:43  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    * imach.c (Repository): Replace "freqsummary" at a correct
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 #define NINTERVMAX 8    parcimony.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.83  2003/06/10 13:39:11  lievre
 #define MAXN 20000    *** empty log message ***
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.82  2003/06/05 15:57:20  brouard
 #define AGEBASE 40    Add log in  imach.c and  fullversion number is now printed.
   
   */
 int nvar;  /*
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;     Interpolated Markov Chain
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Short summary of the programme:
 int ndeath=1; /* Number of dead states */    
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    This program computes Healthy Life Expectancies from
 int popbased=0;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 int *wav; /* Number of waves for this individuual 0 is possible */    interviewed on their health status or degree of disability (in the
 int maxwav; /* Maxim number of waves */    case of a health survey which is our main interest) -2- at least a
 int jmin, jmax; /* min, max spacing between 2 waves */    second wave of interviews ("longitudinal") which measure each change
 int mle, weightopt;    (if any) in individual health status.  Health expectancies are
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    computed from the time spent in each health state according to a
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    model. More health states you consider, more time is necessary to reach the
 double jmean; /* Mean space between 2 waves */    Maximum Likelihood of the parameters involved in the model.  The
 double **oldm, **newm, **savm; /* Working pointers to matrices */    simplest model is the multinomial logistic model where pij is the
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    probability to be observed in state j at the second wave
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    conditional to be observed in state i at the first wave. Therefore
 FILE *ficgp, *fichtm,*ficresprob;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 FILE *ficreseij;    'age' is age and 'sex' is a covariate. If you want to have a more
   char filerese[FILENAMELENGTH];    complex model than "constant and age", you should modify the program
  FILE  *ficresvij;    where the markup *Covariates have to be included here again* invites
   char fileresv[FILENAMELENGTH];    you to do it.  More covariates you add, slower the
  FILE  *ficresvpl;    convergence.
   char fileresvpl[FILENAMELENGTH];  
     The advantage of this computer programme, compared to a simple
 #define NR_END 1    multinomial logistic model, is clear when the delay between waves is not
 #define FREE_ARG char*    identical for each individual. Also, if a individual missed an
 #define FTOL 1.0e-10    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 #define NRANSI  
 #define ITMAX 200    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
 #define TOL 2.0e-4    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 #define CGOLD 0.3819660    semester or year) is modelled as a multinomial logistic.  The hPx
 #define ZEPS 1.0e-10    matrix is simply the matrix product of nh*stepm elementary matrices
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    and the contribution of each individual to the likelihood is simply
     hPijx.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Also this programme outputs the covariance matrix of the parameters but also
 #define TINY 1.0e-20    of the life expectancies. It also computes the stable prevalence. 
     
 static double maxarg1,maxarg2;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))             Institut national d'études démographiques, Paris.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    This software have been partly granted by Euro-REVES, a concerted action
      from the European Union.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    It is copyrighted identically to a GNU software product, ie programme and
 #define rint(a) floor(a+0.5)    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 int imx;    **********************************************************************/
 int stepm;  /*
 /* Stepm, step in month: minimum step interpolation*/    main
     read parameterfile
 int m,nb;    read datafile
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    concatwav
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    freqsummary
 double **pmmij, ***probs, ***mobaverage;    if (mle >= 1)
       mlikeli
 double *weight;    print results files
 int **s; /* Status */    if mle==1 
 double *agedc, **covar, idx;       computes hessian
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    open gnuplot file
 double ftolhess; /* Tolerance for computing hessian */    open html file
     stable prevalence
 /**************** split *************************/     for age prevalim()
 static  int split( char *path, char *dirc, char *name )    h Pij x
 {    variance of p varprob
    char *s;                             /* pointer */    forecasting if prevfcast==1 prevforecast call prevalence()
    int  l1, l2;                         /* length counters */    health expectancies
     Variance-covariance of DFLE
    l1 = strlen( path );                 /* length of path */    prevalence()
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );     movingaverage()
    s = strrchr( path, '\\' );           /* find last / */    varevsij() 
    if ( s == NULL ) {                   /* no directory, so use current */    if popbased==1 varevsij(,popbased)
 #if     defined(__bsd__)                /* get current working directory */    total life expectancies
       extern char       *getwd( );    Variance of stable prevalence
    end
       if ( getwd( dirc ) == NULL ) {  */
 #else  
       extern char       *getcwd( );  
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {   
 #endif  #include <math.h>
          return( GLOCK_ERROR_GETCWD );  #include <stdio.h>
       }  #include <stdlib.h>
       strcpy( name, path );             /* we've got it */  #include <unistd.h>
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  #include <sys/time.h>
       l2 = strlen( s );                 /* length of filename */  #include <time.h>
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #include "timeval.h"
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define MAXLINE 256
       dirc[l1-l2] = 0;                  /* add zero */  #define GNUPLOTPROGRAM "gnuplot"
    }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
    l1 = strlen( dirc );                 /* length of directory */  #define FILENAMELENGTH 132
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  /*#define DEBUG*/
    return( 0 );                         /* we're done */  /*#define windows*/
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 /******************************************/  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 void replace(char *s, char*t)  
 {  #define NINTERVMAX 8
   int i;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   int lg=20;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   i=0;  #define NCOVMAX 8 /* Maximum number of covariates */
   lg=strlen(t);  #define MAXN 20000
   for(i=0; i<= lg; i++) {  #define YEARM 12. /* Number of months per year */
     (s[i] = t[i]);  #define AGESUP 130
     if (t[i]== '\\') s[i]='/';  #define AGEBASE 40
   }  #ifdef unix
 }  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 int nbocc(char *s, char occ)  #else
 {  #define DIRSEPARATOR '\\'
   int i,j=0;  #define ODIRSEPARATOR '/'
   int lg=20;  #endif
   i=0;  
   lg=strlen(s);  /* $Id$ */
   for(i=0; i<= lg; i++) {  /* $State$ */
   if  (s[i] == occ ) j++;  
   }  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
   return j;  char fullversion[]="$Revision$ $Date$"; 
 }  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nvar;
 void cutv(char *u,char *v, char*t, char occ)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 {  int npar=NPARMAX;
   int i,lg,j,p=0;  int nlstate=2; /* Number of live states */
   i=0;  int ndeath=1; /* Number of dead states */
   for(j=0; j<=strlen(t)-1; j++) {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  int popbased=0;
   }  
   int *wav; /* Number of waves for this individuual 0 is possible */
   lg=strlen(t);  int maxwav; /* Maxim number of waves */
   for(j=0; j<p; j++) {  int jmin, jmax; /* min, max spacing between 2 waves */
     (u[j] = t[j]);  int gipmx, gsw; /* Global variables on the number of contributions 
   }                     to the likelihood and the sum of weights (done by funcone)*/
      u[p]='\0';  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    for(j=0; j<= lg; j++) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     if (j>=(p+1))(v[j-p-1] = t[j]);  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. */
 }  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 /********************** nrerror ********************/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 void nrerror(char error_text[])  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   fprintf(stderr,"ERREUR ...\n");  double fretone; /* Only one call to likelihood */
   fprintf(stderr,"%s\n",error_text);  long ipmx; /* Number of contributions */
   exit(1);  double sw; /* Sum of weights */
 }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 /*********************** vector *******************/  FILE *ficresilk;
 double *vector(int nl, int nh)  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
   double *v;  FILE *fichtm, *fichtmcov; /* Html File */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  FILE *ficreseij;
   if (!v) nrerror("allocation failure in vector");  char filerese[FILENAMELENGTH];
   return v-nl+NR_END;  FILE  *ficresvij;
 }  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 /************************ free vector ******************/  char fileresvpl[FILENAMELENGTH];
 void free_vector(double*v, int nl, int nh)  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 }  char tmpout[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
 /************************ivector *******************************/  int  outcmd=0;
 int *ivector(long nl,long nh)  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  char filelog[FILENAMELENGTH]; /* Log file */
   if (!v) nrerror("allocation failure in ivector");  char filerest[FILENAMELENGTH];
   return v-nl+NR_END;  char fileregp[FILENAMELENGTH];
 }  char popfile[FILENAMELENGTH];
   
 /******************free ivector **************************/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 void free_ivector(int *v, long nl, long nh)  
 {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   free((FREE_ARG)(v+nl-NR_END));  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /******************* imatrix *******************************/  long time_value;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  extern long time();
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  char strcurr[80], strfor[80];
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define NR_END 1
   int **m;  #define FREE_ARG char*
    #define FTOL 1.0e-10
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define NRANSI 
   if (!m) nrerror("allocation failure 1 in matrix()");  #define ITMAX 200 
   m += NR_END;  
   m -= nrl;  #define TOL 2.0e-4 
    
    #define CGOLD 0.3819660 
   /* allocate rows and set pointers to them */  #define ZEPS 1.0e-10 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define GOLD 1.618034 
   m[nrl] -= ncl;  #define GLIMIT 100.0 
    #define TINY 1.0e-20 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    static double maxarg1,maxarg2;
   /* return pointer to array of pointers to rows */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   return m;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /****************** free_imatrix *************************/  #define rint(a) floor(a+0.5)
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  static double sqrarg;
       long nch,ncl,nrh,nrl;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
      /* free an int matrix allocated by imatrix() */  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int imx; 
   free((FREE_ARG) (m+nrl-NR_END));  int stepm;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /******************* matrix *******************************/  int estepm;
 double **matrix(long nrl, long nrh, long ncl, long nch)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int m,nb;
   double **m;  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   if (!m) nrerror("allocation failure 1 in matrix()");  double **pmmij, ***probs;
   m += NR_END;  double dateintmean=0;
   m -= nrl;  
   double *weight;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int **s; /* Status */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double *agedc, **covar, idx;
   m[nrl] += NR_END;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m[nrl] -= ncl;  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double ftolhess; /* Tolerance for computing hessian */
   return m;  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 /*************************free matrix ************************/  {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    char  *ss;                            /* pointer */
 {    int   l1, l2;                         /* length counters */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    l1 = strlen(path );                   /* length of path */
 }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 /******************* ma3x *******************************/    if ( ss == NULL ) {                   /* no directory, so use current */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;      /* get current working directory */
   double ***m;      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));        return( GLOCK_ERROR_GETCWD );
   if (!m) nrerror("allocation failure 1 in matrix()");      }
   m += NR_END;      strcpy( name, path );               /* we've got it */
   m -= nrl;    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      l2 = strlen( ss );                  /* length of filename */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl] += NR_END;      strcpy( name, ss );         /* save file name */
   m[nrl] -= ncl;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    }
     l1 = strlen( dirc );                  /* length of directory */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    /*#ifdef windows
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   m[nrl][ncl] += NR_END;  #else
   m[nrl][ncl] -= nll;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   for (j=ncl+1; j<=nch; j++)  #endif
     m[nrl][j]=m[nrl][j-1]+nlay;    */
      ss = strrchr( name, '.' );            /* find last / */
   for (i=nrl+1; i<=nrh; i++) {    ss++;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    strcpy(ext,ss);                       /* save extension */
     for (j=ncl+1; j<=nch; j++)    l1= strlen( name);
       m[i][j]=m[i][j-1]+nlay;    l2= strlen(ss)+1;
   }    strncpy( finame, name, l1-l2);
   return m;    finame[l1-l2]= 0;
 }    return( 0 );                          /* we're done */
   }
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  /******************************************/
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  void replace_back_to_slash(char *s, char*t)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    int i;
     int lg=0;
 /***************** f1dim *************************/    i=0;
 extern int ncom;    lg=strlen(t);
 extern double *pcom,*xicom;    for(i=0; i<= lg; i++) {
 extern double (*nrfunc)(double []);      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
 double f1dim(double x)    }
 {  }
   int j;  
   double f;  int nbocc(char *s, char occ)
   double *xt;  {
      int i,j=0;
   xt=vector(1,ncom);    int lg=20;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    i=0;
   f=(*nrfunc)(xt);    lg=strlen(s);
   free_vector(xt,1,ncom);    for(i=0; i<= lg; i++) {
   return f;    if  (s[i] == occ ) j++;
 }    }
     return j;
 /*****************brent *************************/  }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  void cutv(char *u,char *v, char*t, char occ)
   int iter;  {
   double a,b,d,etemp;    /* cuts string t into u and v where u is ended by char occ excluding it
   double fu,fv,fw,fx;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   double ftemp;       gives u="abcedf" and v="ghi2j" */
   double p,q,r,tol1,tol2,u,v,w,x,xm;    int i,lg,j,p=0;
   double e=0.0;    i=0;
      for(j=0; j<=strlen(t)-1; j++) {
   a=(ax < cx ? ax : cx);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   b=(ax > cx ? ax : cx);    }
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    lg=strlen(t);
   for (iter=1;iter<=ITMAX;iter++) {    for(j=0; j<p; j++) {
     xm=0.5*(a+b);      (u[j] = t[j]);
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/       u[p]='\0';
     printf(".");fflush(stdout);  
 #ifdef DEBUG     for(j=0; j<= lg; 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);      if (j>=(p+1))(v[j-p-1] = t[j]);
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    }
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /********************** nrerror ********************/
       return fx;  
     }  void nrerror(char error_text[])
     ftemp=fu;  {
     if (fabs(e) > tol1) {    fprintf(stderr,"ERREUR ...\n");
       r=(x-w)*(fx-fv);    fprintf(stderr,"%s\n",error_text);
       q=(x-v)*(fx-fw);    exit(EXIT_FAILURE);
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  /*********************** vector *******************/
       if (q > 0.0) p = -p;  double *vector(int nl, int nh)
       q=fabs(q);  {
       etemp=e;    double *v;
       e=d;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    if (!v) nrerror("allocation failure in vector");
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    return v-nl+NR_END;
       else {  }
         d=p/q;  
         u=x+d;  /************************ free vector ******************/
         if (u-a < tol2 || b-u < tol2)  void free_vector(double*v, int nl, int nh)
           d=SIGN(tol1,xm-x);  {
       }    free((FREE_ARG)(v+nl-NR_END));
     } else {  }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  /************************ivector *******************************/
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int *ivector(long nl,long nh)
     fu=(*f)(u);  {
     if (fu <= fx) {    int *v;
       if (u >= x) a=x; else b=x;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       SHFT(v,w,x,u)    if (!v) nrerror("allocation failure in ivector");
         SHFT(fv,fw,fx,fu)    return v-nl+NR_END;
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /******************free ivector **************************/
             v=w;  void free_ivector(int *v, long nl, long nh)
             w=u;  {
             fv=fw;    free((FREE_ARG)(v+nl-NR_END));
             fw=fu;  }
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /************************lvector *******************************/
             fv=fu;  long *lvector(long nl,long nh)
           }  {
         }    long *v;
   }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   nrerror("Too many iterations in brent");    if (!v) nrerror("allocation failure in ivector");
   *xmin=x;    return v-nl+NR_END;
   return fx;  }
 }  
   /******************free lvector **************************/
 /****************** mnbrak ***********************/  void free_lvector(long *v, long nl, long nh)
   {
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    free((FREE_ARG)(v+nl-NR_END));
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  /******************* imatrix *******************************/
   double fu;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   *fa=(*func)(*ax);  { 
   *fb=(*func)(*bx);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   if (*fb > *fa) {    int **m; 
     SHFT(dum,*ax,*bx,dum)    
       SHFT(dum,*fb,*fa,dum)    /* allocate pointers to rows */ 
       }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   *cx=(*bx)+GOLD*(*bx-*ax);    if (!m) nrerror("allocation failure 1 in matrix()"); 
   *fc=(*func)(*cx);    m += NR_END; 
   while (*fb > *fc) {    m -= nrl; 
     r=(*bx-*ax)*(*fb-*fc);    
     q=(*bx-*cx)*(*fb-*fa);    
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    /* allocate rows and set pointers to them */ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     if ((*bx-u)*(u-*cx) > 0.0) {    m[nrl] += NR_END; 
       fu=(*func)(u);    m[nrl] -= ncl; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    
       fu=(*func)(u);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       if (fu < *fc) {    
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* return pointer to array of pointers to rows */ 
           SHFT(*fb,*fc,fu,(*func)(u))    return m; 
           }  } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /****************** free_imatrix *************************/
       fu=(*func)(u);  void free_imatrix(m,nrl,nrh,ncl,nch)
     } else {        int **m;
       u=(*cx)+GOLD*(*cx-*bx);        long nch,ncl,nrh,nrl; 
       fu=(*func)(u);       /* free an int matrix allocated by imatrix() */ 
     }  { 
     SHFT(*ax,*bx,*cx,u)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       SHFT(*fa,*fb,*fc,fu)    free((FREE_ARG) (m+nrl-NR_END)); 
       }  } 
 }  
   /******************* matrix *******************************/
 /*************** linmin ************************/  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 int ncom;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 double *pcom,*xicom;    double **m;
 double (*nrfunc)(double []);  
      m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   double brent(double ax, double bx, double cx,    m -= nrl;
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
               double *fc, double (*func)(double));    m[nrl] += NR_END;
   int j;    m[nrl] -= ncl;
   double xx,xmin,bx,ax;  
   double fx,fb,fa;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
      return m;
   ncom=n;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   pcom=vector(1,n);     */
   xicom=vector(1,n);  }
   nrfunc=func;  
   for (j=1;j<=n;j++) {  /*************************free matrix ************************/
     pcom[j]=p[j];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     xicom[j]=xi[j];  {
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   ax=0.0;    free((FREE_ARG)(m+nrl-NR_END));
   xx=1.0;  }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /******************* ma3x *******************************/
 #ifdef DEBUG  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  {
 #endif    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (j=1;j<=n;j++) {    double ***m;
     xi[j] *= xmin;  
     p[j] += xi[j];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
   free_vector(xicom,1,n);    m += NR_END;
   free_vector(pcom,1,n);    m -= nrl;
 }  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /*************** powell ************************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    m[nrl] += NR_END;
             double (*func)(double []))    m[nrl] -= ncl;
 {  
   void linmin(double p[], double xi[], int n, double *fret,    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
               double (*func)(double []));  
   int i,ibig,j;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double del,t,*pt,*ptt,*xit;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double fp,fptt;    m[nrl][ncl] += NR_END;
   double *xits;    m[nrl][ncl] -= nll;
   pt=vector(1,n);    for (j=ncl+1; j<=nch; j++) 
   ptt=vector(1,n);      m[nrl][j]=m[nrl][j-1]+nlay;
   xit=vector(1,n);    
   xits=vector(1,n);    for (i=nrl+1; i<=nrh; i++) {
   *fret=(*func)(p);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (j=1;j<=n;j++) pt[j]=p[j];      for (j=ncl+1; j<=nch; j++) 
   for (*iter=1;;++(*iter)) {        m[i][j]=m[i][j-1]+nlay;
     fp=(*fret);    }
     ibig=0;    return m; 
     del=0.0;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     for (i=1;i<=n;i++)    */
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  /*************************free ma3x ************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       fptt=(*fret);  {
 #ifdef DEBUG    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       printf("fret=%lf \n",*fret);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #endif    free((FREE_ARG)(m+nrl-NR_END));
       printf("%d",i);fflush(stdout);  }
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /*************** function subdirf ***********/
         del=fabs(fptt-(*fret));  char *subdirf(char fileres[])
         ibig=i;  {
       }    /* Caution optionfilefiname is hidden */
 #ifdef DEBUG    strcpy(tmpout,optionfilefiname);
       printf("%d %.12e",i,(*fret));    strcat(tmpout,"/"); /* Add to the right */
       for (j=1;j<=n;j++) {    strcat(tmpout,fileres);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    return tmpout;
         printf(" x(%d)=%.12e",j,xit[j]);  }
       }  
       for(j=1;j<=n;j++)  /*************** function subdirf2 ***********/
         printf(" p=%.12e",p[j]);  char *subdirf2(char fileres[], char *preop)
       printf("\n");  {
 #endif    
     }    /* Caution optionfilefiname is hidden */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    strcpy(tmpout,optionfilefiname);
 #ifdef DEBUG    strcat(tmpout,"/");
       int k[2],l;    strcat(tmpout,preop);
       k[0]=1;    strcat(tmpout,fileres);
       k[1]=-1;    return tmpout;
       printf("Max: %.12e",(*func)(p));  }
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /*************** function subdirf3 ***********/
       printf("\n");  char *subdirf3(char fileres[], char *preop, char *preop2)
       for(l=0;l<=1;l++) {  {
         for (j=1;j<=n;j++) {    
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    /* Caution optionfilefiname is hidden */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    strcpy(tmpout,optionfilefiname);
         }    strcat(tmpout,"/");
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    strcat(tmpout,preop);
       }    strcat(tmpout,preop2);
 #endif    strcat(tmpout,fileres);
     return tmpout;
   }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /***************** f1dim *************************/
       free_vector(ptt,1,n);  extern int ncom; 
       free_vector(pt,1,n);  extern double *pcom,*xicom;
       return;  extern double (*nrfunc)(double []); 
     }   
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  double f1dim(double x) 
     for (j=1;j<=n;j++) {  { 
       ptt[j]=2.0*p[j]-pt[j];    int j; 
       xit[j]=p[j]-pt[j];    double f;
       pt[j]=p[j];    double *xt; 
     }   
     fptt=(*func)(ptt);    xt=vector(1,ncom); 
     if (fptt < fp) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    f=(*nrfunc)(xt); 
       if (t < 0.0) {    free_vector(xt,1,ncom); 
         linmin(p,xit,n,fret,func);    return f; 
         for (j=1;j<=n;j++) {  } 
           xi[j][ibig]=xi[j][n];  
           xi[j][n]=xit[j];  /*****************brent *************************/
         }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 #ifdef DEBUG  { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    int iter; 
         for(j=1;j<=n;j++)    double a,b,d,etemp;
           printf(" %.12e",xit[j]);    double fu,fv,fw,fx;
         printf("\n");    double ftemp;
 #endif    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       }    double e=0.0; 
     }   
   }    a=(ax < cx ? ax : cx); 
 }    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
 /**** Prevalence limit ****************/    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      xm=0.5*(a+b); 
 {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      matrix by transitions matrix until convergence is reached */      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   int i, ii,j,k;  #ifdef DEBUG
   double min, max, maxmin, maxmax,sumnew=0.;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double **matprod2();      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double **out, cov[NCOVMAX], **pmij();      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   double **newm;  #endif
   double agefin, delaymax=50 ; /* Max number of years to converge */      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
   for (ii=1;ii<=nlstate+ndeath;ii++)        return fx; 
     for (j=1;j<=nlstate+ndeath;j++){      } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      ftemp=fu;
     }      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
    cov[1]=1.;        q=(x-v)*(fx-fw); 
          p=(x-v)*q-(x-w)*r; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        q=2.0*(q-r); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        if (q > 0.0) p = -p; 
     newm=savm;        q=fabs(q); 
     /* Covariates have to be included here again */        etemp=e; 
      cov[2]=agefin;        e=d; 
          if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       for (k=1; k<=cptcovn;k++) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        else { 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/          d=p/q; 
       }          u=x+d; 
       for (k=1; k<=cptcovage;k++)          if (u-a < tol2 || b-u < tol2) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            d=SIGN(tol1,xm-x); 
       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]]];      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      } 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
     savm=oldm;        SHFT(v,w,x,u) 
     oldm=newm;          SHFT(fv,fw,fx,fu) 
     maxmax=0.;          } else { 
     for(j=1;j<=nlstate;j++){            if (u < x) a=u; else b=u; 
       min=1.;            if (fu <= fw || w == x) { 
       max=0.;              v=w; 
       for(i=1; i<=nlstate; i++) {              w=u; 
         sumnew=0;              fv=fw; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];              fw=fu; 
         prlim[i][j]= newm[i][j]/(1-sumnew);            } else if (fu <= fv || v == x || v == w) { 
         max=FMAX(max,prlim[i][j]);              v=u; 
         min=FMIN(min,prlim[i][j]);              fv=fu; 
       }            } 
       maxmin=max-min;          } 
       maxmax=FMAX(maxmax,maxmin);    } 
     }    nrerror("Too many iterations in brent"); 
     if(maxmax < ftolpl){    *xmin=x; 
       return prlim;    return fx; 
     }  } 
   }  
 }  /****************** mnbrak ***********************/
   
 /*************** transition probabilities ***************/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  { 
 {    double ulim,u,r,q, dum;
   double s1, s2;    double fu; 
   /*double t34;*/   
   int i,j,j1, nc, ii, jj;    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
     for(i=1; i<= nlstate; i++){    if (*fb > *fa) { 
     for(j=1; j<i;j++){      SHFT(dum,*ax,*bx,dum) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        SHFT(dum,*fb,*fa,dum) 
         /*s2 += param[i][j][nc]*cov[nc];*/        } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    *cx=(*bx)+GOLD*(*bx-*ax); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    *fc=(*func)(*cx); 
       }    while (*fb > *fc) { 
       ps[i][j]=s2;      r=(*bx-*ax)*(*fb-*fc); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      q=(*bx-*cx)*(*fb-*fa); 
     }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(j=i+1; j<=nlstate+ndeath;j++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      if ((*bx-u)*(u-*cx) > 0.0) { 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        fu=(*func)(u); 
       }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       ps[i][j]=(s2);        fu=(*func)(u); 
     }        if (fu < *fc) { 
   }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     /*ps[3][2]=1;*/            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
   for(i=1; i<= nlstate; i++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
      s1=0;        u=ulim; 
     for(j=1; j<i; j++)        fu=(*func)(u); 
       s1+=exp(ps[i][j]);      } else { 
     for(j=i+1; j<=nlstate+ndeath; j++)        u=(*cx)+GOLD*(*cx-*bx); 
       s1+=exp(ps[i][j]);        fu=(*func)(u); 
     ps[i][i]=1./(s1+1.);      } 
     for(j=1; j<i; j++)      SHFT(*ax,*bx,*cx,u) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        SHFT(*fa,*fb,*fc,fu) 
     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 */  
   } /* end i */  /*************** linmin ************************/
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  int ncom; 
     for(jj=1; jj<= nlstate+ndeath; jj++){  double *pcom,*xicom;
       ps[ii][jj]=0;  double (*nrfunc)(double []); 
       ps[ii][ii]=1;   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   }  { 
     double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double f1dim(double x); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
      printf("%lf ",ps[ii][jj]);                double *fc, double (*func)(double)); 
    }    int j; 
     printf("\n ");    double xx,xmin,bx,ax; 
     }    double fx,fb,fa;
     printf("\n ");printf("%lf ",cov[2]);*/   
 /*    ncom=n; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    pcom=vector(1,n); 
   goto end;*/    xicom=vector(1,n); 
     return ps;    nrfunc=func; 
 }    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
 /**************** Product of 2 matrices ******************/      xicom[j]=xi[j]; 
     } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    ax=0.0; 
 {    xx=1.0; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   /* in, b, out are matrice of pointers which should have been initialized  #ifdef DEBUG
      before: only the contents of out is modified. The function returns    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      a pointer to pointers identical to out */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   long i, j, k;  #endif
   for(i=nrl; i<= nrh; i++)    for (j=1;j<=n;j++) { 
     for(k=ncolol; k<=ncoloh; k++)      xi[j] *= xmin; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      p[j] += xi[j]; 
         out[i][k] +=in[i][j]*b[j][k];    } 
     free_vector(xicom,1,n); 
   return out;    free_vector(pcom,1,n); 
 }  } 
   
   char *asc_diff_time(long time_sec, char ascdiff[])
 /************* Higher Matrix Product ***************/  {
     long sec_left, days, hours, minutes;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    days = (time_sec) / (60*60*24);
 {    sec_left = (time_sec) % (60*60*24);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    hours = (sec_left) / (60*60) ;
      duration (i.e. until    sec_left = (sec_left) %(60*60);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    minutes = (sec_left) /60;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    sec_left = (sec_left) % (60);
      (typically every 2 years instead of every month which is too big).    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
      Model is determined by parameters x and covariates have to be    return ascdiff;
      included manually here.  }
   
      */  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   int i, j, d, h, k;              double (*func)(double [])) 
   double **out, cov[NCOVMAX];  { 
   double **newm;    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   /* Hstepm could be zero and should return the unit matrix */    int i,ibig,j; 
   for (i=1;i<=nlstate+ndeath;i++)    double del,t,*pt,*ptt,*xit;
     for (j=1;j<=nlstate+ndeath;j++){    double fp,fptt;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double *xits;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    int niterf, itmp;
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    pt=vector(1,n); 
   for(h=1; h <=nhstepm; h++){    ptt=vector(1,n); 
     for(d=1; d <=hstepm; d++){    xit=vector(1,n); 
       newm=savm;    xits=vector(1,n); 
       /* Covariates have to be included here again */    *fret=(*func)(p); 
       cov[1]=1.;    for (j=1;j<=n;j++) pt[j]=p[j]; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    for (*iter=1;;++(*iter)) { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      fp=(*fret); 
       for (k=1; k<=cptcovage;k++)      ibig=0; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      del=0.0; 
       for (k=1; k<=cptcovprod;k++)      last_time=curr_time;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      (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);
       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);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for (i=1;i<=n;i++) {
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        printf(" %d %.12f",i, p[i]);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        fprintf(ficlog," %d %.12lf",i, p[i]);
       savm=oldm;        fprintf(ficrespow," %.12lf", p[i]);
       oldm=newm;      }
     }      printf("\n");
     for(i=1; i<=nlstate+ndeath; i++)      fprintf(ficlog,"\n");
       for(j=1;j<=nlstate+ndeath;j++) {      fprintf(ficrespow,"\n");fflush(ficrespow);
         po[i][j][h]=newm[i][j];      if(*iter <=3){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        tm = *localtime(&curr_time.tv_sec);
          */        strcpy(strcurr,asctime(&tmf));
       }  /*       asctime_r(&tm,strcurr); */
   } /* end h */        forecast_time=curr_time;
   return po;        itmp = strlen(strcurr);
 }        if(strcurr[itmp-1]=='\n')
           strcurr[itmp-1]='\0';
         printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 /*************** log-likelihood *************/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 double func( double *x)        for(niterf=10;niterf<=30;niterf+=10){
 {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   int i, ii, j, k, mi, d, kk;          tmf = *localtime(&forecast_time.tv_sec);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /*      asctime_r(&tmf,strfor); */
   double **out;          strcpy(strfor,asctime(&tmf));
   double sw; /* Sum of weights */          itmp = strlen(strfor);
   double lli; /* Individual log likelihood */          if(strfor[itmp-1]=='\n')
   long ipmx;          strfor[itmp-1]='\0';
   /*extern weight */          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   /* We are differentiating ll according to initial status */          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        }
   /*for(i=1;i<imx;i++)      }
     printf(" %d\n",s[4][i]);      for (i=1;i<=n;i++) { 
   */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   cov[1]=1.;        fptt=(*fret); 
   #ifdef DEBUG
   for(k=1; k<=nlstate; k++) ll[k]=0.;        printf("fret=%lf \n",*fret);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        fprintf(ficlog,"fret=%lf \n",*fret);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  #endif
     for(mi=1; mi<= wav[i]-1; mi++){        printf("%d",i);fflush(stdout);
       for (ii=1;ii<=nlstate+ndeath;ii++)        fprintf(ficlog,"%d",i);fflush(ficlog);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        linmin(p,xit,n,fret,func); 
       for(d=0; d<dh[mi][i]; d++){        if (fabs(fptt-(*fret)) > del) { 
         newm=savm;          del=fabs(fptt-(*fret)); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          ibig=i; 
         for (kk=1; kk<=cptcovage;kk++) {        } 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  #ifdef DEBUG
         }        printf("%d %.12e",i,(*fret));
                fprintf(ficlog,"%d %.12e",i,(*fret));
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        for (j=1;j<=n;j++) {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         savm=oldm;          printf(" x(%d)=%.12e",j,xit[j]);
         oldm=newm;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
                }
                for(j=1;j<=n;j++) {
       } /* end mult */          printf(" p=%.12e",p[j]);
                fprintf(ficlog," p=%.12e",p[j]);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        printf("\n");
       ipmx +=1;        fprintf(ficlog,"\n");
       sw += weight[i];  #endif
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      } 
     } /* end of wave */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   } /* end of individual */  #ifdef DEBUG
         int k[2],l;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        k[0]=1;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        k[1]=-1;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        printf("Max: %.12e",(*func)(p));
   return -l;        fprintf(ficlog,"Max: %.12e",(*func)(p));
 }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
 /*********** Maximum Likelihood Estimation ***************/        }
         printf("\n");
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        fprintf(ficlog,"\n");
 {        for(l=0;l<=1;l++) {
   int i,j, iter;          for (j=1;j<=n;j++) {
   double **xi,*delti;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   double fret;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   xi=matrix(1,npar,1,npar);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1;i<=npar;i++)          }
     for (j=1;j<=npar;j++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       xi[i][j]=(i==j ? 1.0 : 0.0);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   printf("Powell\n");        }
   powell(p,xi,npar,ftol,&iter,&fret,func);  #endif
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
 }        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 /**** Computes Hessian and covariance matrix ***/        return; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      } 
 {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double  **a,**y,*x,pd;      for (j=1;j<=n;j++) { 
   double **hess;        ptt[j]=2.0*p[j]-pt[j]; 
   int i, j,jk;        xit[j]=p[j]-pt[j]; 
   int *indx;        pt[j]=p[j]; 
       } 
   double hessii(double p[], double delta, int theta, double delti[]);      fptt=(*func)(ptt); 
   double hessij(double p[], double delti[], int i, int j);      if (fptt < fp) { 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
   hess=matrix(1,npar,1,npar);          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
   printf("\nCalculation of the hessian matrix. Wait...\n");            xi[j][n]=xit[j]; 
   for (i=1;i<=npar;i++){          }
     printf("%d",i);fflush(stdout);  #ifdef DEBUG
     hess[i][i]=hessii(p,ftolhess,i,delti);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     /*printf(" %f ",p[i]);*/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     /*printf(" %lf ",hess[i][i]);*/          for(j=1;j<=n;j++){
   }            printf(" %.12e",xit[j]);
              fprintf(ficlog," %.12e",xit[j]);
   for (i=1;i<=npar;i++) {          }
     for (j=1;j<=npar;j++)  {          printf("\n");
       if (j>i) {          fprintf(ficlog,"\n");
         printf(".%d%d",i,j);fflush(stdout);  #endif
         hess[i][j]=hessij(p,delti,i,j);        }
         hess[j][i]=hess[i][j];          } 
         /*printf(" %lf ",hess[i][j]);*/    } 
       }  } 
     }  
   }  /**** Prevalence limit (stable prevalence)  ****************/
   printf("\n");  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  {
      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   a=matrix(1,npar,1,npar);       matrix by transitions matrix until convergence is reached */
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);    int i, ii,j,k;
   indx=ivector(1,npar);    double min, max, maxmin, maxmax,sumnew=0.;
   for (i=1;i<=npar;i++)    double **matprod2();
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    double **out, cov[NCOVMAX], **pmij();
   ludcmp(a,npar,indx,&pd);    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    for (ii=1;ii<=nlstate+ndeath;ii++)
     x[j]=1;      for (j=1;j<=nlstate+ndeath;j++){
     lubksb(a,npar,indx,x);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++){      }
       matcov[i][j]=x[i];  
     }     cov[1]=1.;
   }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   printf("\n#Hessian matrix#\n");    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for (i=1;i<=npar;i++) {      newm=savm;
     for (j=1;j<=npar;j++) {      /* Covariates have to be included here again */
       printf("%.3e ",hess[i][j]);       cov[2]=agefin;
     }    
     printf("\n");        for (k=1; k<=cptcovn;k++) {
   }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   /* Recompute Inverse */        }
   for (i=1;i<=npar;i++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        for (k=1; k<=cptcovprod;k++)
   ludcmp(a,npar,indx,&pd);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   /*  printf("\n#Hessian matrix recomputed#\n");        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   for (j=1;j<=npar;j++) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for (i=1;i<=npar;i++) x[i]=0;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     x[j]=1;  
     lubksb(a,npar,indx,x);      savm=oldm;
     for (i=1;i<=npar;i++){      oldm=newm;
       y[i][j]=x[i];      maxmax=0.;
       printf("%.3e ",y[i][j]);      for(j=1;j<=nlstate;j++){
     }        min=1.;
     printf("\n");        max=0.;
   }        for(i=1; i<=nlstate; i++) {
   */          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   free_matrix(a,1,npar,1,npar);          prlim[i][j]= newm[i][j]/(1-sumnew);
   free_matrix(y,1,npar,1,npar);          max=FMAX(max,prlim[i][j]);
   free_vector(x,1,npar);          min=FMIN(min,prlim[i][j]);
   free_ivector(indx,1,npar);        }
   free_matrix(hess,1,npar,1,npar);        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
       }
 }      if(maxmax < ftolpl){
         return prlim;
 /*************** hessian matrix ****************/      }
 double hessii( double x[], double delta, int theta, double delti[])    }
 {  }
   int i;  
   int l=1, lmax=20;  /*************** transition probabilities ***************/ 
   double k1,k2;  
   double p2[NPARMAX+1];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   double res;  {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double s1, s2;
   double fx;    /*double t34;*/
   int k=0,kmax=10;    int i,j,j1, nc, ii, jj;
   double l1;  
       for(i=1; i<= nlstate; i++){
   fx=func(x);      for(j=1; j<i;j++){
   for (i=1;i<=npar;i++) p2[i]=x[i];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for(l=0 ; l <=lmax; l++){          /*s2 += param[i][j][nc]*cov[nc];*/
     l1=pow(10,l);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     delts=delt;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
     for(k=1 ; k <kmax; k=k+1){        }
       delt = delta*(l1*k);        ps[i][j]=s2;
       p2[theta]=x[theta] +delt;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       k1=func(p2)-fx;      }
       p2[theta]=x[theta]-delt;      for(j=i+1; j<=nlstate+ndeath;j++){
       k2=func(p2)-fx;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       /*res= (k1-2.0*fx+k2)/delt/delt; */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
              }
 #ifdef DEBUG        ps[i][j]=s2;
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      }
 #endif    }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      /*ps[3][2]=1;*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    for(i=1; i<= nlstate; i++){
       }       s1=0;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for(j=1; j<i; j++)
         k=kmax; l=lmax*10.;        s1+=exp(ps[i][j]);
       }      for(j=i+1; j<=nlstate+ndeath; j++)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        s1+=exp(ps[i][j]);
         delts=delt;      ps[i][i]=1./(s1+1.);
       }      for(j=1; j<i; j++)
     }        ps[i][j]= exp(ps[i][j])*ps[i][i];
   }      for(j=i+1; j<=nlstate+ndeath; j++)
   delti[theta]=delts;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   return res;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      } /* end i */
 }  
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 double hessij( double x[], double delti[], int thetai,int thetaj)      for(jj=1; jj<= nlstate+ndeath; jj++){
 {        ps[ii][jj]=0;
   int i;        ps[ii][ii]=1;
   int l=1, l1, lmax=20;      }
   double k1,k2,k3,k4,res,fx;    }
   double p2[NPARMAX+1];  
   int k;  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   fx=func(x);      for(jj=1; jj<= nlstate+ndeath; jj++){
   for (k=1; k<=2; k++) {       printf("%lf ",ps[ii][jj]);
     for (i=1;i<=npar;i++) p2[i]=x[i];     }
     p2[thetai]=x[thetai]+delti[thetai]/k;      printf("\n ");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      }
     k1=func(p2)-fx;      printf("\n ");printf("%lf ",cov[2]);*/
    /*
     p2[thetai]=x[thetai]+delti[thetai]/k;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    goto end;*/
     k2=func(p2)-fx;      return ps;
    }
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /**************** Product of 2 matrices ******************/
     k3=func(p2)-fx;  
    double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     k4=func(p2)-fx;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    /* in, b, out are matrice of pointers which should have been initialized 
 #ifdef DEBUG       before: only the contents of out is modified. The function returns
     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);       a pointer to pointers identical to out */
 #endif    long i, j, k;
   }    for(i=nrl; i<= nrh; i++)
   return res;      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];
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    return out;
 {  }
   int i,imax,j,k;  
   double big,dum,sum,temp;  
   double *vv;  /************* Higher Matrix Product ***************/
    
   vv=vector(1,n);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   *d=1.0;  {
   for (i=1;i<=n;i++) {    /* Computes the transition matrix starting at age 'age' over 
     big=0.0;       'nhstepm*hstepm*stepm' months (i.e. until
     for (j=1;j<=n;j++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       if ((temp=fabs(a[i][j])) > big) big=temp;       nhstepm*hstepm matrices. 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     vv[i]=1.0/big;       (typically every 2 years instead of every month which is too big 
   }       for the memory).
   for (j=1;j<=n;j++) {       Model is determined by parameters x and covariates have to be 
     for (i=1;i<j;i++) {       included manually here. 
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];       */
       a[i][j]=sum;  
     }    int i, j, d, h, k;
     big=0.0;    double **out, cov[NCOVMAX];
     for (i=j;i<=n;i++) {    double **newm;
       sum=a[i][j];  
       for (k=1;k<j;k++)    /* Hstepm could be zero and should return the unit matrix */
         sum -= a[i][k]*a[k][j];    for (i=1;i<=nlstate+ndeath;i++)
       a[i][j]=sum;      for (j=1;j<=nlstate+ndeath;j++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
         big=dum;        po[i][j][0]=(i==j ? 1.0 : 0.0);
         imax=i;      }
       }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
     if (j != imax) {      for(d=1; d <=hstepm; d++){
       for (k=1;k<=n;k++) {        newm=savm;
         dum=a[imax][k];        /* Covariates have to be included here again */
         a[imax][k]=a[j][k];        cov[1]=1.;
         a[j][k]=dum;        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]]];
       *d = -(*d);        for (k=1; k<=cptcovage;k++)
       vv[imax]=vv[j];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }        for (k=1; k<=cptcovprod;k++)
     indx[j]=imax;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  
       dum=1.0/(a[j][j]);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        /*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, 
   }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_vector(vv,1,n);  /* Doesn't work */        savm=oldm;
 ;        oldm=newm;
 }      }
       for(i=1; i<=nlstate+ndeath; i++)
 void lubksb(double **a, int n, int *indx, double b[])        for(j=1;j<=nlstate+ndeath;j++) {
 {          po[i][j][h]=newm[i][j];
   int i,ii=0,ip,j;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   double sum;           */
          }
   for (i=1;i<=n;i++) {    } /* end h */
     ip=indx[i];    return po;
     sum=b[ip];  }
     b[ip]=b[i];  
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /*************** log-likelihood *************/
     else if (sum) ii=i;  double func( double *x)
     b[i]=sum;  {
   }    int i, ii, j, k, mi, d, kk;
   for (i=n;i>=1;i--) {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     sum=b[i];    double **out;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    double sw; /* Sum of weights */
     b[i]=sum/a[i][i];    double lli; /* Individual log likelihood */
   }    int s1, s2;
 }    double bbh, survp;
     long ipmx;
 /************ Frequencies ********************/    /*extern weight */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)    /* We are differentiating ll according to initial status */
 {  /* Some frequencies */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      printf(" %d\n",s[4][i]);
   double ***freq; /* Frequencies */    */
   double *pp;    cov[1]=1.;
   double pos;  
   FILE *ficresp;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   char fileresp[FILENAMELENGTH];  
     if(mle==1){
   pp=vector(1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  probs= ma3x(1,130 ,1,8, 1,8);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcpy(fileresp,"p");        for(mi=1; mi<= wav[i]-1; mi++){
   strcat(fileresp,fileres);          for (ii=1;ii<=nlstate+ndeath;ii++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {            for (j=1;j<=nlstate+ndeath;j++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     exit(0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          for(d=0; d<dh[mi][i]; d++){
   j1=0;            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   j=cptcoveff;            for (kk=1; kk<=cptcovage;kk++) {
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   for(k1=1; k1<=j;k1++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    for(i1=1; i1<=ncodemax[k1];i1++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
        j1++;            savm=oldm;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            oldm=newm;
          scanf("%d", i);*/          } /* end mult */
         for (i=-1; i<=nlstate+ndeath; i++)          
          for (jk=-1; jk<=nlstate+ndeath; jk++)            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            for(m=agemin; m <= agemax+3; m++)          /* But now since version 0.9 we anticipate for bias and large stepm.
              freq[i][jk][m]=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
                   * (in months) between two waves is not a multiple of stepm, we rounded to 
        for (i=1; i<=imx; i++) {           * the nearest (and in case of equal distance, to the lowest) interval but now
          bool=1;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
          if  (cptcovn>0) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            for (z1=1; z1<=cptcoveff; z1++)           * probability in order to take into account the bias as a fraction of the way
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                bool=0;           * -stepm/2 to stepm/2 .
          }           * For stepm=1 the results are the same as for previous versions of Imach.
           if (bool==1) {           * For stepm > 1 the results are less biased than in previous versions. 
            for(m=fprev1; m<=lprev1; m++){           */
              if(agev[m][i]==0) agev[m][i]=agemax+1;          s1=s[mw[mi][i]][i];
              if(agev[m][i]==1) agev[m][i]=agemax+2;          s2=s[mw[mi+1][i]][i];
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          bbh=(double)bh[mi][i]/(double)stepm; 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          /* bias is positive if real duration
            }           * is higher than the multiple of stepm and negative otherwise.
          }           */
        }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         if  (cptcovn>0) {          if( s2 > nlstate){ 
          fprintf(ficresp, "\n#********** Variable ");            /* i.e. if s2 is a death state and if the date of death is known then the contribution
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);               to the likelihood is the probability to die between last step unit time and current 
        fprintf(ficresp, "**********\n#");               step unit time, which is also the differences between probability to die before dh 
         }               and probability to die before dh-stepm . 
        for(i=1; i<=nlstate;i++)               In version up to 0.92 likelihood was computed
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          as if date of death was unknown. Death was treated as any other
        fprintf(ficresp, "\n");          health state: the date of the interview describes the actual state
                  and not the date of a change in health state. The former idea was
   for(i=(int)agemin; i <= (int)agemax+3; i++){          to consider that at each interview the state was recorded
     if(i==(int)agemax+3)          (healthy, disable or death) and IMaCh was corrected; but when we
       printf("Total");          introduced the exact date of death then we should have modified
     else          the contribution of an exact death to the likelihood. This new
       printf("Age %d", i);          contribution is smaller and very dependent of the step unit
     for(jk=1; jk <=nlstate ; jk++){          stepm. It is no more the probability to die between last interview
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          and month of death but the probability to survive from last
         pp[jk] += freq[jk][m][i];          interview up to one month before death multiplied by the
     }          probability to die within a month. Thanks to Chris
     for(jk=1; jk <=nlstate ; jk++){          Jackson for correcting this bug.  Former versions increased
       for(m=-1, pos=0; m <=0 ; m++)          mortality artificially. The bad side is that we add another loop
         pos += freq[jk][m][i];          which slows down the processing. The difference can be up to 10%
       if(pp[jk]>=1.e-10)          lower mortality.
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            */
       else            lli=log(out[s1][s2] - savm[s1][s2]);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          }else{
     }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
      for(jk=1; jk <=nlstate ; jk++){          } 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         pp[jk] += freq[jk][m][i];          /*if(lli ==000.0)*/
      }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
     for(jk=1,pos=0; jk <=nlstate ; jk++)          sw += weight[i];
       pos += pp[jk];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
       if(pos>=1.e-5)      } /* end of individual */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    }  else if(mle==2){
       else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if( i <= (int) agemax){        for(mi=1; mi<= wav[i]-1; mi++){
         if(pos>=1.e-5){          for (ii=1;ii<=nlstate+ndeath;ii++)
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for (j=1;j<=nlstate+ndeath;j++){
           probs[i][jk][j1]= pp[jk]/pos;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
       else          for(d=0; d<=dh[mi][i]; d++){
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     for(jk=-1; jk <=nlstate+ndeath; jk++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(m=-1; m <=nlstate+ndeath; m++)            }
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if(i <= (int) agemax)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       fprintf(ficresp,"\n");            savm=oldm;
     printf("\n");            oldm=newm;
     }          } /* end mult */
     }        
  }          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   fclose(ficresp);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   free_vector(pp,1,nlstate);          ipmx +=1;
           sw += weight[i];
 }  /* End of Freq */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 /************ Prevalence ********************/      } /* end of individual */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)    }  else if(mle==3){  /* exponential inter-extrapolation */
 {  /* Some frequencies */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***freq; /* Frequencies */          for (ii=1;ii<=nlstate+ndeath;ii++)
   double *pp;            for (j=1;j<=nlstate+ndeath;j++){
   double pos;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   pp=vector(1,nlstate);            }
   probs= ma3x(1,130 ,1,8, 1,8);          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   j1=0;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   j=cptcoveff;            }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  for(k1=1; k1<=j;k1++){            savm=oldm;
     for(i1=1; i1<=ncodemax[k1];i1++){            oldm=newm;
       j1++;          } /* end mult */
          
       for (i=-1; i<=nlstate+ndeath; i++)            s1=s[mw[mi][i]][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)            s2=s[mw[mi+1][i]][i];
           for(m=agemin; m <= agemax+3; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
           freq[i][jk][m]=0;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
                ipmx +=1;
       for (i=1; i<=imx; i++) {          sw += weight[i];
         bool=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if  (cptcovn>0) {        } /* end of wave */
           for (z1=1; z1<=cptcoveff; z1++)      } /* end of individual */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    }else if (mle==4){  /* ml=4 no inter-extrapolation */
               bool=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if (bool==1) {        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=fprev1; m<=lprev1; m++){          for (ii=1;ii<=nlstate+ndeath;ii++)
             if(agev[m][i]==0) agev[m][i]=agemax+1;            for (j=1;j<=nlstate+ndeath;j++){
             if(agev[m][i]==1) agev[m][i]=agemax+2;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        for(i=(int)agemin; i <= (int)agemax+3; i++){            for (kk=1; kk<=cptcovage;kk++) {
         for(jk=1; jk <=nlstate ; jk++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            }
             pp[jk] += freq[jk][m][i];          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=-1, pos=0; m <=0 ; m++)            savm=oldm;
             pos += freq[jk][m][i];            oldm=newm;
         }          } /* end mult */
                
          for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          s2=s[mw[mi+1][i]][i];
              pp[jk] += freq[jk][m][i];          if( s2 > nlstate){ 
          }            lli=log(out[s1][s2] - savm[s1][s2]);
                    }else{
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
          for(jk=1; jk <=nlstate ; jk++){                    ipmx +=1;
            if( i <= (int) agemax){          sw += weight[i];
              if(pos>=1.e-5){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                probs[i][jk][j1]= pp[jk]/pos;  /*      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 */
          }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(pp,1,nlstate);            }
            for(d=0; d<dh[mi][i]; d++){
 }  /* End of Freq */            newm=savm;
 /************* Waves Concatenation ***************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 {            }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          
      Death is a valid wave (if date is known).            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            savm=oldm;
      and mw[mi+1][i]. dh depends on stepm.            oldm=newm;
      */          } /* end mult */
         
   int i, mi, m;          s1=s[mw[mi][i]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          s2=s[mw[mi+1][i]][i];
      double sum=0., jmean=0.;*/          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
   int j, k=0,jk, ju, jl;          sw += weight[i];
   double sum=0.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   jmin=1e+5;          /*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]);*/
   jmax=-1;        } /* end of wave */
   jmean=0.;      } /* end of individual */
   for(i=1; i<=imx; i++){    } /* End of if */
     mi=0;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     m=firstpass;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     while(s[m][i] <= nlstate){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       if(s[m][i]>=1)    return -l;
         mw[++mi][i]=m;  }
       if(m >=lastpass)  
         break;  /*************** log-likelihood *************/
       else  double funcone( double *x)
         m++;  {
     }/* end while */    /* Same as likeli but slower because of a lot of printf and if */
     if (s[m][i] > nlstate){    int i, ii, j, k, mi, d, kk;
       mi++;     /* Death is another wave */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       /* if(mi==0)  never been interviewed correctly before death */    double **out;
          /* Only death is a correct wave */    double lli; /* Individual log likelihood */
       mw[mi][i]=m;    double llt;
     }    int s1, s2;
     double bbh, survp;
     wav[i]=mi;    /*extern weight */
     if(mi==0)    /* We are differentiating ll according to initial status */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   for(i=1; i<=imx; i++){    */
     for(mi=1; mi<wav[i];mi++){    cov[1]=1.;
       if (stepm <=0)  
         dh[mi][i]=1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           if (agedc[i] < 2*AGESUP) {      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for(mi=1; mi<= wav[i]-1; mi++){
           if(j==0) j=1;  /* Survives at least one month after exam */        for (ii=1;ii<=nlstate+ndeath;ii++)
           k=k+1;          for (j=1;j<=nlstate+ndeath;j++){
           if (j >= jmax) jmax=j;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (j <= jmin) jmin=j;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           sum=sum+j;          }
           /* if (j<10) printf("j=%d num=%d ",j,i); */        for(d=0; d<dh[mi][i]; d++){
           }          newm=savm;
         }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         else{          for (kk=1; kk<=cptcovage;kk++) {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           k=k+1;          }
           if (j >= jmax) jmax=j;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           else if (j <= jmin)jmin=j;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          savm=oldm;
           sum=sum+j;          oldm=newm;
         }        } /* end mult */
         jk= j/stepm;        
         jl= j -jk*stepm;        s1=s[mw[mi][i]][i];
         ju= j -(jk+1)*stepm;        s2=s[mw[mi+1][i]][i];
         if(jl <= -ju)        bbh=(double)bh[mi][i]/(double)stepm; 
           dh[mi][i]=jk;        /* bias is positive if real duration
         else         * is higher than the multiple of stepm and negative otherwise.
           dh[mi][i]=jk+1;         */
         if(dh[mi][i]==0)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           dh[mi][i]=1; /* At least one step */          lli=log(out[s1][s2] - savm[s1][s2]);
       }        } else if (mle==1){
     }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }        } else if(mle==2){
   jmean=sum/k;          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 */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        } 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 */
 /*********** Tricode ****************************/        } else if (mle==4){  /* mle=4 no inter-extrapolation */
 void tricode(int *Tvar, int **nbcode, int imx)          lli=log(out[s1][s2]); /* Original formula */
 {        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   int Ndum[20],ij=1, k, j, i;          lli=log(out[s1][s2]); /* Original formula */
   int cptcode=0;        } /* End of if */
   cptcoveff=0;        ipmx +=1;
          sw += weight[i];
   for (k=0; k<19; k++) Ndum[k]=0;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (k=1; k<=7; k++) ncodemax[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]); */
         if(globpr){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     for (i=1; i<=imx; i++) {   %10.6f %10.6f %10.6f ", \
       ij=(int)(covar[Tvar[j]][i]);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       Ndum[ij]++;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       if (ij > cptcode) cptcode=ij;            llt +=ll[k]*gipmx/gsw;
     }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
     for (i=0; i<=cptcode; i++) {          fprintf(ficresilk," %10.6f\n", -llt);
       if(Ndum[i]!=0) ncodemax[j]++;        }
     }      } /* end of wave */
     ij=1;    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for (i=1; i<=ncodemax[j]; i++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for (k=0; k<=19; k++) {    if(globpr==0){ /* First time we count the contributions and weights */
         if (Ndum[k] != 0) {      gipmx=ipmx;
           nbcode[Tvar[j]][ij]=k;      gsw=sw;
           ij++;    }
         }    return -l;
         if (ij > ncodemax[j]) break;  }
       }    
     }  
   }    /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
  for (k=0; k<19; k++) Ndum[k]=0;  {
     /* This routine should help understanding what is done with 
  for (i=1; i<=ncovmodel-2; i++) {       the selection of individuals/waves and
       ij=Tvar[i];       to check the exact contribution to the likelihood.
       Ndum[ij]++;       Plotting could be done.
     }     */
     int k;
  ij=1;  
  for (i=1; i<=10; i++) {    if(*globpri !=0){ /* Just counts and sums, no printings */
    if((Ndum[i]!=0) && (i<=ncov)){      strcpy(fileresilk,"ilk"); 
      Tvaraff[ij]=i;      strcat(fileresilk,fileres);
      ij++;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
    }        printf("Problem with resultfile: %s\n", fileresilk);
  }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
        }
     cptcoveff=ij-1;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
 }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 /*********** Health Expectancies ****************/      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 {    }
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h;    *fretone=(*funcone)(p);
   double age, agelim,hf;    if(*globpri !=0){
   double ***p3mat;      fclose(ficresilk);
        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   fprintf(ficreseij,"# Health expectancies\n");      fflush(fichtm); 
   fprintf(ficreseij,"# Age");    } 
   for(i=1; i<=nlstate;i++)    return;
     for(j=1; j<=nlstate;j++)  }
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");  
   /*********** Maximum Likelihood Estimation ***************/
   hstepm=1*YEARM; /*  Every j years of age (in month) */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   agelim=AGESUP;    int i,j, iter;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double **xi;
     /* nhstepm age range expressed in number of stepm */    double fret;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    double fretone; /* Only one call to likelihood */
     /* Typically if 20 years = 20*12/6=40 stepm */    char filerespow[FILENAMELENGTH];
     if (stepm >= YEARM) hstepm=1;    xi=matrix(1,npar,1,npar);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    for (i=1;i<=npar;i++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=npar;j++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        xi[i][j]=(i==j ? 1.0 : 0.0);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(i=1; i<=nlstate;i++)      printf("Problem with resultfile: %s\n", filerespow);
       for(j=1; j<=nlstate;j++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    }
           eij[i][j][(int)age] +=p3mat[i][j][h];    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         }    for (i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate+ndeath;j++)
     hf=1;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     if (stepm >= YEARM) hf=stepm/YEARM;    fprintf(ficrespow,"\n");
     fprintf(ficreseij,"%.0f",age );  
     for(i=1; i<=nlstate;i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    fclose(ficrespow);
       }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficreseij,"\n");    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   }  
 }  }
   
 /************ Variance ******************/  /**** Computes Hessian and covariance matrix ***/
 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)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 {  {
   /* Variance of health expectancies */    double  **a,**y,*x,pd;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double **hess;
   double **newm;    int i, j,jk;
   double **dnewm,**doldm;    int *indx;
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;    double hessii(double p[], double delta, int theta, double delti[]);
   double *xp;    double hessij(double p[], double delti[], int i, int j);
   double **gp, **gm;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double ***gradg, ***trgradg;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double ***p3mat;  
   double age,agelim;    hess=matrix(1,npar,1,npar);
   int theta;  
     printf("\nCalculation of the hessian matrix. Wait...\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficresvij,"# Age");    for (i=1;i<=npar;i++){
   for(i=1; i<=nlstate;i++)      printf("%d",i);fflush(stdout);
     for(j=1; j<=nlstate;j++)      fprintf(ficlog,"%d",i);fflush(ficlog);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      hess[i][i]=hessii(p,ftolhess,i,delti);
   fprintf(ficresvij,"\n");      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1;i<=npar;i++) {
        for (j=1;j<=npar;j++)  {
   hstepm=1*YEARM; /* Every year of age */        if (j>i) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          printf(".%d%d",i,j);fflush(stdout);
   agelim = AGESUP;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          hess[i][j]=hessij(p,delti,i,j);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          hess[j][i]=hess[i][j];    
     if (stepm >= YEARM) hstepm=1;          /*printf(" %lf ",hess[i][j]);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    }
     gp=matrix(0,nhstepm,1,nlstate);    printf("\n");
     gm=matrix(0,nhstepm,1,nlstate);    fprintf(ficlog,"\n");
   
     for(theta=1; theta <=npar; theta++){    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);    
       }    a=matrix(1,npar,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      y=matrix(1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    x=vector(1,npar);
     indx=ivector(1,npar);
       if (popbased==1) {    for (i=1;i<=npar;i++)
         for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           prlim[i][i]=probs[(int)age][i][ij];    ludcmp(a,npar,indx,&pd);
       }  
          for (j=1;j<=npar;j++) {
       for(j=1; j<= nlstate; j++){      for (i=1;i<=npar;i++) x[i]=0;
         for(h=0; h<=nhstepm; h++){      x[j]=1;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      lubksb(a,npar,indx,x);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (i=1;i<=npar;i++){ 
         }        matcov[i][j]=x[i];
       }      }
        }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    printf("\n#Hessian matrix#\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      fprintf(ficlog,"\n#Hessian matrix#\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
       if (popbased==1) {        printf("%.3e ",hess[i][j]);
         for(i=1; i<=nlstate;i++)        fprintf(ficlog,"%.3e ",hess[i][j]);
           prlim[i][i]=probs[(int)age][i][ij];      }
       }      printf("\n");
       fprintf(ficlog,"\n");
       for(j=1; j<= nlstate; j++){    }
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    /* Recompute Inverse */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    for (i=1;i<=npar;i++)
         }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       }    ludcmp(a,npar,indx,&pd);
   
       for(j=1; j<= nlstate; j++)    /*  printf("\n#Hessian matrix recomputed#\n");
         for(h=0; h<=nhstepm; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
     } /* End theta */      x[j]=1;
       lubksb(a,npar,indx,x);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
     for(h=0; h<=nhstepm; h++)        printf("%.3e ",y[i][j]);
       for(j=1; j<=nlstate;j++)        fprintf(ficlog,"%.3e ",y[i][j]);
         for(theta=1; theta <=npar; theta++)      }
           trgradg[h][j][theta]=gradg[h][theta][j];      printf("\n");
       fprintf(ficlog,"\n");
     for(i=1;i<=nlstate;i++)    }
       for(j=1;j<=nlstate;j++)    */
         vareij[i][j][(int)age] =0.;  
     for(h=0;h<=nhstepm;h++){    free_matrix(a,1,npar,1,npar);
       for(k=0;k<=nhstepm;k++){    free_matrix(y,1,npar,1,npar);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    free_vector(x,1,npar);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    free_ivector(indx,1,npar);
         for(i=1;i<=nlstate;i++)    free_matrix(hess,1,npar,1,npar);
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];  
       }  }
     }  
     h=1;  /*************** hessian matrix ****************/
     if (stepm >= YEARM) h=stepm/YEARM;  double hessii( double x[], double delta, int theta, double delti[])
     fprintf(ficresvij,"%.0f ",age );  {
     for(i=1; i<=nlstate;i++)    int i;
       for(j=1; j<=nlstate;j++){    int l=1, lmax=20;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double k1,k2;
       }    double p2[NPARMAX+1];
     fprintf(ficresvij,"\n");    double res;
     free_matrix(gp,0,nhstepm,1,nlstate);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     free_matrix(gm,0,nhstepm,1,nlstate);    double fx;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    int k=0,kmax=10;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double l1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */    fx=func(x);
      for (i=1;i<=npar;i++) p2[i]=x[i];
   free_vector(xp,1,npar);    for(l=0 ; l <=lmax; l++){
   free_matrix(doldm,1,nlstate,1,npar);      l1=pow(10,l);
   free_matrix(dnewm,1,nlstate,1,nlstate);      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
 }        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
 /************ Variance of prevlim ******************/        k1=func(p2)-fx;
 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)        p2[theta]=x[theta]-delt;
 {        k2=func(p2)-fx;
   /* Variance of prevalence limit */        /*res= (k1-2.0*fx+k2)/delt/delt; */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double **newm;        
   double **dnewm,**doldm;  #ifdef DEBUG
   int i, j, nhstepm, hstepm;        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);
   int k, cptcode;        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);
   double *xp;  #endif
   double *gp, *gm;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   double **gradg, **trgradg;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   double age,agelim;          k=kmax;
   int theta;        }
            else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          k=kmax; l=lmax*10.;
   fprintf(ficresvpl,"# Age");        }
   for(i=1; i<=nlstate;i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       fprintf(ficresvpl," %1d-%1d",i,i);          delts=delt;
   fprintf(ficresvpl,"\n");        }
       }
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);    delti[theta]=delts;
   doldm=matrix(1,nlstate,1,nlstate);    return res; 
      
   hstepm=1*YEARM; /* Every year of age */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  double hessij( double x[], double delti[], int thetai,int thetaj)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    int i;
     if (stepm >= YEARM) hstepm=1;    int l=1, l1, lmax=20;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double k1,k2,k3,k4,res,fx;
     gradg=matrix(1,npar,1,nlstate);    double p2[NPARMAX+1];
     gp=vector(1,nlstate);    int k;
     gm=vector(1,nlstate);  
     fx=func(x);
     for(theta=1; theta <=npar; theta++){    for (k=1; k<=2; k++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (i=1;i<=npar;i++) p2[i]=x[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      k1=func(p2)-fx;
       for(i=1;i<=nlstate;i++)    
         gp[i] = prlim[i][i];      p2[thetai]=x[thetai]+delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(i=1; i<=npar; i++) /* Computes gradient */      k2=func(p2)-fx;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      p2[thetai]=x[thetai]-delti[thetai]/k;
       for(i=1;i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         gm[i] = prlim[i][i];      k3=func(p2)-fx;
     
       for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     } /* End theta */      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     trgradg =matrix(1,nlstate,1,npar);  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     for(j=1; j<=nlstate;j++)      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);
       for(theta=1; theta <=npar; theta++)  #endif
         trgradg[j][theta]=gradg[theta][j];    }
     return res;
     for(i=1;i<=nlstate;i++)  }
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  /************** Inverse of matrix **************/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  void ludcmp(double **a, int n, int *indx, double *d) 
     for(i=1;i<=nlstate;i++)  { 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    int i,imax,j,k; 
     double big,dum,sum,temp; 
     fprintf(ficresvpl,"%.0f ",age );    double *vv; 
     for(i=1; i<=nlstate;i++)   
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    vv=vector(1,n); 
     fprintf(ficresvpl,"\n");    *d=1.0; 
     free_vector(gp,1,nlstate);    for (i=1;i<=n;i++) { 
     free_vector(gm,1,nlstate);      big=0.0; 
     free_matrix(gradg,1,npar,1,nlstate);      for (j=1;j<=n;j++) 
     free_matrix(trgradg,1,nlstate,1,npar);        if ((temp=fabs(a[i][j])) > big) big=temp; 
   } /* End age */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   free_vector(xp,1,npar);    } 
   free_matrix(doldm,1,nlstate,1,npar);    for (j=1;j<=n;j++) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
 }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
 /************ Variance of one-step probabilities  ******************/      } 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      big=0.0; 
 {      for (i=j;i<=n;i++) { 
   int i, j;        sum=a[i][j]; 
   int k=0, cptcode;        for (k=1;k<j;k++) 
   double **dnewm,**doldm;          sum -= a[i][k]*a[k][j]; 
   double *xp;        a[i][j]=sum; 
   double *gp, *gm;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   double **gradg, **trgradg;          big=dum; 
   double age,agelim, cov[NCOVMAX];          imax=i; 
   int theta;        } 
   char fileresprob[FILENAMELENGTH];      } 
       if (j != imax) { 
   strcpy(fileresprob,"prob");        for (k=1;k<=n;k++) { 
   strcat(fileresprob,fileres);          dum=a[imax][k]; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          a[imax][k]=a[j][k]; 
     printf("Problem with resultfile: %s\n", fileresprob);          a[j][k]=dum; 
   }        } 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        *d = -(*d); 
          vv[imax]=vv[j]; 
       } 
   xp=vector(1,npar);      indx[j]=imax; 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      if (j != n) { 
          dum=1.0/(a[j][j]); 
   cov[1]=1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   for (age=bage; age<=fage; age ++){      } 
     cov[2]=age;    } 
     gradg=matrix(1,npar,1,9);    free_vector(vv,1,n);  /* Doesn't work */
     trgradg=matrix(1,9,1,npar);  ;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  } 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
      void lubksb(double **a, int n, int *indx, double b[]) 
     for(theta=1; theta <=npar; theta++){  { 
       for(i=1; i<=npar; i++)    int i,ii=0,ip,j; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double sum; 
         
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    for (i=1;i<=n;i++) { 
          ip=indx[i]; 
       k=0;      sum=b[ip]; 
       for(i=1; i<= (nlstate+ndeath); i++){      b[ip]=b[i]; 
         for(j=1; j<=(nlstate+ndeath);j++){      if (ii) 
            k=k+1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           gp[k]=pmmij[i][j];      else if (sum) ii=i; 
         }      b[i]=sum; 
       }    } 
     for (i=n;i>=1;i--) { 
       for(i=1; i<=npar; i++)      sum=b[i]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
          b[i]=sum/a[i][i]; 
     } 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  } 
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){  /************ Frequencies ********************/
         for(j=1; j<=(nlstate+ndeath);j++){  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=k+1;  {  /* Some frequencies */
           gm[k]=pmmij[i][j];    
         }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       }    int first;
          double ***freq; /* Frequencies */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    double *pp, **prop;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double pos,posprop, k2, dateintsum=0,k2cpt=0;
     }    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    
       for(theta=1; theta <=npar; theta++)    pp=vector(1,nlstate);
       trgradg[j][theta]=gradg[theta][j];    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    strcat(fileresp,fileres);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
      pmij(pmmij,cov,ncovmodel,x,nlstate);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
      k=0;    }
      for(i=1; i<=(nlstate+ndeath); i++){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
        for(j=1; j<=(nlstate+ndeath);j++){    j1=0;
          k=k+1;    
          gm[k]=pmmij[i][j];    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      }  
          first=1;
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for(k1=1; k1<=j;k1++){
              for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
      }*/          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
   fprintf(ficresprob,"\n%d ",(int)age);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              freq[i][jk][m]=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]);      for (i=1; i<=nlstate; i++)  
   }        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        dateintsum=0;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        k2cpt=0;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for (i=1; i<=imx; i++) {
 }          bool=1;
  free_vector(xp,1,npar);          if  (cptcovn>0) {
 fclose(ficresprob);            for (z1=1; z1<=cptcoveff; z1++) 
  exit(0);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 }                bool=0;
           }
 /***********************************************/          if (bool==1){
 /**************** Main Program *****************/            for(m=firstpass; m<=lastpass; m++){
 /***********************************************/              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 /*int main(int argc, char *argv[])*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 int main()                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   double agedeb, agefin,hf;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   double agemin=1.e20, agemax=-1.e20;                }
                 
   double fret;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   double **xi,tmp,delta;                  dateintsum=dateintsum+k2;
                   k2cpt++;
   double dum; /* Dummy variable */                }
   double ***p3mat;                /*}*/
   int *indx;            }
   char line[MAXLINE], linepar[MAXLINE];          }
   char title[MAXLINE];        }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];         
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];        if  (cptcovn>0) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          fprintf(ficresp, "\n#********** Variable "); 
   int firstobs=1, lastobs=10;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int sdeb, sfin; /* Status at beginning and end */          fprintf(ficresp, "**********\n#");
   int c,  h , cpt,l;        }
   int ju,jl, mi;        for(i=1; i<=nlstate;i++) 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        fprintf(ficresp, "\n");
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast;        
   int hstepm, nhstepm;        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   double bage, fage, age, agelim, agebase;            fprintf(ficlog,"Total");
   double ftolpl=FTOL;          }else{
   double **prlim;            if(first==1){
   double *severity;              first=0;
   double ***param; /* Matrix of parameters */              printf("See log file for details...\n");
   double  *p;            }
   double **matcov; /* Matrix of covariance */            fprintf(ficlog,"Age %d", i);
   double ***delti3; /* Scale */          }
   double *delti; /* Scale */          for(jk=1; jk <=nlstate ; jk++){
   double ***eij, ***vareij;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   double **varpl; /* Variances of prevalence limits by age */              pp[jk] += freq[jk][m][i]; 
   double *epj, vepp;          }
   double kk1;          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";              pos += freq[jk][m][i];
   char *alph[]={"a","a","b","c","d","e"}, str[4];            if(pp[jk]>=1.e-10){
               if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   char z[1]="c", occ;              }
 #include <sys/time.h>              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 #include <time.h>            }else{
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              if(first==1)
   /* long total_usecs;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   struct timeval start_time, end_time;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          }
   
           for(jk=1; jk <=nlstate ; jk++){
   printf("\nIMACH, Version 0.64b");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   printf("\nEnter the parameter file name: ");              pp[jk] += freq[jk][m][i];
           }       
 #ifdef windows          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   scanf("%s",pathtot);            pos += pp[jk];
   getcwd(pathcd, size);            posprop += prop[jk][i];
   /*cygwin_split_path(pathtot,path,optionfile);          }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for(jk=1; jk <=nlstate ; jk++){
   /* cutv(path,optionfile,pathtot,'\\');*/            if(pos>=1.e-5){
               if(first==1)
 split(pathtot, path,optionfile);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   chdir(path);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   replace(pathc,path);            }else{
 #endif              if(first==1)
 #ifdef unix                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   scanf("%s",optionfile);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #endif            }
             if( i <= iagemax){
 /*-------- arguments in the command line --------*/              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   strcpy(fileres,"r");                /*probs[i][jk][j1]= pp[jk]/pos;*/
   strcat(fileres, optionfile);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
   /*---------arguments file --------*/              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            }
     printf("Problem with optionfile %s\n",optionfile);          }
     goto end;          
   }          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
   strcpy(filereso,"o");              if(freq[jk][m][i] !=0 ) {
   strcat(filereso,fileres);              if(first==1)
   if((ficparo=fopen(filereso,"w"))==NULL) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   }              }
           if(i <= iagemax)
   /* Reads comments: lines beginning with '#' */            fprintf(ficresp,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){          if(first==1)
     ungetc(c,ficpar);            printf("Others in log...\n");
     fgets(line, MAXLINE, ficpar);          fprintf(ficlog,"\n");
     puts(line);        }
     fputs(line,ficparo);      }
   }    }
   ungetc(c,ficpar);    dateintmean=dateintsum/k2cpt; 
    
   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);    fclose(ficresp);
   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);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   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);    free_vector(pp,1,nlstate);
 while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     ungetc(c,ficpar);    /* End of Freq */
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /************ Prevalence ********************/
   }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   ungetc(c,ficpar);  {  
      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);       in each health status at the date of interview (if between dateprev1 and dateprev2).
  while((c=getc(ficpar))=='#' && c!= EOF){       We still use firstpass and lastpass as another selection.
     ungetc(c,ficpar);    */
     fgets(line, MAXLINE, ficpar);   
     puts(line);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     fputs(line,ficparo);    double ***freq; /* Frequencies */
   }    double *pp, **prop;
   ungetc(c,ficpar);    double pos,posprop; 
      double  y2; /* in fractional years */
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);    int iagemin, iagemax;
    
   covar=matrix(0,NCOVMAX,1,n);    iagemin= (int) agemin;
   cptcovn=0;    iagemax= (int) agemax;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
   ncovmodel=2+cptcovn;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    j1=0;
      
   /* Read guess parameters */    j=cptcoveff;
   /* Reads comments: lines beginning with '#' */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    for(k1=1; k1<=j;k1++){
     fgets(line, MAXLINE, ficpar);      for(i1=1; i1<=ncodemax[k1];i1++){
     puts(line);        j1++;
     fputs(line,ficparo);        
   }        for (i=1; i<=nlstate; i++)  
   ungetc(c,ficpar);          for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0.0;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       
     for(i=1; i <=nlstate; i++)        for (i=1; i<=imx; i++) { /* Each individual */
     for(j=1; j <=nlstate+ndeath-1; j++){          bool=1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);          if  (cptcovn>0) {
       fprintf(ficparo,"%1d%1d",i1,j1);            for (z1=1; z1<=cptcoveff; z1++) 
       printf("%1d%1d",i,j);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(k=1; k<=ncovmodel;k++){                bool=0;
         fscanf(ficpar," %lf",&param[i][j][k]);          } 
         printf(" %lf",param[i][j][k]);          if (bool==1) { 
         fprintf(ficparo," %lf",param[i][j][k]);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       fscanf(ficpar,"\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       printf("\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       fprintf(ficparo,"\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                  /*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];
   p=param[1][1];                  prop[s[m][i]][iagemax+3] += weight[i]; 
                  } 
   /* Reads comments: lines beginning with '#' */              }
   while((c=getc(ficpar))=='#' && c!= EOF){            } /* end selection of waves */
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        for(i=iagemin; i <= iagemax+3; i++){  
     fputs(line,ficparo);          
   }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   ungetc(c,ficpar);            posprop += prop[jk][i]; 
           } 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          for(jk=1; jk <=nlstate ; jk++){     
   for(i=1; i <=nlstate; i++){            if( i <=  iagemax){ 
     for(j=1; j <=nlstate+ndeath-1; j++){              if(posprop>=1.e-5){ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);                probs[i][jk][j1]= prop[jk][i]/posprop;
       printf("%1d%1d",i,j);              } 
       fprintf(ficparo,"%1d%1d",i1,j1);            } 
       for(k=1; k<=ncovmodel;k++){          }/* end jk */ 
         fscanf(ficpar,"%le",&delti3[i][j][k]);        }/* end i */ 
         printf(" %le",delti3[i][j][k]);      } /* end i1 */
         fprintf(ficparo," %le",delti3[i][j][k]);    } /* end k1 */
       }    
       fscanf(ficpar,"\n");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       printf("\n");    /*free_vector(pp,1,nlstate);*/
       fprintf(ficparo,"\n");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     }  }  /* End of prevalence */
   }  
   delti=delti3[1][1];  /************* Waves Concatenation ***************/
    
   /* Reads comments: lines beginning with '#' */  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)
   while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fgets(line, MAXLINE, ficpar);       Death is a valid wave (if date is known).
     puts(line);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     fputs(line,ficparo);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   }       and mw[mi+1][i]. dh depends on stepm.
   ungetc(c,ficpar);       */
    
   matcov=matrix(1,npar,1,npar);    int i, mi, m;
   for(i=1; i <=npar; i++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     fscanf(ficpar,"%s",&str);       double sum=0., jmean=0.;*/
     printf("%s",str);    int first;
     fprintf(ficparo,"%s",str);    int j, k=0,jk, ju, jl;
     for(j=1; j <=i; j++){    double sum=0.;
       fscanf(ficpar," %le",&matcov[i][j]);    first=0;
       printf(" %.5le",matcov[i][j]);    jmin=1e+5;
       fprintf(ficparo," %.5le",matcov[i][j]);    jmax=-1;
     }    jmean=0.;
     fscanf(ficpar,"\n");    for(i=1; i<=imx; i++){
     printf("\n");      mi=0;
     fprintf(ficparo,"\n");      m=firstpass;
   }      while(s[m][i] <= nlstate){
   for(i=1; i <=npar; i++)        if(s[m][i]>=1)
     for(j=i+1;j<=npar;j++)          mw[++mi][i]=m;
       matcov[i][j]=matcov[j][i];        if(m >=lastpass)
              break;
   printf("\n");        else
           m++;
       }/* end while */
     /*-------- data file ----------*/      if (s[m][i] > nlstate){
     if((ficres =fopen(fileres,"w"))==NULL) {        mi++;     /* Death is another wave */
       printf("Problem with resultfile: %s\n", fileres);goto end;        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
     fprintf(ficres,"#%s\n",version);        mw[mi][i]=m;
          }
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;      wav[i]=mi;
     }      if(mi==0){
         nbwarn++;
     n= lastobs;        if(first==0){
     severity = vector(1,maxwav);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     outcome=imatrix(1,maxwav+1,1,n);          first=1;
     num=ivector(1,n);        }
     moisnais=vector(1,n);        if(first==1){
     annais=vector(1,n);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     moisdc=vector(1,n);        }
     andc=vector(1,n);      } /* end mi==0 */
     agedc=vector(1,n);    } /* End individuals */
     cod=ivector(1,n);  
     weight=vector(1,n);    for(i=1; i<=imx; i++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      for(mi=1; mi<wav[i];mi++){
     mint=matrix(1,maxwav,1,n);        if (stepm <=0)
     anint=matrix(1,maxwav,1,n);          dh[mi][i]=1;
     s=imatrix(1,maxwav+1,1,n);        else{
     adl=imatrix(1,maxwav+1,1,n);              if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     tab=ivector(1,NCOVMAX);            if (agedc[i] < 2*AGESUP) {
     ncodemax=ivector(1,8);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
     i=1;              else if(j<0){
     while (fgets(line, MAXLINE, fic) != NULL)    {                nberr++;
       if ((i >= firstobs) && (i <=lastobs)) {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                        j=1; /* Temporary Dangerous patch */
         for (j=maxwav;j>=1;j--){                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                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]);
           strcpy(line,stra);                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);
           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);              k=k+1;
         }              if (j >= jmax) jmax=j;
                      if (j <= jmin) jmin=j;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              sum=sum+j;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          }
           else{
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         for (j=ncov;j>=1;j--){            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            k=k+1;
         }            if (j >= jmax) jmax=j;
         num[i]=atol(stra);            else if (j <= jmin)jmin=j;
                    /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            /*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]);*/
           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;}*/            if(j<0){
               nberr++;
         i=i+1;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       }              fprintf(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]);
     }            }
     /* printf("ii=%d", ij);            sum=sum+j;
        scanf("%d",i);*/          }
   imx=i-1; /* Number of individuals */          jk= j/stepm;
           jl= j -jk*stepm;
   /* for (i=1; i<=imx; i++){          ju= j -(jk+1)*stepm;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            if(jl==0){
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;              dh[mi][i]=jk;
     }              bh[mi][i]=0;
     for (i=1; i<=imx; i++) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/            }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
   /* Calculation of the number of parameter from char model*/              dh[mi][i]=jk+1;
   Tvar=ivector(1,15);              bh[mi][i]=ju;
   Tprod=ivector(1,15);            }
   Tvaraff=ivector(1,15);          }else{
   Tvard=imatrix(1,15,1,2);            if(jl <= -ju){
   Tage=ivector(1,15);                    dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
   if (strlen(model) >1){                                   * is higher than the multiple of stepm and negative otherwise.
     j=0, j1=0, k1=1, k2=1;                                   */
     j=nbocc(model,'+');            }
     j1=nbocc(model,'*');            else{
     cptcovn=j+1;              dh[mi][i]=jk+1;
     cptcovprod=j1;              bh[mi][i]=ju;
                }
                if(dh[mi][i]==0){
     strcpy(modelsav,model);              dh[mi][i]=1; /* At least one step */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){              bh[mi][i]=ju; /* At least one step */
       printf("Error. Non available option model=%s ",model);              /*  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);*/
       goto end;            }
     }          } /* end if mle */
            }
     for(i=(j+1); i>=1;i--){      } /* end wave */
       cutv(stra,strb,modelsav,'+');    }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    jmean=sum/k;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       /*scanf("%d",i);*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       if (strchr(strb,'*')) {   }
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  /*********** Tricode ****************************/
           cptcovprod--;  void tricode(int *Tvar, int **nbcode, int imx)
           cutv(strb,stre,strd,'V');  {
           Tvar[i]=atoi(stre);    
           cptcovage++;    int Ndum[20],ij=1, k, j, i, maxncov=19;
             Tage[cptcovage]=i;    int cptcode=0;
             /*printf("stre=%s ", stre);*/    cptcoveff=0; 
         }   
         else if (strcmp(strd,"age")==0) {    for (k=0; k<maxncov; k++) Ndum[k]=0;
           cptcovprod--;    for (k=1; k<=7; k++) ncodemax[k]=0;
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           cptcovage++;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           Tage[cptcovage]=i;                                 modality*/ 
         }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         else {        Ndum[ij]++; /*store the modality */
           cutv(strb,stre,strc,'V');        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           Tvar[i]=ncov+k1;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           cutv(strb,strc,strd,'V');                                         Tvar[j]. If V=sex and male is 0 and 
           Tprod[k1]=i;                                         female is 1, then  cptcode=1.*/
           Tvard[k1][1]=atoi(strc);      }
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];      for (i=0; i<=cptcode; i++) {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        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 */
           for (k=1; k<=lastobs;k++)      }
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;      ij=1; 
           k2=k2+2;      for (i=1; i<=ncodemax[j]; i++) {
         }        for (k=0; k<= maxncov; k++) {
       }          if (Ndum[k] != 0) {
       else {            nbcode[Tvar[j]][ij]=k; 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /* 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; */
        /*  scanf("%d",i);*/            
       cutv(strd,strc,strb,'V');            ij++;
       Tvar[i]=atoi(strc);          }
       }          if (ij > ncodemax[j]) break; 
       strcpy(modelsav,stra);          }  
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      } 
         scanf("%d",i);*/    }  
     }  
 }   for (k=0; k< maxncov; k++) Ndum[k]=0;
    
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   for (i=1; i<=ncovmodel-2; i++) { 
   printf("cptcovprod=%d ", cptcovprod);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   scanf("%d ",i);*/     ij=Tvar[i];
     fclose(fic);     Ndum[ij]++;
    }
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/   ij=1;
       for(i=1;i<=n;i++) weight[i]=1.0;   for (i=1; i<= maxncov; i++) {
     }     if((Ndum[i]!=0) && (i<=ncovcol)){
     /*-calculation of age at interview from date of interview and age at death -*/       Tvaraff[ij]=i; /*For printing */
     agev=matrix(1,maxwav,1,imx);       ij++;
      }
    for (i=1; i<=imx; i++)   }
      for(m=2; (m<= maxwav); m++)   
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){   cptcoveff=ij-1; /*Number of simple covariates*/
          anint[m][i]=9999;  }
          s[m][i]=-1;  
        }  /*********** Health Expectancies ****************/
      
     for (i=1; i<=imx; i++)  {  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 )
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  {
         if(s[m][i] >0){    /* Health expectancies */
           if (s[m][i] == nlstate+1) {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
             if(agedc[i]>0)    double age, agelim, hf;
               if(moisdc[i]!=99 && andc[i]!=9999)    double ***p3mat,***varhe;
               agev[m][i]=agedc[i];    double **dnewm,**doldm;
             else {    double *xp;
               if (andc[i]!=9999){    double **gp, **gm;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double ***gradg, ***trgradg;
               agev[m][i]=-1;    int theta;
               }  
             }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
           }    xp=vector(1,npar);
           else if(s[m][i] !=9){ /* Should no more exist */    dnewm=matrix(1,nlstate*nlstate,1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
             if(mint[m][i]==99 || anint[m][i]==9999)    
               agev[m][i]=1;    fprintf(ficreseij,"# Health expectancies\n");
             else if(agev[m][i] <agemin){    fprintf(ficreseij,"# Age");
               agemin=agev[m][i];    for(i=1; i<=nlstate;i++)
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      for(j=1; j<=nlstate;j++)
             }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
             else if(agev[m][i] >agemax){    fprintf(ficreseij,"\n");
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    if(estepm < stepm){
             }      printf ("Problem %d lower than %d\n",estepm, stepm);
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/    else  hstepm=estepm;   
           }    /* We compute the life expectancy from trapezoids spaced every estepm months
           else { /* =9 */     * This is mainly to measure the difference between two models: for example
             agev[m][i]=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
             s[m][i]=-1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
           }     * progression in between and thus overestimating or underestimating according
         }     * to the curvature of the survival function. If, for the same date, we 
         else /*= 0 Unknown */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           agev[m][i]=1;     * to compare the new estimate of Life expectancy with the same linear 
       }     * hypothesis. A more precise result, taking into account a more precise
         * curvature will be obtained if estepm is as small as stepm. */
     }  
     for (i=1; i<=imx; i++)  {    /* For example we decided to compute the life expectancy with the smallest unit */
       for(m=1; (m<= maxwav); m++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         if (s[m][i] > (nlstate+ndeath)) {       nhstepm is the number of hstepm from age to agelim 
           printf("Error: Wrong value in nlstate or ndeath\n");         nstepm is the number of stepm from age to agelin. 
           goto end;       Look at hpijx to understand the reason of that which relies in memory size
         }       and note for a fixed period like estepm months */
       }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     free_vector(severity,1,maxwav);    */
     free_imatrix(outcome,1,maxwav+1,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    agelim=AGESUP;
     free_matrix(mint,1,maxwav,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     free_matrix(anint,1,maxwav,1,n);      /* nhstepm age range expressed in number of stepm */
     free_vector(moisdc,1,n);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     free_vector(andc,1,n);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     wav=ivector(1,imx);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
          gm=matrix(0,nhstepm,1,nlstate*nlstate);
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       Tcode=ivector(1,100);   
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
            /* Computing Variances of health expectancies */
    codtab=imatrix(1,100,1,10);  
    h=0;       for(theta=1; theta <=npar; theta++){
    m=pow(2,cptcoveff);        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
    for(k=1;k<=cptcoveff; k++){        }
      for(i=1; i <=(m/pow(2,k));i++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        for(j=1; j <= ncodemax[k]; j++){    
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        cptj=0;
            h++;        for(j=1; j<= nlstate; j++){
            if (h>m) h=1;codtab[h][k]=j;          for(i=1; i<=nlstate; i++){
          }            cptj=cptj+1;
        }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
      }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/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);        for(i=1; i<=npar; i++) 
      }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      printf("\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    }        
    scanf("%d",i);*/        cptj=0;
            for(j=1; j<= nlstate; j++){
    /* Calculates basic frequencies. Computes observed prevalence at single age          for(i=1;i<=nlstate;i++){
        and prints on file fileres'p'. */            cptj=cptj+1;
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     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(j=1; j<= nlstate*nlstate; j++)
                for(h=0; h<=nhstepm-1; h++){
     /* For Powell, parameters are in a vector p[] starting at p[1]            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
        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) */       } 
      
     if(mle==1){  /* End theta */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      
     /*--------- results files --------------*/       for(h=0; h<=nhstepm-1; h++)
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);        for(j=1; j<=nlstate*nlstate;j++)
              for(theta=1; theta <=npar; theta++)
    jk=1;            trgradg[h][j][theta]=gradg[h][theta][j];
    fprintf(ficres,"# Parameters\n");       
    printf("# Parameters\n");  
    for(i=1,jk=1; i <=nlstate; i++){       for(i=1;i<=nlstate*nlstate;i++)
      for(k=1; k <=(nlstate+ndeath); k++){        for(j=1;j<=nlstate*nlstate;j++)
        if (k != i)          varhe[i][j][(int)age] =0.;
          {  
            printf("%d%d ",i,k);       printf("%d|",(int)age);fflush(stdout);
            fprintf(ficres,"%1d%1d ",i,k);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
            for(j=1; j <=ncovmodel; j++){       for(h=0;h<=nhstepm-1;h++){
              printf("%f ",p[jk]);        for(k=0;k<=nhstepm-1;k++){
              fprintf(ficres,"%f ",p[jk]);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
              jk++;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
            }          for(i=1;i<=nlstate*nlstate;i++)
            printf("\n");            for(j=1;j<=nlstate*nlstate;j++)
            fprintf(ficres,"\n");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
          }        }
      }      }
    }      /* Computing expectancies */
  if(mle==1){      for(i=1; i<=nlstate;i++)
     /* Computing hessian and covariance matrix */        for(j=1; j<=nlstate;j++)
     ftolhess=ftol; /* Usually correct */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     hesscov(matcov, p, npar, delti, ftolhess, func);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
  }            
     fprintf(ficres,"# Scales\n");  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     printf("# Scales\n");  
      for(i=1,jk=1; i <=nlstate; i++){          }
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {      fprintf(ficreseij,"%3.0f",age );
           fprintf(ficres,"%1d%1d",i,j);      cptj=0;
           printf("%1d%1d",i,j);      for(i=1; i<=nlstate;i++)
           for(k=1; k<=ncovmodel;k++){        for(j=1; j<=nlstate;j++){
             printf(" %.5e",delti[jk]);          cptj++;
             fprintf(ficres," %.5e",delti[jk]);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             jk++;        }
           }      fprintf(ficreseij,"\n");
           printf("\n");     
           fprintf(ficres,"\n");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     k=1;    }
     fprintf(ficres,"# Covariance\n");    printf("\n");
     printf("# Covariance\n");    fprintf(ficlog,"\n");
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;    free_vector(xp,1,npar);
       i1=(i-1)/(ncovmodel*nlstate)+1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       fprintf(ficres,"%3d",i);  }
       printf("%3d",i);  
       for(j=1; j<=i;j++){  /************ Variance ******************/
         fprintf(ficres," %.5e",matcov[i][j]);  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)
         printf(" %.5e",matcov[i][j]);  {
       }    /* Variance of health expectancies */
       fprintf(ficres,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       printf("\n");    /* double **newm;*/
       k++;    double **dnewm,**doldm;
     }    double **dnewmp,**doldmp;
        int i, j, nhstepm, hstepm, h, nstepm ;
     while((c=getc(ficpar))=='#' && c!= EOF){    int k, cptcode;
       ungetc(c,ficpar);    double *xp;
       fgets(line, MAXLINE, ficpar);    double **gp, **gm;  /* for var eij */
       puts(line);    double ***gradg, ***trgradg; /*for var eij */
       fputs(line,ficparo);    double **gradgp, **trgradgp; /* for var p point j */
     }    double *gpp, *gmp; /* for var p point j */
     ungetc(c,ficpar);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      double ***p3mat;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    double age,agelim, hf;
        double ***mobaverage;
     if (fage <= 2) {    int theta;
       bage = agemin;    char digit[4];
       fage = agemax;    char digitp[25];
     }  
     char fileresprobmorprev[FILENAMELENGTH];
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    if(popbased==1){
       if(mobilav!=0)
            strcpy(digitp,"-populbased-mobilav-");
 /*------------ gnuplot -------------*/      else strcpy(digitp,"-populbased-nomobil-");
 chdir(pathcd);    }
   if((ficgp=fopen("graph.plt","w"))==NULL) {    else 
     printf("Problem with file graph.gp");goto end;      strcpy(digitp,"-stablbased-");
   }  
 #ifdef windows    if (mobilav!=0) {
   fprintf(ficgp,"cd \"%s\" \n",pathc);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #endif      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 m=pow(2,cptcoveff);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
  /* 1eme*/      }
   for (cpt=1; cpt<= nlstate ; cpt ++) {    }
    for (k1=1; k1<= m ; k1 ++) {  
     strcpy(fileresprobmorprev,"prmorprev"); 
 #ifdef windows    sprintf(digit,"%-d",ij);
     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);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
 #endif    strcat(fileresprobmorprev,digit); /* Tvar to be done */
 #ifdef unix    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    strcat(fileresprobmorprev,fileres);
 #endif    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
 for (i=1; i<= nlstate ; i ++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(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);
     for (i=1; i<= nlstate ; i ++) {    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficresprobmorprev," p.%-d SE",j);
 }      for(i=1; i<=nlstate;i++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      for (i=1; i<= nlstate ; i ++) {    }  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresprobmorprev,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficgp,"\n# Routine varevsij");
 }      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 #ifdef unix  /*   } */
 fprintf(ficgp,"\nset ter gif small size 400,300");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    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");
    }    fprintf(ficresvij,"# Age");
   }    for(i=1; i<=nlstate;i++)
   /*2 eme*/      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   for (k1=1; k1<= m ; k1 ++) {    fprintf(ficresvij,"\n");
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
        xp=vector(1,npar);
     for (i=1; i<= nlstate+1 ; i ++) {    dnewm=matrix(1,nlstate,1,npar);
       k=2*i;    doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for (j=1; j<= nlstate+1 ; j ++) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 }      gpp=vector(nlstate+1,nlstate+ndeath);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    gmp=vector(nlstate+1,nlstate+ndeath);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {    if(estepm < stepm){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      printf ("Problem %d lower than %d\n",estepm, stepm);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }      else  hstepm=estepm;   
       fprintf(ficgp,"\" t\"\" w l 0,");    /* For example we decided to compute the life expectancy with the smallest unit */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for (j=1; j<= nlstate+1 ; j ++) {       nhstepm is the number of hstepm from age to agelim 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       nstepm is the number of stepm from age to agelin. 
   else fprintf(ficgp," \%%*lf (\%%*lf)");       Look at hpijx to understand the reason of that which relies in memory size
 }         and note for a fixed period like k years */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       else fprintf(ficgp,"\" t\"\" w l 0,");       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed every two years of age and if
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   }       results. So we changed our mind and took the option of the best precision.
      */
   /*3eme*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   for (k1=1; k1<= m ; k1 ++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for (cpt=1; cpt<= nlstate ; cpt ++) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       k=2+nlstate*(cpt-1);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       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);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for (i=1; i< nlstate ; i ++) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         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);      gp=matrix(0,nhstepm,1,nlstate);
       }      gm=matrix(0,nhstepm,1,nlstate);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  
   }      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   /* CV preval stat */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<nlstate ; cpt ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       k=3;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)        if (popbased==1) {
         fprintf(ficgp,"+$%d",k+i+1);          if(mobilav ==0){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
       l=3+(nlstate+ndeath)*cpt;          }else{ /* mobilav */ 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {              prlim[i][i]=mobaverage[(int)age][i][ij];
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);        }
       }    
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for(j=1; j<= nlstate; j++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          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];
           }
   /* proba elementaires */        }
    for(i=1,jk=1; i <=nlstate; i++){        /* This for computing probability of death (h=1 means
     for(k=1; k <=(nlstate+ndeath); k++){           computed over hstepm matrices product = hstepm*stepm months) 
       if (k != i) {           as a weighted average of prlim.
         for(j=1; j <=ncovmodel; j++){        */
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           /*fprintf(ficgp,"%s",alph[1]);*/          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
           jk++;        }    
           fprintf(ficgp,"\n");        /* end probability of death */
         }  
       }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   for(jk=1; jk <=m; jk++) {   
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        if (popbased==1) {
    i=1;          if(mobilav ==0){
    for(k2=1; k2<=nlstate; k2++) {            for(i=1; i<=nlstate;i++)
      k3=i;              prlim[i][i]=probs[(int)age][i][ij];
      for(k=1; k<=(nlstate+ndeath); k++) {          }else{ /* mobilav */ 
        if (k != k2){            for(i=1; i<=nlstate;i++)
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              prlim[i][i]=mobaverage[(int)age][i][ij];
 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]]]);        for(j=1; j<= nlstate; j++){
             ij++;          for(h=0; h<=nhstepm; h++){
           }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           else              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
         }        }
           fprintf(ficgp,")/(1");        /* This for computing probability of death (h=1 means
                   computed over hstepm matrices product = hstepm*stepm months) 
         for(k1=1; k1 <=nlstate; k1++){             as a weighted average of prlim.
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        */
 ij=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(j=3; j <=ncovmodel; j++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        }    
             ij++;        /* end probability of death */
           }  
           else        for(j=1; j<= nlstate; j++) /* vareij */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(h=0; h<=nhstepm; h++){
           }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           fprintf(ficgp,")");          }
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         i=i+ncovmodel;        }
        }  
      }      } /* End theta */
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   }  
          for(h=0; h<=nhstepm; h++) /* veij */
   fclose(ficgp);        for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
 chdir(path);            trgradg[h][j][theta]=gradg[h][theta][j];
      
     free_ivector(wav,1,imx);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(theta=1; theta <=npar; theta++)
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            trgradgp[j][theta]=gradgp[theta][j];
     free_ivector(num,1,n);    
     free_vector(agedc,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fclose(ficparo);      for(i=1;i<=nlstate;i++)
     fclose(ficres);        for(j=1;j<=nlstate;j++)
     /*  }*/          vareij[i][j][(int)age] =0.;
      
    /*________fin mle=1_________*/      for(h=0;h<=nhstepm;h++){
            for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     /* No more information from the sample is required now */          for(i=1;i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */            for(j=1;j<=nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    
     fputs(line,ficparo);      /* pptj */
   }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   ungetc(c,ficpar);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          varppt[j][i]=doldmp[j][i];
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      /* end ppptj */
 /*--------- index.htm --------*/      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   strcpy(optionfilehtm,optionfile);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   strcat(optionfilehtm,".htm");   
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      if (popbased==1) {
     printf("Problem with %s \n",optionfilehtm);goto end;        if(mobilav ==0){
   }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">        }else{ /* mobilav */ 
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          for(i=1; i<=nlstate;i++)
 Total number of observations=%d <br>            prlim[i][i]=mobaverage[(int)age][i][ij];
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        }
 <hr  size=\"2\" color=\"#EC5E5E\">      }
 <li>Outputs files<br><br>\n               
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      /* This for computing probability of death (h=1 means
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>         as a weighted average of prlim.
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      }    
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      /* end probability of death */
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>  
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
  fprintf(fichtm," <li>Graphs</li><p>");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
  m=cptcoveff;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        }
       } 
  j1=0;      fprintf(ficresprobmorprev,"\n");
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      fprintf(ficresvij,"%.0f ",age );
        j1++;      for(i=1; i<=nlstate;i++)
        if (cptcovn > 0) {        for(j=1; j<=nlstate;j++){
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          for (cpt=1; cpt<=cptcoveff;cpt++)        }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      fprintf(ficresvij,"\n");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      free_matrix(gp,0,nhstepm,1,nlstate);
        }      free_matrix(gm,0,nhstepm,1,nlstate);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        for(cpt=1; cpt<nlstate;cpt++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    } /* End age */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
        }    free_vector(gmp,nlstate+1,nlstate+ndeath);
     for(cpt=1; cpt<=nlstate;cpt++) {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 interval) in state (%d): v%s%d%d.gif <br>    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
      for(cpt=1; cpt<=nlstate;cpt++) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
 health expectancies in states (1) and (2): e%s%d.gif<br>    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
 fprintf(fichtm,"\n</body>");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    }    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
  }  */
 fclose(fichtm);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /*--------------- Prevalence limit --------------*/  
      free_vector(xp,1,npar);
   strcpy(filerespl,"pl");    free_matrix(doldm,1,nlstate,1,nlstate);
   strcat(filerespl,fileres);    free_matrix(dnewm,1,nlstate,1,npar);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficrespl,"#Prevalence limit\n");    fclose(ficresprobmorprev);
   fprintf(ficrespl,"#Age ");    fflush(ficgp);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fflush(fichtm); 
   fprintf(ficrespl,"\n");  }  /* end varevsij */
    
   prlim=matrix(1,nlstate,1,nlstate);  /************ Variance of prevlim ******************/
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  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)
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  {
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* Variance of prevalence limit */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double **newm;
   k=0;    double **dnewm,**doldm;
   agebase=agemin;    int i, j, nhstepm, hstepm;
   agelim=agemax;    int k, cptcode;
   ftolpl=1.e-10;    double *xp;
   i1=cptcoveff;    double *gp, *gm;
   if (cptcovn < 1){i1=1;}    double **gradg, **trgradg;
     double age,agelim;
   for(cptcov=1;cptcov<=i1;cptcov++){    int theta;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     
         k=k+1;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    fprintf(ficresvpl,"# Age");
         fprintf(ficrespl,"\n#******");    for(i=1; i<=nlstate;i++)
         for(j=1;j<=cptcoveff;j++)        fprintf(ficresvpl," %1d-%1d",i,i);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresvpl,"\n");
         fprintf(ficrespl,"******\n");  
            xp=vector(1,npar);
         for (age=agebase; age<=agelim; age++){    dnewm=matrix(1,nlstate,1,npar);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    doldm=matrix(1,nlstate,1,nlstate);
           fprintf(ficrespl,"%.0f",age );    
           for(i=1; i<=nlstate;i++)    hstepm=1*YEARM; /* Every year of age */
           fprintf(ficrespl," %.5f", prlim[i][i]);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
           fprintf(ficrespl,"\n");    agelim = AGESUP;
         }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }      if (stepm >= YEARM) hstepm=1;
   fclose(ficrespl);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
   /*------------- h Pij x at various ages ------------*/      gp=vector(1,nlstate);
        gm=vector(1,nlstate);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      for(theta=1; theta <=npar; theta++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        for(i=1; i<=npar; i++){ /* Computes gradient */
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   printf("Computing pij: result on file '%s' \n", filerespij);        }
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(i=1;i<=nlstate;i++)
   /*if (stepm<=24) stepsize=2;*/          gp[i] = prlim[i][i];
       
   agelim=AGESUP;        for(i=1; i<=npar; i++) /* Computes gradient */
   hstepm=stepsize*YEARM; /* Every year of age */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   k=0;          gm[i] = prlim[i][i];
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1;i<=nlstate;i++)
       k=k+1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         fprintf(ficrespij,"\n#****** ");      } /* End theta */
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      trgradg =matrix(1,nlstate,1,npar);
         fprintf(ficrespij,"******\n");  
              for(j=1; j<=nlstate;j++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for(theta=1; theta <=npar; theta++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          trgradg[j][theta]=gradg[theta][j];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1;i<=nlstate;i++)
           oldm=oldms;savm=savms;        varpl[i][(int)age] =0.;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           fprintf(ficrespij,"# Age");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           for(i=1; i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");      fprintf(ficresvpl,"%.0f ",age );
           for (h=0; h<=nhstepm; h++){      for(i=1; i<=nlstate;i++)
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             for(i=1; i<=nlstate;i++)      fprintf(ficresvpl,"\n");
               for(j=1; j<=nlstate+ndeath;j++)      free_vector(gp,1,nlstate);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      free_vector(gm,1,nlstate);
             fprintf(ficrespij,"\n");      free_matrix(gradg,1,npar,1,nlstate);
           }      free_matrix(trgradg,1,nlstate,1,npar);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } /* End age */
           fprintf(ficrespij,"\n");  
         }    free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  }
   
   fclose(ficrespij);  /************ 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)
   /*---------- Forecasting ------------------*/  {
     int i, j=0,  i1, k1, l1, t, tj;
   strcpy(fileresf,"f");    int k2, l2, j1,  z1;
   strcat(fileresf,fileres);    int k=0,l, cptcode;
   if((ficresf=fopen(fileresf,"w"))==NULL) {    int first=1, first1;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   }    double **dnewm,**doldm;
   printf("Computing forecasting: result on file '%s' \n", fileresf);    double *xp;
     double *gp, *gm;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);    double **gradg, **trgradg;
     double **mu;
  free_matrix(agev,1,maxwav,1,imx);    double age,agelim, cov[NCOVMAX];
   /* Mobile average */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
   if (mobilav==1) {    char fileresprobcor[FILENAMELENGTH];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    double ***varpij;
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    strcpy(fileresprob,"prob"); 
           mobaverage[(int)agedeb][i][cptcod]=0.;    strcat(fileresprob,fileres);
        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     for (agedeb=bage+4; agedeb<=fage; agedeb++){      printf("Problem with resultfile: %s\n", fileresprob);
       for (i=1; i<=nlstate;i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
           for (cpt=0;cpt<=4;cpt++){    strcpy(fileresprobcov,"probcov"); 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    strcat(fileresprobcov,fileres);
           }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      printf("Problem with resultfile: %s\n", fileresprobcov);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       }    }
     }      strcpy(fileresprobcor,"probcor"); 
   }    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;      printf("Problem with resultfile: %s\n", fileresprobcor);
   if (stepm<=12) stepsize=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
   agelim=AGESUP;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   hstepm=stepsize*YEARM; /* Every year of age */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    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);
    k=0;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       fprintf(ficresf,"\n#****** ");    fprintf(ficresprob,"# Age");
       for(j=1;j<=cptcoveff;j++) {    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcov,"# Age");
       }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       fprintf(ficresf,"******\n");    fprintf(ficresprobcov,"# Age");
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
     for(i=1; i<=nlstate;i++)
       for (agedeb=fage; agedeb>=bage; agedeb--){      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresf,"\n%d %.f %.f 0 ",k,agedeb, agedeb);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        if (mobilav==1) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         for(j=1; j<=nlstate;j++)        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           fprintf(ficresf," %.5f ",mobaverage[(int)agedeb][j][cptcod]);      }  
         }   /* fprintf(ficresprob,"\n");
         else {    fprintf(ficresprobcov,"\n");
           for(j=1; j<=nlstate;j++)    fprintf(ficresprobcor,"\n");
           fprintf(ficresf," %.5f ",probs[(int)agedeb][j][cptcod]);   */
         }     xp=vector(1,npar);
       for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       for (cpt=1; cpt<=nforecast;cpt++)      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
            first=1;
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficgp,"\n# Routine varprob");
         nhstepm = nhstepm/hstepm;    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    fprintf(fichtm,"\n");
   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
         oldm=oldms;savm=savms;    fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      file %s<br>\n",optionfilehtmcov);
                    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         for (h=0; h<=nhstepm; h++){  and drawn. It helps understanding how is the covariance between two incidences.\
           They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
          if (h*hstepm/YEARM*stepm==cpt)    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. \
             fprintf(ficresf,"\n%d %.f %.f %.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
            would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
            standard deviations wide on each axis. <br>\
           for(j=1; j<=nlstate+ndeath;j++) {   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
             kk1=0.;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
             for(i=1; i<=nlstate;i++) {          To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
               if (mobilav==1)  
               kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];    cov[1]=1;
               else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];    tj=cptcoveff;
             }        if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           if (h*hstepm/YEARM*stepm==cpt) fprintf(ficresf," %.5f ", kk1);    j1=0;
           }    for(t=1; t<=tj;t++){
         }      for(i1=1; i1<=ncodemax[t];i1++){ 
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        j1++;
       }        if  (cptcovn>0) {
     }          fprintf(ficresprob, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresprob, "**********\n#\n");
   free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficresprobcov, "\n#********** Variable "); 
   free_vector(weight,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fclose(ficresf);          fprintf(ficresprobcov, "**********\n#\n");
   /*---------- Health expectancies and variances ------------*/          
           fprintf(ficgp, "\n#********** Variable "); 
   strcpy(filerest,"t");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(filerest,fileres);          fprintf(ficgp, "**********\n#\n");
   if((ficrest=fopen(filerest,"w"))==NULL) {          
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          
   }          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
   strcpy(filerese,"e");          fprintf(ficresprobcor, "\n#********** Variable ");    
   strcat(filerese,fileres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficreseij=fopen(filerese,"w"))==NULL) {          fprintf(ficresprobcor, "**********\n#");    
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        }
   }        
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
  strcpy(fileresv,"v");          for (k=1; k<=cptcovn;k++) {
   strcat(fileresv,fileres);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   }          for (k=1; k<=cptcovprod;k++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   k=0;          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   for(cptcov=1;cptcov<=i1;cptcov++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          gp=vector(1,(nlstate)*(nlstate+ndeath));
       k=k+1;          gm=vector(1,(nlstate)*(nlstate+ndeath));
       fprintf(ficrest,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)          for(theta=1; theta <=npar; theta++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(i=1; i<=npar; i++)
       fprintf(ficrest,"******\n");              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
       fprintf(ficreseij,"\n#****** ");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       for(j=1;j<=cptcoveff;j++)            
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            k=0;
       fprintf(ficreseij,"******\n");            for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficresvij,"\n#****** ");                k=k+1;
       for(j=1;j<=cptcoveff;j++)                gp[k]=pmmij[i][j];
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);              }
       fprintf(ficresvij,"******\n");            }
             
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            for(i=1; i<=npar; i++)
       oldm=oldms;savm=savms;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       oldm=oldms;savm=savms;            k=0;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            for(i=1; i<=(nlstate); i++){
                    for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                k=k+1;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                gm[k]=pmmij[i][j];
       fprintf(ficrest,"\n");              }
                    }
       hf=1;       
       if (stepm >= YEARM) hf=stepm/YEARM;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       epj=vector(1,nlstate+1);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       for(age=bage; age <=fage ;age++){          }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
           for(i=1; i<=nlstate;i++)            for(theta=1; theta <=npar; theta++)
             prlim[i][i]=probs[(int)age][i][k];              trgradg[j][theta]=gradg[theta][j];
         }          
                  matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         fprintf(ficrest," %.0f",age);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           epj[nlstate+1] +=epj[j];  
         }          pmij(pmmij,cov,ncovmodel,x,nlstate);
         for(i=1, vepp=0.;i <=nlstate;i++)          
           for(j=1;j <=nlstate;j++)          k=0;
             vepp += vareij[i][j][(int)age];          for(i=1; i<=(nlstate); i++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            for(j=1; j<=(nlstate+ndeath);j++){
         for(j=1;j <=nlstate;j++){              k=k+1;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));              mu[k][(int) age]=pmmij[i][j];
         }            }
         fprintf(ficrest,"\n");          }
       }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   }              varpij[i][j][(int)age] = doldm[i][j];
          
                  /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  fclose(ficreseij);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  fclose(ficresvij);            }*/
   fclose(ficrest);  
   fclose(ficpar);          fprintf(ficresprob,"\n%d ",(int)age);
   free_vector(epj,1,nlstate+1);          fprintf(ficresprobcov,"\n%d ",(int)age);
   /*  scanf("%d ",i); */          fprintf(ficresprobcor,"\n%d ",(int)age);
   
   /*------- Variance limit prevalence------*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
 strcpy(fileresvpl,"vpl");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   strcat(fileresvpl,fileres);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          }
     exit(0);          i=0;
   }          for (k=1; k<=(nlstate);k++){
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
  k=0;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
  for(cptcov=1;cptcov<=i1;cptcov++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              for (j=1; j<=i;j++){
      k=k+1;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
      fprintf(ficresvpl,"\n#****** ");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
      for(j=1;j<=cptcoveff;j++)              }
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
      fprintf(ficresvpl,"******\n");          }/* end of loop for state */
              } /* end of loop for age */
      varpl=matrix(1,nlstate,(int) bage, (int) fage);  
      oldm=oldms;savm=savms;        /* Confidence intervalle of pij  */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        /*
    }          fprintf(ficgp,"\nset noparametric;unset label");
  }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   fclose(ficresvpl);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   /*---------- End : free ----------------*/          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
          */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
          first1=1;
          for (k2=1; k2<=(nlstate);k2++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            if(l2==k2) continue;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            j=(k2-1)*(nlstate+ndeath)+l2;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            for (k1=1; k1<=(nlstate);k1++){
                for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   free_matrix(matcov,1,npar,1,npar);                if(l1==k1) continue;
   free_vector(delti,1,npar);                i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
   printf("End of Imach\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /* 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);*/                    mu1=mu[i][(int) age]/stepm*YEARM ;
   /*printf("Total time was %d uSec.\n", total_usecs);*/                    mu2=mu[j][(int) age]/stepm*YEARM;
   /*------ End -----------*/                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
  end:                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 #ifdef windows                    /* Eigen vectors */
  chdir(pathcd);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 #endif                    /*v21=sqrt(1.-v11*v11); *//* error */
                      v21=(lc1-v1)/cv12*v11;
  system("..\\gp37mgw\\wgnuplot graph.plt");                    v12=-v21;
                     v22=v11;
 #ifdef windows                    tnalp=v21/v11;
   while (z[0] != 'q') {                    if(first1==1){
     chdir(pathcd);                      first1=0;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");                      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);
     scanf("%s",z);                    }
     if (z[0] == 'c') system("./imach");                    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);
     else if (z[0] == 'e') {                    /*printf(fignu*/
       chdir(path);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       system(optionfilehtm);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     }                    if(first==1){
     else if (z[0] == 'q') exit(0);                      first=0;
   }                      fprintf(ficgp,"\nset parametric;unset label");
 #endif                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
 }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
   /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   /*   } */
   
      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 \
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>", \
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
    - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            rfileres,rfileres,\
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
            subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** 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, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  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]; 
     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;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     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;
    
     /*   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(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",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 */
    
     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);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* 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);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     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 paramater 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);
       
     /*-------- 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=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); 
   
     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);
     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 */
     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*/
     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);
     
   
     jk=1;
     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");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     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.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     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(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  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);
   
     /*---------- 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 ----------------*/
     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);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     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 warnings %d\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,GNUPLOTPROGRAM);
     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') 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);
     }
   }
   
   
   

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  Added in v.1.94


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