Diff for /imach/src/imach.c between versions 1.37 and 1.93

version 1.37, 2002/03/29 15:31:59 version 1.93, 2003/06/25 16:33:55
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
   This program computes Healthy Life Expectancies from    exist so I changed back to asctime which exists.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (Module): Version 0.96b
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.92  2003/06/25 16:30:45  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): On windows (cygwin) function asctime_r doesn't
   second wave of interviews ("longitudinal") which measure each change    exist so I changed back to asctime which exists.
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.91  2003/06/25 15:30:29  brouard
   model. More health states you consider, more time is necessary to reach the    * imach.c (Repository): Duplicated warning errors corrected.
   Maximum Likelihood of the parameters involved in the model.  The    (Repository): Elapsed time after each iteration is now output. It
   simplest model is the multinomial logistic model where pij is the    helps to forecast when convergence will be reached. Elapsed time
   probabibility to be observed in state j at the second wave    is stamped in powell.  We created a new html file for the graphs
   conditional to be observed in state i at the first wave. Therefore    concerning matrix of covariance. It has extension -cov.htm.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.90  2003/06/24 12:34:15  brouard
   complex model than "constant and age", you should modify the program    (Module): Some bugs corrected for windows. Also, when
   where the markup *Covariates have to be included here again* invites    mle=-1 a template is output in file "or"mypar.txt with the design
   you to do it.  More covariates you add, slower the    of the covariance matrix to be input.
   convergence.  
     Revision 1.89  2003/06/24 12:30:52  brouard
   The advantage of this computer programme, compared to a simple    (Module): Some bugs corrected for windows. Also, when
   multinomial logistic model, is clear when the delay between waves is not    mle=-1 a template is output in file "or"mypar.txt with the design
   identical for each individual. Also, if a individual missed an    of the covariance matrix to be input.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.88  2003/06/23 17:54:56  brouard
     * 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.
   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    Revision 1.87  2003/06/18 12:26:01  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Version 0.96
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.86  2003/06/17 20:04:08  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Change position of html and gnuplot routines and added
   and the contribution of each individual to the likelihood is simply    routine fileappend.
   hPijx.  
     Revision 1.85  2003/06/17 13:12:43  brouard
   Also this programme outputs the covariance matrix of the parameters but also    * imach.c (Repository): Check when date of death was earlier that
   of the life expectancies. It also computes the prevalence limits.    current date of interview. It may happen when the death was just
      prior to the death. In this case, dh was negative and likelihood
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    was wrong (infinity). We still send an "Error" but patch by
            Institut national d'études démographiques, Paris.    assuming that the date of death was just one stepm after the
   This software have been partly granted by Euro-REVES, a concerted action    interview.
   from the European Union.    (Repository): Because some people have very long ID (first column)
   It is copyrighted identically to a GNU software product, ie programme and    we changed int to long in num[] and we added a new lvector for
   software can be distributed freely for non commercial use. Latest version    memory allocation. But we also truncated to 8 characters (left
   can be accessed at http://euroreves.ined.fr/imach .    truncation)
   **********************************************************************/    (Repository): No more line truncation errors.
    
 #include <math.h>    Revision 1.84  2003/06/13 21:44:43  brouard
 #include <stdio.h>    * imach.c (Repository): Replace "freqsummary" at a correct
 #include <stdlib.h>    place. It differs from routine "prevalence" which may be called
 #include <unistd.h>    many times. Probs is memory consuming and must be used with
     parcimony.
 #define MAXLINE 256    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.83  2003/06/10 13:39:11  lievre
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.82  2003/06/05 15:57:20  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Add log in  imach.c and  fullversion number is now printed.
 #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 */     Interpolated Markov Chain
   
 #define NINTERVMAX 8    Short summary of the programme:
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    This program computes Healthy Life Expectancies from
 #define NCOVMAX 8 /* Maximum number of covariates */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define MAXN 20000    first survey ("cross") where individuals from different ages are
 #define YEARM 12. /* Number of months per year */    interviewed on their health status or degree of disability (in the
 #define AGESUP 130    case of a health survey which is our main interest) -2- at least a
 #define AGEBASE 40    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 int erreur; /* Error number */    model. More health states you consider, more time is necessary to reach the
 int nvar;    Maximum Likelihood of the parameters involved in the model.  The
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    simplest model is the multinomial logistic model where pij is the
 int npar=NPARMAX;    probability to be observed in state j at the second wave
 int nlstate=2; /* Number of live states */    conditional to be observed in state i at the first wave. Therefore
 int ndeath=1; /* Number of dead states */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    'age' is age and 'sex' is a covariate. If you want to have a more
 int popbased=0;    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 int *wav; /* Number of waves for this individuual 0 is possible */    you to do it.  More covariates you add, slower the
 int maxwav; /* Maxim number of waves */    convergence.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    The advantage of this computer programme, compared to a simple
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    multinomial logistic model, is clear when the delay between waves is not
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    identical for each individual. Also, if a individual missed an
 double jmean; /* Mean space between 2 waves */    intermediate interview, the information is lost, but taken into
 double **oldm, **newm, **savm; /* Working pointers to matrices */    account using an interpolation or extrapolation.  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    hPijx is the probability to be observed in state i at age x+h
 FILE *ficgp,*ficresprob,*ficpop;    conditional to the observed state i at age x. The delay 'h' can be
 FILE *ficreseij;    split into an exact number (nh*stepm) of unobserved intermediate
   char filerese[FILENAMELENGTH];    states. This elementary transition (by month, quarter,
  FILE  *ficresvij;    semester or year) is modelled as a multinomial logistic.  The hPx
   char fileresv[FILENAMELENGTH];    matrix is simply the matrix product of nh*stepm elementary matrices
  FILE  *ficresvpl;    and the contribution of each individual to the likelihood is simply
   char fileresvpl[FILENAMELENGTH];    hPijx.
   
 #define NR_END 1    Also this programme outputs the covariance matrix of the parameters but also
 #define FREE_ARG char*    of the life expectancies. It also computes the stable prevalence. 
 #define FTOL 1.0e-10    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define NRANSI             Institut national d'études démographiques, Paris.
 #define ITMAX 200    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 #define TOL 2.0e-4    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define CGOLD 0.3819660    can be accessed at http://euroreves.ined.fr/imach .
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define GOLD 1.618034    
 #define GLIMIT 100.0    **********************************************************************/
 #define TINY 1.0e-20  /*
     main
 static double maxarg1,maxarg2;    read parameterfile
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    read datafile
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    concatwav
      freqsummary
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    if (mle >= 1)
 #define rint(a) floor(a+0.5)      mlikeli
     print results files
 static double sqrarg;    if mle==1 
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)       computes hessian
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 int imx;    open gnuplot file
 int stepm;    open html file
 /* Stepm, step in month: minimum step interpolation*/    stable prevalence
      for age prevalim()
 int estepm;    h Pij x
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 int m,nb;    health expectancies
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Variance-covariance of DFLE
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    prevalence()
 double **pmmij, ***probs, ***mobaverage;     movingaverage()
 double dateintmean=0;    varevsij() 
     if popbased==1 varevsij(,popbased)
 double *weight;    total life expectancies
 int **s; /* Status */    Variance of stable prevalence
 double *agedc, **covar, idx;   end
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  */
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  
    
 /**************** split *************************/  #include <math.h>
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #include <stdio.h>
 {  #include <stdlib.h>
    char *s;                             /* pointer */  #include <unistd.h>
    int  l1, l2;                         /* length counters */  
   #include <sys/time.h>
    l1 = strlen( path );                 /* length of path */  #include <time.h>
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #include "timeval.h"
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  #define MAXLINE 256
 #else  #define GNUPLOTPROGRAM "gnuplot"
    s = strrchr( path, '/' );            /* find last / */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #endif  #define FILENAMELENGTH 132
    if ( s == NULL ) {                   /* no directory, so use current */  /*#define DEBUG*/
 #if     defined(__bsd__)                /* get current working directory */  /*#define windows*/
       extern char       *getwd( );  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       if ( getwd( dirc ) == NULL ) {  
 #else  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
       extern char       *getcwd( );  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define NINTERVMAX 8
 #endif  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
          return( GLOCK_ERROR_GETCWD );  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       }  #define NCOVMAX 8 /* Maximum number of covariates */
       strcpy( name, path );             /* we've got it */  #define MAXN 20000
    } else {                             /* strip direcotry from path */  #define YEARM 12. /* Number of months per year */
       s++;                              /* after this, the filename */  #define AGESUP 130
       l2 = strlen( s );                 /* length of filename */  #define AGEBASE 40
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #ifdef unix
       strcpy( name, s );                /* save file name */  #define DIRSEPARATOR '/'
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define ODIRSEPARATOR '\\'
       dirc[l1-l2] = 0;                  /* add zero */  #else
    }  #define DIRSEPARATOR '\\'
    l1 = strlen( dirc );                 /* length of directory */  #define ODIRSEPARATOR '/'
 #ifdef windows  #endif
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  /* $Id$ */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  /* $State$ */
 #endif  
    s = strrchr( name, '.' );            /* find last / */  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
    s++;  char fullversion[]="$Revision$ $Date$"; 
    strcpy(ext,s);                       /* save extension */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    l1= strlen( name);  int nvar;
    l2= strlen( s)+1;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    strncpy( finame, name, l1-l2);  int npar=NPARMAX;
    finame[l1-l2]= 0;  int nlstate=2; /* Number of live states */
    return( 0 );                         /* we're done */  int ndeath=1; /* Number of dead states */
 }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   
 /******************************************/  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 void replace(char *s, char*t)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   int i;                     to the likelihood and the sum of weights (done by funcone)*/
   int lg=20;  int mle, weightopt;
   i=0;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   lg=strlen(t);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for(i=0; i<= lg; i++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     (s[i] = t[i]);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     if (t[i]== '\\') s[i]='/';  double jmean; /* Mean space between 2 waves */
   }  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int nbocc(char *s, char occ)  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   int i,j=0;  double fretone; /* Only one call to likelihood */
   int lg=20;  long ipmx; /* Number of contributions */
   i=0;  double sw; /* Sum of weights */
   lg=strlen(s);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for(i=0; i<= lg; i++) {  FILE *ficresilk;
   if  (s[i] == occ ) j++;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   }  FILE *ficresprobmorprev;
   return j;  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  FILE  *ficresvij;
 {  char fileresv[FILENAMELENGTH];
   int i,lg,j,p=0;  FILE  *ficresvpl;
   i=0;  char fileresvpl[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  char title[MAXLINE];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   }  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH]; 
   lg=strlen(t);  char command[FILENAMELENGTH];
   for(j=0; j<p; j++) {  int  outcmd=0;
     (u[j] = t[j]);  
   }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
      u[p]='\0';  char lfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
    for(j=0; j<= lg; j++) {  char filerest[FILENAMELENGTH];
     if (j>=(p+1))(v[j-p-1] = t[j]);  char fileregp[FILENAMELENGTH];
   }  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /********************** nrerror ********************/  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 void nrerror(char error_text[])  struct timezone tzp;
 {  extern int gettimeofday();
   fprintf(stderr,"ERREUR ...\n");  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   fprintf(stderr,"%s\n",error_text);  long time_value;
   exit(1);  extern long time();
 }  char strcurr[80], strfor[80];
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  #define NR_END 1
 {  #define FREE_ARG char*
   double *v;  #define FTOL 1.0e-10
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define NRANSI 
   return v-nl+NR_END;  #define ITMAX 200 
 }  
   #define TOL 2.0e-4 
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   free((FREE_ARG)(v+nl-NR_END));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /************************ivector *******************************/  #define GLIMIT 100.0 
 int *ivector(long nl,long nh)  #define TINY 1.0e-20 
 {  
   int *v;  static double maxarg1,maxarg2;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   if (!v) nrerror("allocation failure in ivector");  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   return v-nl+NR_END;    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   free((FREE_ARG)(v+nl-NR_END));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  
   int imx; 
 /******************* imatrix *******************************/  int stepm;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /* Stepm, step in month: minimum step interpolation*/
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  int estepm;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   int **m;  
    int m,nb;
   /* allocate pointers to rows */  long *num;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   if (!m) nrerror("allocation failure 1 in matrix()");  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   m += NR_END;  double **pmmij, ***probs;
   m -= nrl;  double dateintmean=0;
    
    double *weight;
   /* allocate rows and set pointers to them */  int **s; /* Status */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  double *agedc, **covar, idx;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    double ftolhess; /* Tolerance for computing hessian */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /**************** split *************************/
   /* return pointer to array of pointers to rows */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   return m;  {
 }    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    l1 = strlen(path );                   /* length of path */
       int **m;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       long nch,ncl,nrh,nrl;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      /* free an int matrix allocated by imatrix() */    if ( ss == NULL ) {                   /* no directory, so use current */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   free((FREE_ARG) (m[nrl]+ncl-NR_END));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   free((FREE_ARG) (m+nrl-NR_END));      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 /******************* matrix *******************************/        return( GLOCK_ERROR_GETCWD );
 double **matrix(long nrl, long nrh, long ncl, long nch)      }
 {      strcpy( name, path );               /* we've got it */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    } else {                              /* strip direcotry from path */
   double **m;      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   if (!m) nrerror("allocation failure 1 in matrix()");      strcpy( name, ss );         /* save file name */
   m += NR_END;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m -= nrl;      dirc[l1-l2] = 0;                    /* add zero */
     }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    l1 = strlen( dirc );                  /* length of directory */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    /*#ifdef windows
   m[nrl] += NR_END;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   m[nrl] -= ncl;  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #endif
   return m;    */
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 /*************************free matrix ************************/    strcpy(ext,ss);                       /* save extension */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    l1= strlen( name);
 {    l2= strlen(ss)+1;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    strncpy( finame, name, l1-l2);
   free((FREE_ARG)(m+nrl-NR_END));    finame[l1-l2]= 0;
 }    return( 0 );                          /* we're done */
   }
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  /******************************************/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  void replace_back_to_slash(char *s, char*t)
   {
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int i;
   if (!m) nrerror("allocation failure 1 in matrix()");    int lg=0;
   m += NR_END;    i=0;
   m -= nrl;    lg=strlen(t);
     for(i=0; i<= lg; i++) {
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      (s[i] = t[i]);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      if (t[i]== '\\') s[i]='/';
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int nbocc(char *s, char occ)
   {
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    int i,j=0;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    int lg=20;
   m[nrl][ncl] += NR_END;    i=0;
   m[nrl][ncl] -= nll;    lg=strlen(s);
   for (j=ncl+1; j<=nch; j++)    for(i=0; i<= lg; i++) {
     m[nrl][j]=m[nrl][j-1]+nlay;    if  (s[i] == occ ) j++;
      }
   for (i=nrl+1; i<=nrh; i++) {    return j;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  }
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  void cutv(char *u,char *v, char*t, char occ)
   }  {
   return m;    /* cuts string t into u and v where u is ended by char occ excluding it
 }       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
        gives u="abcedf" and v="ghi2j" */
 /*************************free ma3x ************************/    int i,lg,j,p=0;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    i=0;
 {    for(j=0; j<=strlen(t)-1; j++) {
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    }
   free((FREE_ARG)(m+nrl-NR_END));  
 }    lg=strlen(t);
     for(j=0; j<p; j++) {
 /***************** f1dim *************************/      (u[j] = t[j]);
 extern int ncom;    }
 extern double *pcom,*xicom;       u[p]='\0';
 extern double (*nrfunc)(double []);  
       for(j=0; j<= lg; j++) {
 double f1dim(double x)      if (j>=(p+1))(v[j-p-1] = t[j]);
 {    }
   int j;  }
   double f;  
   double *xt;  /********************** nrerror ********************/
    
   xt=vector(1,ncom);  void nrerror(char error_text[])
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  {
   f=(*nrfunc)(xt);    fprintf(stderr,"ERREUR ...\n");
   free_vector(xt,1,ncom);    fprintf(stderr,"%s\n",error_text);
   return f;    exit(EXIT_FAILURE);
 }  }
   /*********************** vector *******************/
 /*****************brent *************************/  double *vector(int nl, int nh)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  {
 {    double *v;
   int iter;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double a,b,d,etemp;    if (!v) nrerror("allocation failure in vector");
   double fu,fv,fw,fx;    return v-nl+NR_END;
   double ftemp;  }
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  /************************ free vector ******************/
    void free_vector(double*v, int nl, int nh)
   a=(ax < cx ? ax : cx);  {
   b=(ax > cx ? ax : cx);    free((FREE_ARG)(v+nl-NR_END));
   x=w=v=bx;  }
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  /************************ivector *******************************/
     xm=0.5*(a+b);  int *ivector(long nl,long nh)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  {
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    int *v;
     printf(".");fflush(stdout);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in ivector");
     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);    return v-nl+NR_END;
     /*          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))){  /******************free ivector **************************/
       *xmin=x;  void free_ivector(int *v, long nl, long nh)
       return fx;  {
     }    free((FREE_ARG)(v+nl-NR_END));
     ftemp=fu;  }
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  /************************lvector *******************************/
       q=(x-v)*(fx-fw);  long *lvector(long nl,long nh)
       p=(x-v)*q-(x-w)*r;  {
       q=2.0*(q-r);    long *v;
       if (q > 0.0) p = -p;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       q=fabs(q);    if (!v) nrerror("allocation failure in ivector");
       etemp=e;    return v-nl+NR_END;
       e=d;  }
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  /******************free lvector **************************/
       else {  void free_lvector(long *v, long nl, long nh)
         d=p/q;  {
         u=x+d;    free((FREE_ARG)(v+nl-NR_END));
         if (u-a < tol2 || b-u < tol2)  }
           d=SIGN(tol1,xm-x);  
       }  /******************* imatrix *******************************/
     } else {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     }  { 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     fu=(*f)(u);    int **m; 
     if (fu <= fx) {    
       if (u >= x) a=x; else b=x;    /* allocate pointers to rows */ 
       SHFT(v,w,x,u)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         SHFT(fv,fw,fx,fu)    if (!m) nrerror("allocation failure 1 in matrix()"); 
         } else {    m += NR_END; 
           if (u < x) a=u; else b=u;    m -= nrl; 
           if (fu <= fw || w == x) {    
             v=w;    
             w=u;    /* allocate rows and set pointers to them */ 
             fv=fw;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
             fw=fu;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
           } else if (fu <= fv || v == x || v == w) {    m[nrl] += NR_END; 
             v=u;    m[nrl] -= ncl; 
             fv=fu;    
           }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         }    
   }    /* return pointer to array of pointers to rows */ 
   nrerror("Too many iterations in brent");    return m; 
   *xmin=x;  } 
   return fx;  
 }  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
 /****************** mnbrak ***********************/        int **m;
         long nch,ncl,nrh,nrl; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,       /* free an int matrix allocated by imatrix() */ 
             double (*func)(double))  { 
 {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double ulim,u,r,q, dum;    free((FREE_ARG) (m+nrl-NR_END)); 
   double fu;  } 
    
   *fa=(*func)(*ax);  /******************* matrix *******************************/
   *fb=(*func)(*bx);  double **matrix(long nrl, long nrh, long ncl, long nch)
   if (*fb > *fa) {  {
     SHFT(dum,*ax,*bx,dum)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       SHFT(dum,*fb,*fa,dum)    double **m;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   *fc=(*func)(*cx);    if (!m) nrerror("allocation failure 1 in matrix()");
   while (*fb > *fc) {    m += NR_END;
     r=(*bx-*ax)*(*fb-*fc);    m -= nrl;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m[nrl] += NR_END;
     if ((*bx-u)*(u-*cx) > 0.0) {    m[nrl] -= ncl;
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       fu=(*func)(u);    return m;
       if (fu < *fc) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))     */
           SHFT(*fb,*fc,fu,(*func)(u))  }
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /*************************free matrix ************************/
       u=ulim;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       fu=(*func)(u);  {
     } else {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       u=(*cx)+GOLD*(*cx-*bx);    free((FREE_ARG)(m+nrl-NR_END));
       fu=(*func)(u);  }
     }  
     SHFT(*ax,*bx,*cx,u)  /******************* ma3x *******************************/
       SHFT(*fa,*fb,*fc,fu)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       }  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /*************** linmin ************************/  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 int ncom;    if (!m) nrerror("allocation failure 1 in matrix()");
 double *pcom,*xicom;    m += NR_END;
 double (*nrfunc)(double []);    m -= nrl;
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double brent(double ax, double bx, double cx,    m[nrl] += NR_END;
                double (*f)(double), double tol, double *xmin);    m[nrl] -= ncl;
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
               double *fc, double (*func)(double));  
   int j;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double xx,xmin,bx,ax;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double fx,fb,fa;    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
   ncom=n;    for (j=ncl+1; j<=nch; j++) 
   pcom=vector(1,n);      m[nrl][j]=m[nrl][j-1]+nlay;
   xicom=vector(1,n);    
   nrfunc=func;    for (i=nrl+1; i<=nrh; i++) {
   for (j=1;j<=n;j++) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     pcom[j]=p[j];      for (j=ncl+1; j<=nch; j++) 
     xicom[j]=xi[j];        m[i][j]=m[i][j-1]+nlay;
   }    }
   ax=0.0;    return m; 
   xx=1.0;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    */
 #ifdef DEBUG  }
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  /*************************free ma3x ************************/
   for (j=1;j<=n;j++) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     xi[j] *= xmin;  {
     p[j] += xi[j];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   free_vector(xicom,1,n);    free((FREE_ARG)(m+nrl-NR_END));
   free_vector(pcom,1,n);  }
 }  
   /***************** f1dim *************************/
 /*************** powell ************************/  extern int ncom; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  extern double *pcom,*xicom;
             double (*func)(double []))  extern double (*nrfunc)(double []); 
 {   
   void linmin(double p[], double xi[], int n, double *fret,  double f1dim(double x) 
               double (*func)(double []));  { 
   int i,ibig,j;    int j; 
   double del,t,*pt,*ptt,*xit;    double f;
   double fp,fptt;    double *xt; 
   double *xits;   
   pt=vector(1,n);    xt=vector(1,ncom); 
   ptt=vector(1,n);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   xit=vector(1,n);    f=(*nrfunc)(xt); 
   xits=vector(1,n);    free_vector(xt,1,ncom); 
   *fret=(*func)(p);    return f; 
   for (j=1;j<=n;j++) pt[j]=p[j];  } 
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /*****************brent *************************/
     ibig=0;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     del=0.0;  { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    int iter; 
     for (i=1;i<=n;i++)    double a,b,d,etemp;
       printf(" %d %.12f",i, p[i]);    double fu,fv,fw,fx;
     printf("\n");    double ftemp;
     for (i=1;i<=n;i++) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double e=0.0; 
       fptt=(*fret);   
 #ifdef DEBUG    a=(ax < cx ? ax : cx); 
       printf("fret=%lf \n",*fret);    b=(ax > cx ? ax : cx); 
 #endif    x=w=v=bx; 
       printf("%d",i);fflush(stdout);    fw=fv=fx=(*f)(x); 
       linmin(p,xit,n,fret,func);    for (iter=1;iter<=ITMAX;iter++) { 
       if (fabs(fptt-(*fret)) > del) {      xm=0.5*(a+b); 
         del=fabs(fptt-(*fret));      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         ibig=i;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       }      printf(".");fflush(stdout);
 #ifdef DEBUG      fprintf(ficlog,".");fflush(ficlog);
       printf("%d %.12e",i,(*fret));  #ifdef DEBUG
       for (j=1;j<=n;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);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      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);
         printf(" x(%d)=%.12e",j,xit[j]);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       }  #endif
       for(j=1;j<=n;j++)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         printf(" p=%.12e",p[j]);        *xmin=x; 
       printf("\n");        return fx; 
 #endif      } 
     }      ftemp=fu;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      if (fabs(e) > tol1) { 
 #ifdef DEBUG        r=(x-w)*(fx-fv); 
       int k[2],l;        q=(x-v)*(fx-fw); 
       k[0]=1;        p=(x-v)*q-(x-w)*r; 
       k[1]=-1;        q=2.0*(q-r); 
       printf("Max: %.12e",(*func)(p));        if (q > 0.0) p = -p; 
       for (j=1;j<=n;j++)        q=fabs(q); 
         printf(" %.12e",p[j]);        etemp=e; 
       printf("\n");        e=d; 
       for(l=0;l<=1;l++) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         for (j=1;j<=n;j++) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        else { 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);          d=p/q; 
         }          u=x+d; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
 #endif        } 
       } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       free_vector(xit,1,n);      } 
       free_vector(xits,1,n);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       free_vector(ptt,1,n);      fu=(*f)(u); 
       free_vector(pt,1,n);      if (fu <= fx) { 
       return;        if (u >= x) a=x; else b=x; 
     }        SHFT(v,w,x,u) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          SHFT(fv,fw,fx,fu) 
     for (j=1;j<=n;j++) {          } else { 
       ptt[j]=2.0*p[j]-pt[j];            if (u < x) a=u; else b=u; 
       xit[j]=p[j]-pt[j];            if (fu <= fw || w == x) { 
       pt[j]=p[j];              v=w; 
     }              w=u; 
     fptt=(*func)(ptt);              fv=fw; 
     if (fptt < fp) {              fw=fu; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);            } else if (fu <= fv || v == x || v == w) { 
       if (t < 0.0) {              v=u; 
         linmin(p,xit,n,fret,func);              fv=fu; 
         for (j=1;j<=n;j++) {            } 
           xi[j][ibig]=xi[j][n];          } 
           xi[j][n]=xit[j];    } 
         }    nrerror("Too many iterations in brent"); 
 #ifdef DEBUG    *xmin=x; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    return fx; 
         for(j=1;j<=n;j++)  } 
           printf(" %.12e",xit[j]);  
         printf("\n");  /****************** mnbrak ***********************/
 #endif  
       }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     }              double (*func)(double)) 
   }  { 
 }    double ulim,u,r,q, dum;
     double fu; 
 /**** Prevalence limit ****************/   
     *fa=(*func)(*ax); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    *fb=(*func)(*bx); 
 {    if (*fb > *fa) { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      SHFT(dum,*ax,*bx,dum) 
      matrix by transitions matrix until convergence is reached */        SHFT(dum,*fb,*fa,dum) 
         } 
   int i, ii,j,k;    *cx=(*bx)+GOLD*(*bx-*ax); 
   double min, max, maxmin, maxmax,sumnew=0.;    *fc=(*func)(*cx); 
   double **matprod2();    while (*fb > *fc) { 
   double **out, cov[NCOVMAX], **pmij();      r=(*bx-*ax)*(*fb-*fc); 
   double **newm;      q=(*bx-*cx)*(*fb-*fa); 
   double agefin, delaymax=50 ; /* Max number of years to converge */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for (ii=1;ii<=nlstate+ndeath;ii++)      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     for (j=1;j<=nlstate+ndeath;j++){      if ((*bx-u)*(u-*cx) > 0.0) { 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
    cov[1]=1.;        if (fu < *fc) { 
            SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */            SHFT(*fb,*fc,fu,(*func)(u)) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            } 
     newm=savm;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     /* Covariates have to be included here again */        u=ulim; 
      cov[2]=agefin;        fu=(*func)(u); 
        } else { 
       for (k=1; k<=cptcovn;k++) {        u=(*cx)+GOLD*(*cx-*bx); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fu=(*func)(u); 
         /*      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]]);*/      } 
       }      SHFT(*ax,*bx,*cx,u) 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        SHFT(*fa,*fb,*fc,fu) 
       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]]];  } 
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /*************** linmin ************************/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  int ncom; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  double *pcom,*xicom;
   double (*nrfunc)(double []); 
     savm=oldm;   
     oldm=newm;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     maxmax=0.;  { 
     for(j=1;j<=nlstate;j++){    double brent(double ax, double bx, double cx, 
       min=1.;                 double (*f)(double), double tol, double *xmin); 
       max=0.;    double f1dim(double x); 
       for(i=1; i<=nlstate; i++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         sumnew=0;                double *fc, double (*func)(double)); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    int j; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    double xx,xmin,bx,ax; 
         max=FMAX(max,prlim[i][j]);    double fx,fb,fa;
         min=FMIN(min,prlim[i][j]);   
       }    ncom=n; 
       maxmin=max-min;    pcom=vector(1,n); 
       maxmax=FMAX(maxmax,maxmin);    xicom=vector(1,n); 
     }    nrfunc=func; 
     if(maxmax < ftolpl){    for (j=1;j<=n;j++) { 
       return prlim;      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
   }    } 
 }    ax=0.0; 
     xx=1.0; 
 /*************** transition probabilities ***************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #ifdef DEBUG
 {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double s1, s2;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*double t34;*/  #endif
   int i,j,j1, nc, ii, jj;    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
     for(i=1; i<= nlstate; i++){      p[j] += xi[j]; 
     for(j=1; j<i;j++){    } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free_vector(xicom,1,n); 
         /*s2 += param[i][j][nc]*cov[nc];*/    free_vector(pcom,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  } 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  char *asc_diff_time(long time_sec, char ascdiff[])
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    long sec_left, days, hours, minutes;
     }    days = (time_sec) / (60*60*24);
     for(j=i+1; j<=nlstate+ndeath;j++){    sec_left = (time_sec) % (60*60*24);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    hours = (sec_left) / (60*60) ;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    sec_left = (sec_left) %(60*60);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    minutes = (sec_left) /60;
       }    sec_left = (sec_left) % (60);
       ps[i][j]=s2;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     }    return ascdiff;
   }  }
     /*ps[3][2]=1;*/  
   /*************** powell ************************/
   for(i=1; i<= nlstate; i++){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
      s1=0;              double (*func)(double [])) 
     for(j=1; j<i; j++)  { 
       s1+=exp(ps[i][j]);    void linmin(double p[], double xi[], int n, double *fret, 
     for(j=i+1; j<=nlstate+ndeath; j++)                double (*func)(double [])); 
       s1+=exp(ps[i][j]);    int i,ibig,j; 
     ps[i][i]=1./(s1+1.);    double del,t,*pt,*ptt,*xit;
     for(j=1; j<i; j++)    double fp,fptt;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double *xits;
     for(j=i+1; j<=nlstate+ndeath; j++)    int niterf, itmp;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    pt=vector(1,n); 
   } /* end i */    ptt=vector(1,n); 
     xit=vector(1,n); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    xits=vector(1,n); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    *fret=(*func)(p); 
       ps[ii][jj]=0;    for (j=1;j<=n;j++) pt[j]=p[j]; 
       ps[ii][ii]=1;    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
   }      ibig=0; 
       del=0.0; 
       last_time=curr_time;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      (void) gettimeofday(&curr_time,&tzp);
     for(jj=1; jj<= nlstate+ndeath; jj++){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
      printf("%lf ",ps[ii][jj]);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
    }      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     printf("\n ");      for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     printf("\n ");printf("%lf ",cov[2]);*/        fprintf(ficlog," %d %.12lf",i, p[i]);
 /*        fprintf(ficrespow," %.12lf", p[i]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      }
   goto end;*/      printf("\n");
     return ps;      fprintf(ficlog,"\n");
 }      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
 /**************** Product of 2 matrices ******************/        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tmf));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /*       asctime_r(&tm,strcurr); */
 {        forecast_time=curr_time;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        itmp = strlen(strcurr);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        if(strcurr[itmp-1]=='\n')
   /* in, b, out are matrice of pointers which should have been initialized          strcurr[itmp-1]='\0';
      before: only the contents of out is modified. The function returns        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
      a pointer to pointers identical to out */        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   long i, j, k;        for(niterf=10;niterf<=30;niterf+=10){
   for(i=nrl; i<= nrh; i++)          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     for(k=ncolol; k<=ncoloh; k++)          tmf = *localtime(&forecast_time.tv_sec);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*      asctime_r(&tmf,strfor); */
         out[i][k] +=in[i][j]*b[j][k];          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
   return out;          if(strfor[itmp-1]=='\n')
 }          strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
           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);
 /************* Higher Matrix Product ***************/        }
       }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      for (i=1;i<=n;i++) { 
 {        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        fptt=(*fret); 
      duration (i.e. until  #ifdef DEBUG
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        printf("fret=%lf \n",*fret);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        fprintf(ficlog,"fret=%lf \n",*fret);
      (typically every 2 years instead of every month which is too big).  #endif
      Model is determined by parameters x and covariates have to be        printf("%d",i);fflush(stdout);
      included manually here.        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
      */        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
   int i, j, d, h, k;          ibig=i; 
   double **out, cov[NCOVMAX];        } 
   double **newm;  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   /* Hstepm could be zero and should return the unit matrix */        fprintf(ficlog,"%d %.12e",i,(*fret));
   for (i=1;i<=nlstate+ndeath;i++)        for (j=1;j<=n;j++) {
     for (j=1;j<=nlstate+ndeath;j++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       oldm[i][j]=(i==j ? 1.0 : 0.0);          printf(" x(%d)=%.12e",j,xit[j]);
       po[i][j][0]=(i==j ? 1.0 : 0.0);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        for(j=1;j<=n;j++) {
   for(h=1; h <=nhstepm; h++){          printf(" p=%.12e",p[j]);
     for(d=1; d <=hstepm; d++){          fprintf(ficlog," p=%.12e",p[j]);
       newm=savm;        }
       /* Covariates have to be included here again */        printf("\n");
       cov[1]=1.;        fprintf(ficlog,"\n");
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  #endif
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      } 
       for (k=1; k<=cptcovage;k++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #ifdef DEBUG
       for (k=1; k<=cptcovprod;k++)        int k[2],l;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        k[0]=1;
         k[1]=-1;
         printf("Max: %.12e",(*func)(p));
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        fprintf(ficlog,"Max: %.12e",(*func)(p));
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        for (j=1;j<=n;j++) {
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          printf(" %.12e",p[j]);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          fprintf(ficlog," %.12e",p[j]);
       savm=oldm;        }
       oldm=newm;        printf("\n");
     }        fprintf(ficlog,"\n");
     for(i=1; i<=nlstate+ndeath; i++)        for(l=0;l<=1;l++) {
       for(j=1;j<=nlstate+ndeath;j++) {          for (j=1;j<=n;j++) {
         po[i][j][h]=newm[i][j];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
          */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       }          }
   } /* end h */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   return po;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 }        }
   #endif
   
 /*************** log-likelihood *************/  
 double func( double *x)        free_vector(xit,1,n); 
 {        free_vector(xits,1,n); 
   int i, ii, j, k, mi, d, kk;        free_vector(ptt,1,n); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        free_vector(pt,1,n); 
   double **out;        return; 
   double sw; /* Sum of weights */      } 
   double lli; /* Individual log likelihood */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   long ipmx;      for (j=1;j<=n;j++) { 
   /*extern weight */        ptt[j]=2.0*p[j]-pt[j]; 
   /* We are differentiating ll according to initial status */        xit[j]=p[j]-pt[j]; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        pt[j]=p[j]; 
   /*for(i=1;i<imx;i++)      } 
     printf(" %d\n",s[4][i]);      fptt=(*func)(ptt); 
   */      if (fptt < fp) { 
   cov[1]=1.;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;          linmin(p,xit,n,fret,func); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          for (j=1;j<=n;j++) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];            xi[j][ibig]=xi[j][n]; 
     for(mi=1; mi<= wav[i]-1; mi++){            xi[j][n]=xit[j]; 
       for (ii=1;ii<=nlstate+ndeath;ii++)          }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #ifdef DEBUG
       for(d=0; d<dh[mi][i]; d++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         newm=savm;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          for(j=1;j<=n;j++){
         for (kk=1; kk<=cptcovage;kk++) {            printf(" %.12e",xit[j]);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];            fprintf(ficlog," %.12e",xit[j]);
         }          }
                  printf("\n");
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          fprintf(ficlog,"\n");
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #endif
         savm=oldm;        }
         oldm=newm;      } 
            } 
          } 
       } /* end mult */  
        /**** Prevalence limit (stable prevalence)  ****************/
       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]]);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       ipmx +=1;  {
       sw += weight[i];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       matrix by transitions matrix until convergence is reached */
     } /* end of wave */  
   } /* end of individual */    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double **matprod2();
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    double **out, cov[NCOVMAX], **pmij();
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    double **newm;
   return -l;    double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
 /*********** Maximum Likelihood Estimation ***************/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {     cov[1]=1.;
   int i,j, iter;   
   double **xi,*delti;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double fret;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   xi=matrix(1,npar,1,npar);      newm=savm;
   for (i=1;i<=npar;i++)      /* Covariates have to be included here again */
     for (j=1;j<=npar;j++)       cov[2]=agefin;
       xi[i][j]=(i==j ? 1.0 : 0.0);    
   printf("Powell\n");        for (k=1; k<=cptcovn;k++) {
   powell(p,xi,npar,ftol,&iter,&fret,func);          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]]);*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 /**** Computes Hessian and covariance matrix ***/        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double  **a,**y,*x,pd;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double **hess;  
   int i, j,jk;      savm=oldm;
   int *indx;      oldm=newm;
       maxmax=0.;
   double hessii(double p[], double delta, int theta, double delti[]);      for(j=1;j<=nlstate;j++){
   double hessij(double p[], double delti[], int i, int j);        min=1.;
   void lubksb(double **a, int npar, int *indx, double b[]) ;        max=0.;
   void ludcmp(double **a, int npar, int *indx, double *d) ;        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   hess=matrix(1,npar,1,npar);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   printf("\nCalculation of the hessian matrix. Wait...\n");          max=FMAX(max,prlim[i][j]);
   for (i=1;i<=npar;i++){          min=FMIN(min,prlim[i][j]);
     printf("%d",i);fflush(stdout);        }
     hess[i][i]=hessii(p,ftolhess,i,delti);        maxmin=max-min;
     /*printf(" %f ",p[i]);*/        maxmax=FMAX(maxmax,maxmin);
     /*printf(" %lf ",hess[i][i]);*/      }
   }      if(maxmax < ftolpl){
          return prlim;
   for (i=1;i<=npar;i++) {      }
     for (j=1;j<=npar;j++)  {    }
       if (j>i) {  }
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  /*************** transition probabilities ***************/ 
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       }  {
     }    double s1, s2;
   }    /*double t34;*/
   printf("\n");    int i,j,j1, nc, ii, jj;
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      for(i=1; i<= nlstate; i++){
        for(j=1; j<i;j++){
   a=matrix(1,npar,1,npar);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   y=matrix(1,npar,1,npar);          /*s2 += param[i][j][nc]*cov[nc];*/
   x=vector(1,npar);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   indx=ivector(1,npar);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        ps[i][j]=s2;
   ludcmp(a,npar,indx,&pd);        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
   for (j=1;j<=npar;j++) {      for(j=i+1; j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++) x[i]=0;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     x[j]=1;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     lubksb(a,npar,indx,x);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     for (i=1;i<=npar;i++){        }
       matcov[i][j]=x[i];        ps[i][j]=s2;
     }      }
   }    }
       /*ps[3][2]=1;*/
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {    for(i=1; i<= nlstate; i++){
     for (j=1;j<=npar;j++) {       s1=0;
       printf("%.3e ",hess[i][j]);      for(j=1; j<i; j++)
     }        s1+=exp(ps[i][j]);
     printf("\n");      for(j=i+1; j<=nlstate+ndeath; j++)
   }        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
   /* Recompute Inverse */      for(j=1; j<i; j++)
   for (i=1;i<=npar;i++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      for(j=i+1; j<=nlstate+ndeath; j++)
   ludcmp(a,npar,indx,&pd);        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   /*  printf("\n#Hessian matrix recomputed#\n");    } /* end i */
   
   for (j=1;j<=npar;j++) {    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for (i=1;i<=npar;i++) x[i]=0;      for(jj=1; jj<= nlstate+ndeath; jj++){
     x[j]=1;        ps[ii][jj]=0;
     lubksb(a,npar,indx,x);        ps[ii][ii]=1;
     for (i=1;i<=npar;i++){      }
       y[i][j]=x[i];    }
       printf("%.3e ",y[i][j]);  
     }  
     printf("\n");    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   }      for(jj=1; jj<= nlstate+ndeath; jj++){
   */       printf("%lf ",ps[ii][jj]);
      }
   free_matrix(a,1,npar,1,npar);      printf("\n ");
   free_matrix(y,1,npar,1,npar);      }
   free_vector(x,1,npar);      printf("\n ");printf("%lf ",cov[2]);*/
   free_ivector(indx,1,npar);  /*
   free_matrix(hess,1,npar,1,npar);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
       return ps;
 }  }
   
 /*************** hessian matrix ****************/  /**************** Product of 2 matrices ******************/
 double hessii( double x[], double delta, int theta, double delti[])  
 {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int i;  {
   int l=1, lmax=20;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double k1,k2;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double p2[NPARMAX+1];    /* in, b, out are matrice of pointers which should have been initialized 
   double res;       before: only the contents of out is modified. The function returns
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;       a pointer to pointers identical to out */
   double fx;    long i, j, k;
   int k=0,kmax=10;    for(i=nrl; i<= nrh; i++)
   double l1;      for(k=ncolol; k<=ncoloh; k++)
         for(j=ncl,out[i][k]=0.; j<=nch; j++)
   fx=func(x);          out[i][k] +=in[i][j]*b[j][k];
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){    return out;
     l1=pow(10,l);  }
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  /************* Higher Matrix Product ***************/
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       p2[theta]=x[theta]-delt;  {
       k2=func(p2)-fx;    /* Computes the transition matrix starting at age 'age' over 
       /*res= (k1-2.0*fx+k2)/delt/delt; */       'nhstepm*hstepm*stepm' months (i.e. until
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
             nhstepm*hstepm matrices. 
 #ifdef DEBUG       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       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);       (typically every 2 years instead of every month which is too big 
 #endif       for the memory).
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       Model is determined by parameters x and covariates have to be 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){       included manually here. 
         k=kmax;  
       }       */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;    int i, j, d, h, k;
       }    double **out, cov[NCOVMAX];
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double **newm;
         delts=delt;  
       }    /* Hstepm could be zero and should return the unit matrix */
     }    for (i=1;i<=nlstate+ndeath;i++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   delti[theta]=delts;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   return res;        po[i][j][0]=(i==j ? 1.0 : 0.0);
        }
 }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
 double hessij( double x[], double delti[], int thetai,int thetaj)      for(d=1; d <=hstepm; d++){
 {        newm=savm;
   int i;        /* Covariates have to be included here again */
   int l=1, l1, lmax=20;        cov[1]=1.;
   double k1,k2,k3,k4,res,fx;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double p2[NPARMAX+1];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int k;        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fx=func(x);        for (k=1; k<=cptcovprod;k++)
   for (k=1; k<=2; k++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     k1=func(p2)-fx;        /*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, 
     p2[thetai]=x[thetai]+delti[thetai]/k;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        savm=oldm;
     k2=func(p2)-fx;        oldm=newm;
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      for(i=1; i<=nlstate+ndeath; i++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(j=1;j<=nlstate+ndeath;j++) {
     k3=func(p2)-fx;          po[i][j][h]=newm[i][j];
            /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     p2[thetai]=x[thetai]-delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k4=func(p2)-fx;    } /* end h */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    return po;
 #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);  
 #endif  
   }  /*************** log-likelihood *************/
   return res;  double func( double *x)
 }  {
     int i, ii, j, k, mi, d, kk;
 /************** Inverse of matrix **************/    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 void ludcmp(double **a, int n, int *indx, double *d)    double **out;
 {    double sw; /* Sum of weights */
   int i,imax,j,k;    double lli; /* Individual log likelihood */
   double big,dum,sum,temp;    int s1, s2;
   double *vv;    double bbh, survp;
      long ipmx;
   vv=vector(1,n);    /*extern weight */
   *d=1.0;    /* We are differentiating ll according to initial status */
   for (i=1;i<=n;i++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     big=0.0;    /*for(i=1;i<imx;i++) 
     for (j=1;j<=n;j++)      printf(" %d\n",s[4][i]);
       if ((temp=fabs(a[i][j])) > big) big=temp;    */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    cov[1]=1.;
     vv[i]=1.0/big;  
   }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {    if(mle==1){
       sum=a[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       a[i][j]=sum;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     big=0.0;            for (j=1;j<=nlstate+ndeath;j++){
     for (i=j;i<=n;i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       sum=a[i][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<j;k++)            }
         sum -= a[i][k]*a[k][j];          for(d=0; d<dh[mi][i]; d++){
       a[i][j]=sum;            newm=savm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         big=dum;            for (kk=1; kk<=cptcovage;kk++) {
         imax=i;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (j != imax) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<=n;k++) {            savm=oldm;
         dum=a[imax][k];            oldm=newm;
         a[imax][k]=a[j][k];          } /* end mult */
         a[j][k]=dum;        
       }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       *d = -(*d);          /* But now since version 0.9 we anticipate for bias and large stepm.
       vv[imax]=vv[j];           * 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 
     indx[j]=imax;           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (a[j][j] == 0.0) a[j][j]=TINY;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     if (j != n) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       dum=1.0/(a[j][j]);           * probability in order to take into account the bias as a fraction of the way
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     }           * -stepm/2 to stepm/2 .
   }           * For stepm=1 the results are the same as for previous versions of Imach.
   free_vector(vv,1,n);  /* Doesn't work */           * For stepm > 1 the results are less biased than in previous versions. 
 ;           */
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 void lubksb(double **a, int n, int *indx, double b[])          bbh=(double)bh[mi][i]/(double)stepm; 
 {          /* bias is positive if real duration
   int i,ii=0,ip,j;           * is higher than the multiple of stepm and negative otherwise.
   double sum;           */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for (i=1;i<=n;i++) {          if( s2 > nlstate){ 
     ip=indx[i];            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     sum=b[ip];               to the likelihood is the probability to die between last step unit time and current 
     b[ip]=b[i];               step unit time, which is also the differences between probability to die before dh 
     if (ii)               and probability to die before dh-stepm . 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];               In version up to 0.92 likelihood was computed
     else if (sum) ii=i;          as if date of death was unknown. Death was treated as any other
     b[i]=sum;          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=n;i>=1;i--) {          to consider that at each interview the state was recorded
     sum=b[i];          (healthy, disable or death) and IMaCh was corrected; but when we
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          introduced the exact date of death then we should have modified
     b[i]=sum/a[i][i];          the contribution of an exact death to the likelihood. This new
   }          contribution is smaller and very dependent of the step unit
 }          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
 /************ Frequencies ********************/          interview up to one month before death multiplied by the
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)          probability to die within a month. Thanks to Chris
 {  /* Some frequencies */          Jackson for correcting this bug.  Former versions increased
            mortality artificially. The bad side is that we add another loop
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          which slows down the processing. The difference can be up to 10%
   double ***freq; /* Frequencies */          lower mortality.
   double *pp;            */
   double pos, k2, dateintsum=0,k2cpt=0;            lli=log(out[s1][s2] - savm[s1][s2]);
   FILE *ficresp;          }else{
   char fileresp[FILENAMELENGTH];            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 */
   pp=vector(1,nlstate);          } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   strcpy(fileresp,"p");          /*if(lli ==000.0)*/
   strcat(fileresp,fileres);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   if((ficresp=fopen(fileresp,"w"))==NULL) {          ipmx +=1;
     printf("Problem with prevalence resultfile: %s\n", fileresp);          sw += weight[i];
     exit(0);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } /* end of individual */
   j1=0;    }  else if(mle==2){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   j=cptcoveff;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   for(k1=1; k1<=j;k1++){            for (j=1;j<=nlstate+ndeath;j++){
     for(i1=1; i1<=ncodemax[k1];i1++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       j1++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            }
         scanf("%d", i);*/          for(d=0; d<=dh[mi][i]; d++){
       for (i=-1; i<=nlstate+ndeath; i++)              newm=savm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=agemin; m <= agemax+3; m++)            for (kk=1; kk<=cptcovage;kk++) {
             freq[i][jk][m]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  }
       dateintsum=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       k2cpt=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (i=1; i<=imx; i++) {            savm=oldm;
         bool=1;            oldm=newm;
         if  (cptcovn>0) {          } /* end mult */
           for (z1=1; z1<=cptcoveff; z1++)        
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
               bool=0;          /* But now since version 0.9 we anticipate for bias and large stepm.
         }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         if (bool==1) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
           for(m=firstpass; m<=lastpass; m++){           * the nearest (and in case of equal distance, to the lowest) interval but now
             k2=anint[m][i]+(mint[m][i]/12.);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             if ((k2>=dateprev1) && (k2<=dateprev2)) {           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
               if(agev[m][i]==0) agev[m][i]=agemax+1;           * probability in order to take into account the bias as a fraction of the way
               if(agev[m][i]==1) agev[m][i]=agemax+2;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
               if (m<lastpass) {           * -stepm/2 to stepm/2 .
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];           * For stepm=1 the results are the same as for previous versions of Imach.
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];           * For stepm > 1 the results are less biased than in previous versions. 
               }           */
                        s1=s[mw[mi][i]][i];
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          s2=s[mw[mi+1][i]][i];
                 dateintsum=dateintsum+k2;          bbh=(double)bh[mi][i]/(double)stepm; 
                 k2cpt++;          /* bias is positive if real duration
               }           * is higher than the multiple of stepm and negative otherwise.
             }           */
           }          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 */
         }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       }          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
                  /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          /*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); */
       if  (cptcovn>0) {          ipmx +=1;
         fprintf(ficresp, "\n#********** Variable ");          sw += weight[i];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresp, "**********\n#");        } /* end of wave */
       }      } /* end of individual */
       for(i=1; i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresp, "\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
       for(i=(int)agemin; i <= (int)agemax+3; i++){          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(i==(int)agemax+3)            for (j=1;j<=nlstate+ndeath;j++){
           printf("Total");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           printf("Age %d", i);            }
         for(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            newm=savm;
             pp[jk] += freq[jk][m][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            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, pos=0; m <=0 ; m++)            }
             pos += freq[jk][m][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if(pp[jk]>=1.e-10)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            savm=oldm;
           else            oldm=newm;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          } /* end mult */
         }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         for(jk=1; jk <=nlstate ; jk++){          /* But now since version 0.9 we anticipate for bias and large stepm.
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             pp[jk] += freq[jk][m][i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
         }           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
         for(jk=1,pos=0; jk <=nlstate ; jk++)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
           pos += pp[jk];           * probability in order to take into account the bias as a fraction of the way
         for(jk=1; jk <=nlstate ; jk++){           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
           if(pos>=1.e-5)           * -stepm/2 to stepm/2 .
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);           * For stepm=1 the results are the same as for previous versions of Imach.
           else           * For stepm > 1 the results are less biased than in previous versions. 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           */
           if( i <= (int) agemax){          s1=s[mw[mi][i]][i];
             if(pos>=1.e-5){          s2=s[mw[mi+1][i]][i];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          bbh=(double)bh[mi][i]/(double)stepm; 
               probs[i][jk][j1]= pp[jk]/pos;          /* bias is positive if real duration
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/           * is higher than the multiple of stepm and negative otherwise.
             }           */
             else          /* 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 */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          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 */
           }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         }          /*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); */
         for(jk=-1; jk <=nlstate+ndeath; jk++)          ipmx +=1;
           for(m=-1; m <=nlstate+ndeath; m++)          sw += weight[i];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if(i <= (int) agemax)        } /* end of wave */
           fprintf(ficresp,"\n");      } /* end of individual */
         printf("\n");    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   dateintmean=dateintsum/k2cpt;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   fclose(ficresp);              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;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /************ Prevalence ********************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            }
 {  /* Some frequencies */          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***freq; /* Frequencies */            savm=oldm;
   double *pp;            oldm=newm;
   double pos, k2;          } /* end mult */
         
   pp=vector(1,nlstate);          s1=s[mw[mi][i]][i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          s2=s[mw[mi+1][i]][i];
            if( s2 > nlstate){ 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            lli=log(out[s1][s2] - savm[s1][s2]);
   j1=0;          }else{
              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   j=cptcoveff;          }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          ipmx +=1;
            sw += weight[i];
  for(k1=1; k1<=j;k1++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i1=1; i1<=ncodemax[k1];i1++){  /*      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]); */
       j1++;        } /* end of wave */
        } /* end of individual */
       for (i=-1; i<=nlstate+ndeath; i++)      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         for (jk=-1; jk<=nlstate+ndeath; jk++)        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(m=agemin; m <= agemax+3; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             freq[i][jk][m]=0;        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=1; i<=imx; i++) {            for (j=1;j<=nlstate+ndeath;j++){
         bool=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         if  (cptcovn>0) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for (z1=1; z1<=cptcoveff; z1++)            }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          for(d=0; d<dh[mi][i]; d++){
               bool=0;            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if (bool==1) {            for (kk=1; kk<=cptcovage;kk++) {
           for(m=firstpass; m<=lastpass; m++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             k2=anint[m][i]+(mint[m][i]/12.);            }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          
               if(agev[m][i]==0) agev[m][i]=agemax+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               if(agev[m][i]==1) agev[m][i]=agemax+2;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            savm=oldm;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            oldm=newm;
             }          } /* end mult */
           }        
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
         for(i=(int)agemin; i <= (int)agemax+3; i++){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          sw += weight[i];
               pp[jk] += freq[jk][m][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
           for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
             for(m=-1, pos=0; m <=0 ; m++)      } /* end of individual */
             pos += freq[jk][m][i];    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          for(jk=1; jk <=nlstate ; jk++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    return -l;
              pp[jk] += freq[jk][m][i];  }
          }  
            /*************** log-likelihood *************/
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  double funcone( double *x)
   {
          for(jk=1; jk <=nlstate ; jk++){              /* Same as likeli but slower because of a lot of printf and if */
            if( i <= (int) agemax){    int i, ii, j, k, mi, d, kk;
              if(pos>=1.e-5){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
                probs[i][jk][j1]= pp[jk]/pos;    double **out;
              }    double lli; /* Individual log likelihood */
            }    double llt;
          }    int s1, s2;
              double bbh, survp;
         }    /*extern weight */
     }    /* We are differentiating ll according to initial status */
   }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    */
   free_vector(pp,1,nlstate);    cov[1]=1.;
    
 }  /* End of Freq */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 /************* Waves Concatenation ***************/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      for(mi=1; mi<= wav[i]-1; mi++){
 {        for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for (j=1;j<=nlstate+ndeath;j++){
      Death is a valid wave (if date is known).            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            savm[ii][j]=(ii==j ? 1.0 : 0.0);
      dh[m][i] of 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.        for(d=0; d<dh[mi][i]; d++){
      */          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, mi, m;          for (kk=1; kk<=cptcovage;kk++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      double sum=0., jmean=0.;*/          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int j, k=0,jk, ju, jl;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double sum=0.;          savm=oldm;
   jmin=1e+5;          oldm=newm;
   jmax=-1;        } /* end mult */
   jmean=0.;        
   for(i=1; i<=imx; i++){        s1=s[mw[mi][i]][i];
     mi=0;        s2=s[mw[mi+1][i]][i];
     m=firstpass;        bbh=(double)bh[mi][i]/(double)stepm; 
     while(s[m][i] <= nlstate){        /* bias is positive if real duration
       if(s[m][i]>=1)         * is higher than the multiple of stepm and negative otherwise.
         mw[++mi][i]=m;         */
       if(m >=lastpass)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         break;          lli=log(out[s1][s2] - savm[s1][s2]);
       else        } else if (mle==1){
         m++;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }/* end while */        } else if(mle==2){
     if (s[m][i] > nlstate){          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 */
       mi++;     /* Death is another wave */        } else if(mle==3){  /* exponential inter-extrapolation */
       /* if(mi==0)  never been interviewed correctly before death */          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 */
          /* Only death is a correct wave */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       mw[mi][i]=m;          lli=log(out[s1][s2]); /* Original formula */
     }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
     wav[i]=mi;        } /* End of if */
     if(mi==0)        ipmx +=1;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        sw += weight[i];
   }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   for(i=1; i<=imx; i++){        if(globpr){
     for(mi=1; mi<wav[i];mi++){          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       if (stepm <=0)   %10.6f %10.6f %10.6f ", \
         dh[mi][i]=1;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       else{                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         if (s[mw[mi+1][i]][i] > nlstate) {          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           if (agedc[i] < 2*AGESUP) {            llt +=ll[k]*gipmx/gsw;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           if(j==0) j=1;  /* Survives at least one month after exam */          }
           k=k+1;          fprintf(ficresilk," %10.6f\n", -llt);
           if (j >= jmax) jmax=j;        }
           if (j <= jmin) jmin=j;      } /* end of wave */
           sum=sum+j;    } /* end of individual */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         else{    if(globpr==0){ /* First time we count the contributions and weights */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      gipmx=ipmx;
           k=k+1;      gsw=sw;
           if (j >= jmax) jmax=j;    }
           else if (j <= jmin)jmin=j;    return -l;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  }
           sum=sum+j;  
         }  char *subdirf(char fileres[])
         jk= j/stepm;  {
         jl= j -jk*stepm;    /* Caution optionfilefiname is hidden */
         ju= j -(jk+1)*stepm;    strcpy(tmpout,optionfilefiname);
         if(jl <= -ju)    strcat(tmpout,"/"); /* Add to the right */
           dh[mi][i]=jk;    strcat(tmpout,fileres);
         else    return tmpout;
           dh[mi][i]=jk+1;  }
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */  char *subdirf2(char fileres[], char *preop)
       }  {
     }    
   }    strcpy(tmpout,optionfilefiname);
   jmean=sum/k;    strcat(tmpout,"/");
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    strcat(tmpout,preop);
  }    strcat(tmpout,fileres);
 /*********** Tricode ****************************/    return tmpout;
 void tricode(int *Tvar, int **nbcode, int imx)  }
 {  char *subdirf3(char fileres[], char *preop, char *preop2)
   int Ndum[20],ij=1, k, j, i;  {
   int cptcode=0;    
   cptcoveff=0;    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/");
   for (k=0; k<19; k++) Ndum[k]=0;    strcat(tmpout,preop);
   for (k=1; k<=7; k++) ncodemax[k]=0;    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    return tmpout;
     for (i=1; i<=imx; i++) {  }
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  {
       if (ij > cptcode) cptcode=ij;    /* This routine should help understanding what is done with 
     }       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
     for (i=0; i<=cptcode; i++) {       Plotting could be done.
       if(Ndum[i]!=0) ncodemax[j]++;     */
     }    int k;
     ij=1;  
     if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
     for (i=1; i<=ncodemax[j]; i++) {      strcat(fileresilk,fileres);
       for (k=0; k<=19; k++) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         if (Ndum[k] != 0) {        printf("Problem with resultfile: %s\n", fileresilk);
           nbcode[Tvar[j]][ij]=k;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/      }
           ij++;      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 ");
         if (ij > ncodemax[j]) break;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       }        for(k=1; k<=nlstate; k++) 
     }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   }        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
  for (k=0; k<19; k++) Ndum[k]=0;  
     *fretone=(*funcone)(p);
  for (i=1; i<=ncovmodel-2; i++) {    if(*globpri !=0){
       ij=Tvar[i];      fclose(ficresilk);
       Ndum[ij]++;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     }      fflush(fichtm); 
     } 
  ij=1;    return;
  for (i=1; i<=10; i++) {  }
    if((Ndum[i]!=0) && (i<=ncovcol)){  
      Tvaraff[ij]=i;  
      ij++;  /*********** Maximum Likelihood Estimation ***************/
    }  
  }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    {
     cptcoveff=ij-1;    int i,j, iter;
 }    double **xi;
     double fret;
 /*********** Health Expectancies ****************/    double fretone; /* Only one call to likelihood */
     char filerespow[FILENAMELENGTH];
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)    xi=matrix(1,npar,1,npar);
 {    for (i=1;i<=npar;i++)
   /* Health expectancies */      for (j=1;j<=npar;j++)
   int i, j, nhstepm, hstepm, h, nstepm;        xi[i][j]=(i==j ? 1.0 : 0.0);
   double age, agelim, hf;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double ***p3mat;    strcpy(filerespow,"pow"); 
      strcat(filerespow,fileres);
   fprintf(ficreseij,"# Health expectancies\n");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   fprintf(ficreseij,"# Age");      printf("Problem with resultfile: %s\n", filerespow);
   for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(j=1; j<=nlstate;j++)    }
       fprintf(ficreseij," %1d-%1d",i,j);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fprintf(ficreseij,"\n");    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
   if(estepm < stepm){        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     printf ("Problem %d lower than %d\n",estepm, stepm);    fprintf(ficrespow,"\n");
   }  
   else  hstepm=estepm;      powell(p,xi,npar,ftol,&iter,&fret,func);
   /* We compute the life expectancy from trapezoids spaced every estepm months  
    * This is mainly to measure the difference between two models: for example    fclose(ficrespow);
    * if stepm=24 months pijx are given only every 2 years and by summing them    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
    * we are calculating an estimate of the Life Expectancy assuming a linear    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    * progression inbetween and thus overestimating or underestimating according    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  }
    * to compare the new estimate of Life expectancy with the same linear  
    * hypothesis. A more precise result, taking into account a more precise  /**** Computes Hessian and covariance matrix ***/
    * curvature will be obtained if estepm is as small as stepm. */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
   /* For example we decided to compute the life expectancy with the smallest unit */    double  **a,**y,*x,pd;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double **hess;
      nhstepm is the number of hstepm from age to agelim    int i, j,jk;
      nstepm is the number of stepm from age to agelin.    int *indx;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */    double hessii(double p[], double delta, int theta, double delti[]);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double hessij(double p[], double delti[], int i, int j);
      survival function given by stepm (the optimization length). Unfortunately it    void lubksb(double **a, int npar, int *indx, double b[]) ;
      means that if the survival funtion is printed only each two years of age and if    void ludcmp(double **a, int npar, int *indx, double *d) ;
      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.    hess=matrix(1,npar,1,npar);
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   agelim=AGESUP;    for (i=1;i<=npar;i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      printf("%d",i);fflush(stdout);
     /* nhstepm age range expressed in number of stepm */      fprintf(ficlog,"%d",i);fflush(ficlog);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      hess[i][i]=hessii(p,ftolhess,i,delti);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      /*printf(" %f ",p[i]);*/
     /* if (stepm >= YEARM) hstepm=1;*/      /*printf(" %lf ",hess[i][i]);*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for (i=1;i<=npar;i++) {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      for (j=1;j<=npar;j++)  {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          if (j>i) { 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          printf(".%d%d",i,j);fflush(stdout);
     for(i=1; i<=nlstate;i++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       for(j=1; j<=nlstate;j++)          hess[i][j]=hessij(p,delti,i,j);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          hess[j][i]=hess[i][j];    
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          /*printf(" %lf ",hess[i][j]);*/
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        }
         }      }
     fprintf(ficreseij,"%3.0f",age );    }
     for(i=1; i<=nlstate;i++)    printf("\n");
       for(j=1; j<=nlstate;j++){    fprintf(ficlog,"\n");
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  
       }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficreseij,"\n");    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
   }    a=matrix(1,npar,1,npar);
 }    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
 /************ Variance ******************/    indx=ivector(1,npar);
 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, int estepm)    for (i=1;i<=npar;i++)
 {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   /* Variance of health expectancies */    ludcmp(a,npar,indx,&pd);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    for (j=1;j<=npar;j++) {
   double **dnewm,**doldm;      for (i=1;i<=npar;i++) x[i]=0;
   int i, j, nhstepm, hstepm, h, nstepm ;      x[j]=1;
   int k, cptcode;      lubksb(a,npar,indx,x);
   double *xp;      for (i=1;i<=npar;i++){ 
   double **gp, **gm;        matcov[i][j]=x[i];
   double ***gradg, ***trgradg;      }
   double ***p3mat;    }
   double age,agelim, hf;  
   int theta;    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");    for (i=1;i<=npar;i++) { 
   fprintf(ficresvij,"# Age");      for (j=1;j<=npar;j++) { 
   for(i=1; i<=nlstate;i++)        printf("%.3e ",hess[i][j]);
     for(j=1; j<=nlstate;j++)        fprintf(ficlog,"%.3e ",hess[i][j]);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      }
   fprintf(ficresvij,"\n");      printf("\n");
       fprintf(ficlog,"\n");
   xp=vector(1,npar);    }
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);    /* Recompute Inverse */
      for (i=1;i<=npar;i++)
   if(estepm < stepm){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     printf ("Problem %d lower than %d\n",estepm, stepm);    ludcmp(a,npar,indx,&pd);
   }  
   else  hstepm=estepm;      /*  printf("\n#Hessian matrix recomputed#\n");
   /* For example we decided to compute the life expectancy with the smallest unit */  
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    for (j=1;j<=npar;j++) {
      nhstepm is the number of hstepm from age to agelim      for (i=1;i<=npar;i++) x[i]=0;
      nstepm is the number of stepm from age to agelin.      x[j]=1;
      Look at hpijx to understand the reason of that which relies in memory size      lubksb(a,npar,indx,x);
      and note for a fixed period like k years */      for (i=1;i<=npar;i++){ 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        y[i][j]=x[i];
      survival function given by stepm (the optimization length). Unfortunately it        printf("%.3e ",y[i][j]);
      means that if the survival funtion is printed only each two years of age and if        fprintf(ficlog,"%.3e ",y[i][j]);
      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.      printf("\n");
   */      fprintf(ficlog,"\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    }
   agelim = AGESUP;    */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_matrix(a,1,npar,1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    free_matrix(y,1,npar,1,npar);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(x,1,npar);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_ivector(indx,1,npar);
     gp=matrix(0,nhstepm,1,nlstate);    free_matrix(hess,1,npar,1,npar);
     gm=matrix(0,nhstepm,1,nlstate);  
   
     for(theta=1; theta <=npar; theta++){  }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /*************** hessian matrix ****************/
       }  double hessii( double x[], double delta, int theta, double delti[])
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i;
     int l=1, lmax=20;
       if (popbased==1) {    double k1,k2;
         for(i=1; i<=nlstate;i++)    double p2[NPARMAX+1];
           prlim[i][i]=probs[(int)age][i][ij];    double res;
       }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      double fx;
       for(j=1; j<= nlstate; j++){    int k=0,kmax=10;
         for(h=0; h<=nhstepm; h++){    double l1;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){
          l1=pow(10,l);
       for(i=1; i<=npar; i++) /* Computes gradient */      delts=delt;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(k=1 ; k <kmax; k=k+1){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          delt = delta*(l1*k);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        p2[theta]=x[theta] +delt;
          k1=func(p2)-fx;
       if (popbased==1) {        p2[theta]=x[theta]-delt;
         for(i=1; i<=nlstate;i++)        k2=func(p2)-fx;
           prlim[i][i]=probs[(int)age][i][ij];        /*res= (k1-2.0*fx+k2)/delt/delt; */
       }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
       for(j=1; j<= nlstate; j++){  #ifdef DEBUG
         for(h=0; h<=nhstepm; h++){        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  #endif
         }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
       for(j=1; j<= nlstate; j++)        }
         for(h=0; h<=nhstepm; h++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          k=kmax; l=lmax*10.;
         }        }
     } /* End theta */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        }
       }
     for(h=0; h<=nhstepm; h++)    }
       for(j=1; j<=nlstate;j++)    delti[theta]=delts;
         for(theta=1; theta <=npar; theta++)    return res; 
           trgradg[h][j][theta]=gradg[h][theta][j];    
   }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1;i<=nlstate;i++)  double hessij( double x[], double delti[], int thetai,int thetaj)
       for(j=1;j<=nlstate;j++)  {
         vareij[i][j][(int)age] =0.;    int i;
     int l=1, l1, lmax=20;
     for(h=0;h<=nhstepm;h++){    double k1,k2,k3,k4,res,fx;
       for(k=0;k<=nhstepm;k++){    double p2[NPARMAX+1];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    int k;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)    fx=func(x);
           for(j=1;j<=nlstate;j++)    for (k=1; k<=2; k++) {
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      for (i=1;i<=npar;i++) p2[i]=x[i];
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
     fprintf(ficresvij,"%.0f ",age );    
     for(i=1; i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(j=1; j<=nlstate;j++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      k2=func(p2)-fx;
       }    
     fprintf(ficresvij,"\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_matrix(gp,0,nhstepm,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     free_matrix(gm,0,nhstepm,1,nlstate);      k3=func(p2)-fx;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   } /* End age */      k4=func(p2)-fx;
        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   free_vector(xp,1,npar);  #ifdef DEBUG
   free_matrix(doldm,1,nlstate,1,npar);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   free_matrix(dnewm,1,nlstate,1,nlstate);      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);
   #endif
 }    }
     return res;
 /************ Variance of prevlim ******************/  }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {  /************** Inverse of matrix **************/
   /* Variance of prevalence limit */  void ludcmp(double **a, int n, int *indx, double *d) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  { 
   double **newm;    int i,imax,j,k; 
   double **dnewm,**doldm;    double big,dum,sum,temp; 
   int i, j, nhstepm, hstepm;    double *vv; 
   int k, cptcode;   
   double *xp;    vv=vector(1,n); 
   double *gp, *gm;    *d=1.0; 
   double **gradg, **trgradg;    for (i=1;i<=n;i++) { 
   double age,agelim;      big=0.0; 
   int theta;      for (j=1;j<=n;j++) 
            if ((temp=fabs(a[i][j])) > big) big=temp; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   fprintf(ficresvpl,"# Age");      vv[i]=1.0/big; 
   for(i=1; i<=nlstate;i++)    } 
       fprintf(ficresvpl," %1d-%1d",i,i);    for (j=1;j<=n;j++) { 
   fprintf(ficresvpl,"\n");      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   xp=vector(1,npar);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   dnewm=matrix(1,nlstate,1,npar);        a[i][j]=sum; 
   doldm=matrix(1,nlstate,1,nlstate);      } 
        big=0.0; 
   hstepm=1*YEARM; /* Every year of age */      for (i=j;i<=n;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        sum=a[i][j]; 
   agelim = AGESUP;        for (k=1;k<j;k++) 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          sum -= a[i][k]*a[k][j]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        a[i][j]=sum; 
     if (stepm >= YEARM) hstepm=1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          big=dum; 
     gradg=matrix(1,npar,1,nlstate);          imax=i; 
     gp=vector(1,nlstate);        } 
     gm=vector(1,nlstate);      } 
       if (j != imax) { 
     for(theta=1; theta <=npar; theta++){        for (k=1;k<=n;k++) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */          dum=a[imax][k]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          a[imax][k]=a[j][k]; 
       }          a[j][k]=dum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } 
       for(i=1;i<=nlstate;i++)        *d = -(*d); 
         gp[i] = prlim[i][i];        vv[imax]=vv[j]; 
          } 
       for(i=1; i<=npar; i++) /* Computes gradient */      indx[j]=imax; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (j != n) { 
       for(i=1;i<=nlstate;i++)        dum=1.0/(a[j][j]); 
         gm[i] = prlim[i][i];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
       for(i=1;i<=nlstate;i++)    } 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    free_vector(vv,1,n);  /* Doesn't work */
     } /* End theta */  ;
   } 
     trgradg =matrix(1,nlstate,1,npar);  
   void lubksb(double **a, int n, int *indx, double b[]) 
     for(j=1; j<=nlstate;j++)  { 
       for(theta=1; theta <=npar; theta++)    int i,ii=0,ip,j; 
         trgradg[j][theta]=gradg[theta][j];    double sum; 
    
     for(i=1;i<=nlstate;i++)    for (i=1;i<=n;i++) { 
       varpl[i][(int)age] =0.;      ip=indx[i]; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      sum=b[ip]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      b[ip]=b[i]; 
     for(i=1;i<=nlstate;i++)      if (ii) 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
     fprintf(ficresvpl,"%.0f ",age );      b[i]=sum; 
     for(i=1; i<=nlstate;i++)    } 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    for (i=n;i>=1;i--) { 
     fprintf(ficresvpl,"\n");      sum=b[i]; 
     free_vector(gp,1,nlstate);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     free_vector(gm,1,nlstate);      b[i]=sum/a[i][i]; 
     free_matrix(gradg,1,npar,1,nlstate);    } 
     free_matrix(trgradg,1,nlstate,1,npar);  } 
   } /* End age */  
   /************ Frequencies ********************/
   free_vector(xp,1,npar);  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)
   free_matrix(doldm,1,nlstate,1,npar);  {  /* Some frequencies */
   free_matrix(dnewm,1,nlstate,1,nlstate);    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
 }    int first;
     double ***freq; /* Frequencies */
 /************ Variance of one-step probabilities  ******************/    double *pp, **prop;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
 {    FILE *ficresp;
   int i, j;    char fileresp[FILENAMELENGTH];
   int k=0, cptcode;    
   double **dnewm,**doldm;    pp=vector(1,nlstate);
   double *xp;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   double *gp, *gm;    strcpy(fileresp,"p");
   double **gradg, **trgradg;    strcat(fileresp,fileres);
   double age,agelim, cov[NCOVMAX];    if((ficresp=fopen(fileresp,"w"))==NULL) {
   int theta;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   char fileresprob[FILENAMELENGTH];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
   strcpy(fileresprob,"prob");    }
   strcat(fileresprob,fileres);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    j1=0;
     printf("Problem with resultfile: %s\n", fileresprob);    
   }    j=cptcoveff;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
     first=1;
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for(k1=1; k1<=j;k1++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
   cov[1]=1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   for (age=bage; age<=fage; age ++){          scanf("%d", i);*/
     cov[2]=age;        for (i=-1; i<=nlstate+ndeath; i++)  
     gradg=matrix(1,npar,1,9);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     trgradg=matrix(1,9,1,npar);            for(m=iagemin; m <= iagemax+3; m++)
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              freq[i][jk][m]=0;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
          for (i=1; i<=nlstate; i++)  
     for(theta=1; theta <=npar; theta++){        for(m=iagemin; m <= iagemax+3; m++)
       for(i=1; i<=npar; i++)          prop[i][m]=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        
              dateintsum=0;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        k2cpt=0;
            for (i=1; i<=imx; i++) {
       k=0;          bool=1;
       for(i=1; i<= (nlstate+ndeath); i++){          if  (cptcovn>0) {
         for(j=1; j<=(nlstate+ndeath);j++){            for (z1=1; z1<=cptcoveff; z1++) 
            k=k+1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           gp[k]=pmmij[i][j];                bool=0;
         }          }
       }          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
       for(i=1; i<=npar; i++)              k2=anint[m][i]+(mint[m][i]/12.);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       k=0;                if (m<lastpass) {
       for(i=1; i<=(nlstate+ndeath); i++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         for(j=1; j<=(nlstate+ndeath);j++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           k=k+1;                }
           gm[k]=pmmij[i][j];                
         }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       }                  dateintsum=dateintsum+k2;
                        k2cpt++;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)                }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  /*}*/
     }            }
           }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        }
       for(theta=1; theta <=npar; theta++)         
       trgradg[j][theta]=gradg[theta][j];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
    
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        if  (cptcovn>0) {
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      pmij(pmmij,cov,ncovmodel,x,nlstate);          fprintf(ficresp, "**********\n#");
         }
      k=0;        for(i=1; i<=nlstate;i++) 
      for(i=1; i<=(nlstate+ndeath); i++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        for(j=1; j<=(nlstate+ndeath);j++){        fprintf(ficresp, "\n");
          k=k+1;        
          gm[k]=pmmij[i][j];        for(i=iagemin; i <= iagemax+3; i++){
         }          if(i==iagemax+3){
      }            fprintf(ficlog,"Total");
                }else{
      /*printf("\n%d ",(int)age);            if(first==1){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              first=0;
                      printf("See log file for details...\n");
             }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            fprintf(ficlog,"Age %d", i);
      }*/          }
           for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresprob,"\n%d ",(int)age);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          }
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          for(jk=1; jk <=nlstate ; jk++){
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for(m=-1, pos=0; m <=0 ; m++)
   }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              if(first==1){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 }            }else{
  free_vector(xp,1,npar);              if(first==1)
 fclose(ficresprob);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }            }
           }
 /******************* Printing html file ***********/  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          for(jk=1; jk <=nlstate ; jk++){
  int lastpass, int stepm, int weightopt, char model[],\            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              pp[jk] += freq[jk][m][i];
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\          }       
  char version[], int popforecast, int estepm ){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   int jj1, k1, i1, cpt;            pos += pp[jk];
   FILE *fichtm;            posprop += prop[jk][i];
   /*char optionfilehtm[FILENAMELENGTH];*/          }
           for(jk=1; jk <=nlstate ; jk++){
   strcpy(optionfilehtm,optionfile);            if(pos>=1.e-5){
   strcat(optionfilehtm,".htm");              if(first==1)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     printf("Problem with %s \n",optionfilehtm), exit(0);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   }            }else{
               if(first==1)
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 \n            }
 Total number of observations=%d <br>\n            if( i <= iagemax){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              if(pos>=1.e-5){
 <hr  size=\"2\" color=\"#EC5E5E\">                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
  <ul><li>Outputs files<br>\n                /*probs[i][jk][j1]= pp[jk]/pos;*/
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n              }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              else
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n            }
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);          }
           
  fprintf(fichtm,"\n          for(jk=-1; jk <=nlstate+ndeath; jk++)
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n            for(m=-1; m <=nlstate+ndeath; m++)
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n              if(freq[jk][m][i] !=0 ) {
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n              if(first==1)
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  if(popforecast==1) fprintf(fichtm,"\n              }
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          if(i <= iagemax)
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n            fprintf(ficresp,"\n");
         <br>",fileres,fileres,fileres,fileres);          if(first==1)
  else            printf("Others in log...\n");
    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(ficlog,"\n");
 fprintf(fichtm," <li>Graphs</li><p>");        }
       }
  m=cptcoveff;    }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    dateintmean=dateintsum/k2cpt; 
    
  jj1=0;    fclose(ficresp);
  for(k1=1; k1<=m;k1++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
    for(i1=1; i1<=ncodemax[k1];i1++){    free_vector(pp,1,nlstate);
        jj1++;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        if (cptcovn > 0) {    /* End of Freq */
          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]]);  /************ Prevalence ********************/
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  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)
        }  {  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           in each health status at the date of interview (if between dateprev1 and dateprev2).
        for(cpt=1; cpt<nlstate;cpt++){       We still use firstpass and lastpass as another selection.
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);   
        }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     for(cpt=1; cpt<=nlstate;cpt++) {    double ***freq; /* Frequencies */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double *pp, **prop;
 interval) in state (%d): v%s%d%d.gif <br>    double pos,posprop; 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      double  y2; /* in fractional years */
      }    int iagemin, iagemax;
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    iagemin= (int) agemin;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    iagemax= (int) agemax;
      }    /*pp=vector(1,nlstate);*/
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    prop=matrix(1,nlstate,iagemin,iagemax+3); 
 health expectancies in states (1) and (2): e%s%d.gif<br>    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    j1=0;
 fprintf(fichtm,"\n</body>");    
    }    j=cptcoveff;
    }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 fclose(fichtm);    
 }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
 /******************* Gnuplot file **************/        j1++;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        
         for (i=1; i<=nlstate; i++)  
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
   strcpy(optionfilegnuplot,optionfilefiname);       
   strcat(optionfilegnuplot,".gp.txt");        for (i=1; i<=imx; i++) { /* Each individual */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          bool=1;
     printf("Problem with file %s",optionfilegnuplot);          if  (cptcovn>0) {
   }            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 #ifdef windows                bool=0;
     fprintf(ficgp,"cd \"%s\" \n",pathc);          } 
 #endif          if (bool==1) { 
 m=pow(2,cptcoveff);            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 */
  /* 1eme*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   for (cpt=1; cpt<= nlstate ; cpt ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
    for (k1=1; k1<= m ; k1 ++) {                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); 
 #ifdef windows                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     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",ageminpar,fage,fileres,k1-1,k1-1);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
 #endif                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 #ifdef unix                  prop[s[m][i]][iagemax+3] += weight[i]; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);                } 
 #endif              }
             } /* end selection of waves */
 for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=iagemin; i <= iagemax+3; i++){  
 }          
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     for (i=1; i<= nlstate ; i ++) {            posprop += prop[jk][i]; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(jk=1; jk <=nlstate ; jk++){     
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            if( i <=  iagemax){ 
      for (i=1; i<= nlstate ; i ++) {              if(posprop>=1.e-5){ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                probs[i][jk][j1]= prop[jk][i]/posprop;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              } 
 }              } 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          }/* end jk */ 
 #ifdef unix        }/* end i */ 
 fprintf(ficgp,"\nset ter gif small size 400,300");      } /* end i1 */
 #endif    } /* end k1 */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
    }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   }    /*free_vector(pp,1,nlstate);*/
   /*2 eme*/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  /************* Waves Concatenation ***************/
      
     for (i=1; i<= nlstate+1 ; i ++) {  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)
       k=2*i;  {
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       for (j=1; j<= nlstate+1 ; j ++) {       Death is a valid wave (if date is known).
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   else fprintf(ficgp," \%%*lf (\%%*lf)");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 }         and mw[mi+1][i]. dh depends on stepm.
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    int i, mi, m;
       for (j=1; j<= nlstate+1 ; j ++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       double sum=0., jmean=0.;*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");    int first;
 }      int j, k=0,jk, ju, jl;
       fprintf(ficgp,"\" t\"\" w l 0,");    double sum=0.;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    first=0;
       for (j=1; j<= nlstate+1 ; j ++) {    jmin=1e+5;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    jmax=-1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    jmean=0.;
 }      for(i=1; i<=imx; i++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      mi=0;
       else fprintf(ficgp,"\" t\"\" w l 0,");      m=firstpass;
     }      while(s[m][i] <= nlstate){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        if(s[m][i]>=1)
   }          mw[++mi][i]=m;
          if(m >=lastpass)
   /*3eme*/          break;
         else
   for (k1=1; k1<= m ; k1 ++) {          m++;
     for (cpt=1; cpt<= nlstate ; cpt ++) {      }/* end while */
       k=2+nlstate*(cpt-1);      if (s[m][i] > nlstate){
       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",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        mi++;     /* Death is another wave */
       for (i=1; i< nlstate ; i ++) {        /* if(mi==0)  never been interviewed correctly before death */
         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);           /* Only death is a correct wave */
       }        mw[mi][i]=m;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      }
     }  
     }      wav[i]=mi;
        if(mi==0){
   /* CV preval stat */        nbwarn++;
     for (k1=1; k1<= m ; k1 ++) {        if(first==0){
     for (cpt=1; cpt<nlstate ; cpt ++) {          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       k=3;          first=1;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        }
         if(first==1){
       for (i=1; i< nlstate ; i ++)          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         fprintf(ficgp,"+$%d",k+i+1);        }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      } /* end mi==0 */
          } /* End individuals */
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    for(i=1; i<=imx; i++){
       for (i=1; i< nlstate ; i ++) {      for(mi=1; mi<wav[i];mi++){
         l=3+(nlstate+ndeath)*cpt;        if (stepm <=0)
         fprintf(ficgp,"+$%d",l+i+1);          dh[mi][i]=1;
       }        else{
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            if (agedc[i] < 2*AGESUP) {
     }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   }                if(j==0) j=1;  /* Survives at least one month after exam */
                else if(j<0){
   /* proba elementaires */                nberr++;
    for(i=1,jk=1; i <=nlstate; i++){                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for(k=1; k <=(nlstate+ndeath); k++){                j=1; /* Temporary Dangerous patch */
       if (k != i) {                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);
         for(j=1; j <=ncovmodel; j++){                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]);
                        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);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              }
           jk++;              k=k+1;
           fprintf(ficgp,"\n");              if (j >= jmax) jmax=j;
         }              if (j <= jmin) jmin=j;
       }              sum=sum+j;
     }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
     for(jk=1; jk <=m; jk++) {          }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          else{
    i=1;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
    for(k2=1; k2<=nlstate; k2++) {            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
      k3=i;            k=k+1;
      for(k=1; k<=(nlstate+ndeath); k++) {            if (j >= jmax) jmax=j;
        if (k != k2){            else if (j <= jmin)jmin=j;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 ij=1;            /*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]);*/
         for(j=3; j <=ncovmodel; j++) {            if(j<0){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              nberr++;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              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]);
             ij++;              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]);
           }            }
           else            sum=sum+j;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
         }          jk= j/stepm;
           fprintf(ficgp,")/(1");          jl= j -jk*stepm;
                  ju= j -(jk+1)*stepm;
         for(k1=1; k1 <=nlstate; k1++){            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            if(jl==0){
 ij=1;              dh[mi][i]=jk;
           for(j=3; j <=ncovmodel; j++){              bh[mi][i]=0;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            }else{ /* We want a negative bias in order to only have interpolation ie
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                    * at the price of an extra matrix product in likelihood */
             ij++;              dh[mi][i]=jk+1;
           }              bh[mi][i]=ju;
           else            }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }else{
           }            if(jl <= -ju){
           fprintf(ficgp,")");              dh[mi][i]=jk;
         }              bh[mi][i]=jl;       /* bias is positive if real duration
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);                                   * is higher than the multiple of stepm and negative otherwise.
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                                   */
         i=i+ncovmodel;            }
        }            else{
      }              dh[mi][i]=jk+1;
    }              bh[mi][i]=ju;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            }
    }            if(dh[mi][i]==0){
                  dh[mi][i]=1; /* At least one step */
   fclose(ficgp);              bh[mi][i]=ju; /* At least one step */
 }  /* end gnuplot */              /*  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);*/
             }
           } /* end if mle */
 /*************** Moving average **************/        }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      } /* end wave */
     }
   int i, cpt, cptcod;    jmean=sum/k;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       for (i=1; i<=nlstate;i++)    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
      /*********** Tricode ****************************/
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  void tricode(int *Tvar, int **nbcode, int imx)
       for (i=1; i<=nlstate;i++){  {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
           for (cpt=0;cpt<=4;cpt++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    int cptcode=0;
           }    cptcoveff=0; 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;   
         }    for (k=0; k<maxncov; k++) Ndum[k]=0;
       }    for (k=1; k<=7; k++) ncodemax[k]=0;
     }  
        for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
 }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 /************** Forecasting ******************/        Ndum[ij]++; /*store the modality */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
          if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                                         Tvar[j]. If V=sex and male is 0 and 
   int *popage;                                         female is 1, then  cptcode=1.*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      }
   double *popeffectif,*popcount;  
   double ***p3mat;      for (i=0; i<=cptcode; i++) {
   char fileresf[FILENAMELENGTH];        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 */
       }
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for (k=0; k<= maxncov; k++) {
            if (Ndum[k] != 0) {
              nbcode[Tvar[j]][ij]=k; 
   strcpy(fileresf,"f");            /* 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; */
   strcat(fileresf,fileres);            
   if((ficresf=fopen(fileresf,"w"))==NULL) {            ij++;
     printf("Problem with forecast resultfile: %s\n", fileresf);          }
   }          if (ij > ncodemax[j]) break; 
   printf("Computing forecasting: result on file '%s' \n", fileresf);        }  
       } 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    }  
   
   if (mobilav==1) {   for (k=0; k< maxncov; k++) Ndum[k]=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);   for (i=1; i<=ncovmodel-2; i++) { 
   }     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i];
   stepsize=(int) (stepm+YEARM-1)/YEARM;     Ndum[ij]++;
   if (stepm<=12) stepsize=1;   }
    
   agelim=AGESUP;   ij=1;
     for (i=1; i<= maxncov; i++) {
   hstepm=1;     if((Ndum[i]!=0) && (i<=ncovcol)){
   hstepm=hstepm/stepm;       Tvaraff[ij]=i; /*For printing */
   yp1=modf(dateintmean,&yp);       ij++;
   anprojmean=yp;     }
   yp2=modf((yp1*12),&yp);   }
   mprojmean=yp;   
   yp1=modf((yp2*30.5),&yp);   cptcoveff=ij-1; /*Number of simple covariates*/
   jprojmean=yp;  }
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;  /*********** Health Expectancies ****************/
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  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 )
    
   for(cptcov=1;cptcov<=i2;cptcov++){  {
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* Health expectancies */
       k=k+1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       fprintf(ficresf,"\n#******");    double age, agelim, hf;
       for(j=1;j<=cptcoveff;j++) {    double ***p3mat,***varhe;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **dnewm,**doldm;
       }    double *xp;
       fprintf(ficresf,"******\n");    double **gp, **gm;
       fprintf(ficresf,"# StartingAge FinalAge");    double ***gradg, ***trgradg;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    int theta;
        
          varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    xp=vector(1,npar);
         fprintf(ficresf,"\n");    dnewm=matrix(1,nlstate*nlstate,1,npar);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficreseij,"# Health expectancies\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficreseij,"# Age");
           nhstepm = nhstepm/hstepm;    for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           oldm=oldms;savm=savms;    fprintf(ficreseij,"\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
            if(estepm < stepm){
           for (h=0; h<=nhstepm; h++){      printf ("Problem %d lower than %d\n",estepm, stepm);
             if (h==(int) (calagedate+YEARM*cpt)) {    }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    else  hstepm=estepm;   
             }    /* We compute the life expectancy from trapezoids spaced every estepm months
             for(j=1; j<=nlstate+ndeath;j++) {     * This is mainly to measure the difference between two models: for example
               kk1=0.;kk2=0;     * if stepm=24 months pijx are given only every 2 years and by summing them
               for(i=1; i<=nlstate;i++) {                   * we are calculating an estimate of the Life Expectancy assuming a linear 
                 if (mobilav==1)     * progression in between and thus overestimating or underestimating according
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     * to the curvature of the survival function. If, for the same date, we 
                 else {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];     * 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. */
               }  
               if (h==(int)(calagedate+12*cpt)){    /* For example we decided to compute the life expectancy with the smallest unit */
                 fprintf(ficresf," %.3f", kk1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                               nhstepm is the number of hstepm from age to agelim 
               }       nstepm is the number of stepm from age to agelin. 
             }       Look at hpijx to understand the reason of that which relies in memory size
           }       and note for a fixed period like estepm months */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* 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
     }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   }       results. So we changed our mind and took the option of the best precision.
            */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
   fclose(ficresf);    agelim=AGESUP;
 }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 /************** Forecasting ******************/      /* nhstepm age range expressed in number of stepm */
 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){      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      /* if (stepm >= YEARM) hstepm=1;*/
   int *popage;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double *popeffectif,*popcount;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   double ***p3mat,***tabpop,***tabpopprev;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   char filerespop[FILENAMELENGTH];      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   agelim=AGESUP;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;   
    
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
        /* Computing Variances of health expectancies */
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);       for(theta=1; theta <=npar; theta++){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        for(i=1; i<=npar; i++){ 
     printf("Problem with forecast resultfile: %s\n", filerespop);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
   printf("Computing forecasting: result on file '%s' \n", filerespop);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        cptj=0;
         for(j=1; j<= nlstate; j++){
   if (mobilav==1) {          for(i=1; i<=nlstate; i++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cptj=cptj+1;
     movingaverage(agedeb, fage, ageminpar, mobaverage);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;        }
         
   agelim=AGESUP;       
          for(i=1; i<=npar; i++) 
   hstepm=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   hstepm=hstepm/stepm;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
   if (popforecast==1) {        cptj=0;
     if((ficpop=fopen(popfile,"r"))==NULL) {        for(j=1; j<= nlstate; j++){
       printf("Problem with population file : %s\n",popfile);exit(0);          for(i=1;i<=nlstate;i++){
     }            cptj=cptj+1;
     popage=ivector(0,AGESUP);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                }
     i=1;            }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        }
            for(j=1; j<= nlstate*nlstate; j++)
     imx=i;          for(h=0; h<=nhstepm-1; h++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
        } 
   for(cptcov=1;cptcov<=i2;cptcov++){     
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /* End theta */
       k=k+1;  
       fprintf(ficrespop,"\n#******");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       for(h=0; h<=nhstepm-1; h++)
       }        for(j=1; j<=nlstate*nlstate;j++)
       fprintf(ficrespop,"******\n");          for(theta=1; theta <=npar; theta++)
       fprintf(ficrespop,"# Age");            trgradg[h][j][theta]=gradg[h][theta][j];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
             for(i=1;i<=nlstate*nlstate;i++)
       for (cpt=0; cpt<=0;cpt++) {        for(j=1;j<=nlstate*nlstate;j++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            varhe[i][j][(int)age] =0.;
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       printf("%d|",(int)age);fflush(stdout);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           nhstepm = nhstepm/hstepm;       for(h=0;h<=nhstepm-1;h++){
                  for(k=0;k<=nhstepm-1;k++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           oldm=oldms;savm=savms;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(i=1;i<=nlstate*nlstate;i++)
                    for(j=1;j<=nlstate*nlstate;j++)
           for (h=0; h<=nhstepm; h++){              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      }
             }      /* Computing expectancies */
             for(j=1; j<=nlstate+ndeath;j++) {      for(i=1; i<=nlstate;i++)
               kk1=0.;kk2=0;        for(j=1; j<=nlstate;j++)
               for(i=1; i<=nlstate;i++) {                        for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                 if (mobilav==1)            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            
                 else {  /* 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]);*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }          }
               }  
               if (h==(int)(calagedate+12*cpt)){      fprintf(ficreseij,"%3.0f",age );
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      cptj=0;
                   /*fprintf(ficrespop," %.3f", kk1);      for(i=1; i<=nlstate;i++)
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        for(j=1; j<=nlstate;j++){
               }          cptj++;
             }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             for(i=1; i<=nlstate;i++){        }
               kk1=0.;      fprintf(ficreseij,"\n");
                 for(j=1; j<=nlstate;j++){     
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                 }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      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);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    printf("\n");
           }    fprintf(ficlog,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    free_vector(xp,1,npar);
       }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   /******/    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    /************ Variance ******************/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  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)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  {
           nhstepm = nhstepm/hstepm;    /* Variance of health expectancies */
              /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* double **newm;*/
           oldm=oldms;savm=savms;    double **dnewm,**doldm;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **dnewmp,**doldmp;
           for (h=0; h<=nhstepm; h++){    int i, j, nhstepm, hstepm, h, nstepm ;
             if (h==(int) (calagedate+YEARM*cpt)) {    int k, cptcode;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    double *xp;
             }    double **gp, **gm;  /* for var eij */
             for(j=1; j<=nlstate+ndeath;j++) {    double ***gradg, ***trgradg; /*for var eij */
               kk1=0.;kk2=0;    double **gradgp, **trgradgp; /* for var p point j */
               for(i=1; i<=nlstate;i++) {                  double *gpp, *gmp; /* for var p point j */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        double **varppt; /* for var p point j nlstate to nlstate+ndeath */
               }    double ***p3mat;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    double age,agelim, hf;
             }    double ***mobaverage;
           }    int theta;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char digit[4];
         }    char digitp[25];
       }  
    }    char fileresprobmorprev[FILENAMELENGTH];
   }  
      if(popbased==1){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
   if (popforecast==1) {      else strcpy(digitp,"-populbased-nomobil-");
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    else 
     free_vector(popcount,0,AGESUP);      strcpy(digitp,"-stablbased-");
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav!=0) {
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrespop);      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);
 /***********************************************/      }
 /**************** Main Program *****************/    }
 /***********************************************/  
     strcpy(fileresprobmorprev,"prmorprev"); 
 int main(int argc, char *argv[])    sprintf(digit,"%-d",ij);
 {    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   double agedeb, agefin,hf;    strcat(fileresprobmorprev,fileres);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   double fret;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   double **xi,tmp,delta;    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double dum; /* Dummy variable */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double ***p3mat;    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);
   int *indx;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   char line[MAXLINE], linepar[MAXLINE];    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   char title[MAXLINE];      fprintf(ficresprobmorprev," p.%-d SE",j);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      for(i=1; i<=nlstate;i++)
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   char filerest[FILENAMELENGTH];    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");
   char fileregp[FILENAMELENGTH];    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   char popfile[FILENAMELENGTH];  /*   } */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */    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");
   int c,  h , cpt,l;    fprintf(ficresvij,"# Age");
   int ju,jl, mi;    for(i=1; i<=nlstate;i++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      for(j=1; j<=nlstate;j++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   int mobilav=0,popforecast=0;    fprintf(ficresvij,"\n");
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   double bage, fage, age, agelim, agebase;    doldm=matrix(1,nlstate,1,nlstate);
   double ftolpl=FTOL;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   double **prlim;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double *severity;  
   double ***param; /* Matrix of parameters */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   double  *p;    gpp=vector(nlstate+1,nlstate+ndeath);
   double **matcov; /* Matrix of covariance */    gmp=vector(nlstate+1,nlstate+ndeath);
   double ***delti3; /* Scale */    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   double *delti; /* Scale */    
   double ***eij, ***vareij;    if(estepm < stepm){
   double **varpl; /* Variances of prevalence limits by age */      printf ("Problem %d lower than %d\n",estepm, stepm);
   double *epj, vepp;    }
   double kk1, kk2;    else  hstepm=estepm;   
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";       nstepm is the number of stepm from age to agelin. 
   char *alph[]={"a","a","b","c","d","e"}, str[4];       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   char z[1]="c", occ;       survival function given by stepm (the optimization length). Unfortunately it
 #include <sys/time.h>       means that if the survival funtion is printed every two years of age and if
 #include <time.h>       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       results. So we changed our mind and took the option of the best precision.
      */
   /* long total_usecs;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   struct timeval start_time, end_time;    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   getcwd(pathcd, size);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("\n%s",version);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   if(argc <=1){      gp=matrix(0,nhstepm,1,nlstate);
     printf("\nEnter the parameter file name: ");      gm=matrix(0,nhstepm,1,nlstate);
     scanf("%s",pathtot);  
   }  
   else{      for(theta=1; theta <=npar; theta++){
     strcpy(pathtot,argv[1]);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        }
   /*cygwin_split_path(pathtot,path,optionfile);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* cutv(path,optionfile,pathtot,'\\');*/  
         if (popbased==1) {
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          if(mobilav ==0){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);            for(i=1; i<=nlstate;i++)
   chdir(path);              prlim[i][i]=probs[(int)age][i][ij];
   replace(pathc,path);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
 /*-------- arguments in the command line --------*/              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   strcpy(fileres,"r");        }
   strcat(fileres, optionfilefiname);    
   strcat(fileres,".txt");    /* Other files have txt extension */        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   /*---------arguments file --------*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          }
     printf("Problem with optionfile %s\n",optionfile);        }
     goto end;        /* This for computing probability of death (h=1 means
   }           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   strcpy(filereso,"o");        */
   strcat(filereso,fileres);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if((ficparo=fopen(filereso,"w"))==NULL) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   }        }    
         /* end probability of death */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     ungetc(c,ficpar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fgets(line, MAXLINE, ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     puts(line);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fputs(line,ficparo);   
   }        if (popbased==1) {
   ungetc(c,ficpar);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);              prlim[i][i]=probs[(int)age][i][ij];
   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);          }else{ /* mobilav */ 
   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);            for(i=1; i<=nlstate;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){              prlim[i][i]=mobaverage[(int)age][i][ij];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);  
     fputs(line,ficparo);        for(j=1; j<= nlstate; j++){
   }          for(h=0; h<=nhstepm; h++){
   ungetc(c,ficpar);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                gm[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
   covar=matrix(0,NCOVMAX,1,n);        }
   cptcovn=0;        /* This for computing probability of death (h=1 means
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   ncovmodel=2+cptcovn;        */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
   /* Read guess parameters */           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   /* Reads comments: lines beginning with '#' */        }    
   while((c=getc(ficpar))=='#' && c!= EOF){        /* end probability of death */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(j=1; j<= nlstate; j++) /* vareij */
     puts(line);          for(h=0; h<=nhstepm; h++){
     fputs(line,ficparo);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   ungetc(c,ficpar);  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     for(i=1; i <=nlstate; i++)        }
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      } /* End theta */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);      for(h=0; h<=nhstepm; h++) /* veij */
         printf(" %lf",param[i][j][k]);        for(j=1; j<=nlstate;j++)
         fprintf(ficparo," %lf",param[i][j][k]);          for(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
       fscanf(ficpar,"\n");  
       printf("\n");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficparo,"\n");        for(theta=1; theta <=npar; theta++)
     }          trgradgp[j][theta]=gradgp[theta][j];
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   p=param[1][1];      for(i=1;i<=nlstate;i++)
          for(j=1;j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          vareij[i][j][(int)age] =0.;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(h=0;h<=nhstepm;h++){
     fgets(line, MAXLINE, ficpar);        for(k=0;k<=nhstepm;k++){
     puts(line);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     fputs(line,ficparo);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   }          for(i=1;i<=nlstate;i++)
   ungetc(c,ficpar);            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   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++){      /* pptj */
       fscanf(ficpar,"%1d%1d",&i1,&j1);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       printf("%1d%1d",i,j);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficparo,"%1d%1d",i1,j1);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       for(k=1; k<=ncovmodel;k++){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);          varppt[j][i]=doldmp[j][i];
         printf(" %le",delti3[i][j][k]);      /* end ppptj */
         fprintf(ficparo," %le",delti3[i][j][k]);      /*  x centered again */
       }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       fscanf(ficpar,"\n");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       printf("\n");   
       fprintf(ficparo,"\n");      if (popbased==1) {
     }        if(mobilav ==0){
   }          for(i=1; i<=nlstate;i++)
   delti=delti3[1][1];            prlim[i][i]=probs[(int)age][i][ij];
          }else{ /* mobilav */ 
   /* Reads comments: lines beginning with '#' */          for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){            prlim[i][i]=mobaverage[(int)age][i][ij];
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      }
     puts(line);               
     fputs(line,ficparo);      /* This for computing probability of death (h=1 means
   }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   ungetc(c,ficpar);         as a weighted average of prlim.
        */
   matcov=matrix(1,npar,1,npar);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   for(i=1; i <=npar; i++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     fscanf(ficpar,"%s",&str);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     printf("%s",str);      }    
     fprintf(ficparo,"%s",str);      /* end probability of death */
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       printf(" %.5le",matcov[i][j]);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo," %.5le",matcov[i][j]);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     }        for(i=1; i<=nlstate;i++){
     fscanf(ficpar,"\n");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     printf("\n");        }
     fprintf(ficparo,"\n");      } 
   }      fprintf(ficresprobmorprev,"\n");
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)      fprintf(ficresvij,"%.0f ",age );
       matcov[i][j]=matcov[j][i];      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++){
   printf("\n");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
     /*-------- Rewriting paramater file ----------*/      free_matrix(gp,0,nhstepm,1,nlstate);
      strcpy(rfileres,"r");    /* "Rparameterfile */      free_matrix(gm,0,nhstepm,1,nlstate);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
      strcat(rfileres,".");    /* */      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if((ficres =fopen(rfileres,"w"))==NULL) {    } /* End age */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    free_vector(gpp,nlstate+1,nlstate+ndeath);
     }    free_vector(gmp,nlstate+1,nlstate+ndeath);
     fprintf(ficres,"#%s\n",version);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     /*-------- data file ----------*/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     if((fic=fopen(datafile,"r"))==NULL)    {    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       printf("Problem with datafile: %s\n", datafile);goto end;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     n= lastobs;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     severity = vector(1,maxwav);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     outcome=imatrix(1,maxwav+1,1,n);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     num=ivector(1,n);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     moisnais=vector(1,n);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     annais=vector(1,n);    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);
     moisdc=vector(1,n);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
     andc=vector(1,n);  */
     agedc=vector(1,n);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     cod=ivector(1,n);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    free_vector(xp,1,npar);
     mint=matrix(1,maxwav,1,n);    free_matrix(doldm,1,nlstate,1,nlstate);
     anint=matrix(1,maxwav,1,n);    free_matrix(dnewm,1,nlstate,1,npar);
     s=imatrix(1,maxwav+1,1,n);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     adl=imatrix(1,maxwav+1,1,n);        free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     tab=ivector(1,NCOVMAX);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ncodemax=ivector(1,8);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     i=1;    fflush(ficgp);
     while (fgets(line, MAXLINE, fic) != NULL)    {    fflush(fichtm); 
       if ((i >= firstobs) && (i <=lastobs)) {  }  /* end varevsij */
          
         for (j=maxwav;j>=1;j--){  /************ Variance of prevlim ******************/
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  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)
           strcpy(line,stra);  {
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* Variance of prevalence limit */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         }    double **newm;
            double **dnewm,**doldm;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    int i, j, nhstepm, hstepm;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    int k, cptcode;
     double *xp;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    double *gp, *gm;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double **gradg, **trgradg;
     double age,agelim;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    int theta;
         for (j=ncovcol;j>=1;j--){     
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         }    fprintf(ficresvpl,"# Age");
         num[i]=atol(stra);    for(i=1; i<=nlstate;i++)
                fprintf(ficresvpl," %1d-%1d",i,i);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    fprintf(ficresvpl,"\n");
           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;}*/  
     xp=vector(1,npar);
         i=i+1;    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
     }    
     /* printf("ii=%d", ij);    hstepm=1*YEARM; /* Every year of age */
        scanf("%d",i);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   imx=i-1; /* Number of individuals */    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /* for (i=1; i<=imx; i++){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      if (stepm >= YEARM) hstepm=1;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      gradg=matrix(1,npar,1,nlstate);
     }*/      gp=vector(1,nlstate);
        gm=vector(1,nlstate);
   /* for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;      for(theta=1; theta <=npar; theta++){
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}        for(i=1; i<=npar; i++){ /* Computes gradient */
   */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
   /* Calculation of the number of parameter from char model*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   Tvar=ivector(1,15);        for(i=1;i<=nlstate;i++)
   Tprod=ivector(1,15);          gp[i] = prlim[i][i];
   Tvaraff=ivector(1,15);      
   Tvard=imatrix(1,15,1,2);        for(i=1; i<=npar; i++) /* Computes gradient */
   Tage=ivector(1,15);                xp[i] = x[i] - (i==theta ?delti[theta]:0);
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if (strlen(model) >1){        for(i=1;i<=nlstate;i++)
     j=0, j1=0, k1=1, k2=1;          gm[i] = prlim[i][i];
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');        for(i=1;i<=nlstate;i++)
     cptcovn=j+1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     cptcovprod=j1;      } /* End theta */
      
     strcpy(modelsav,model);      trgradg =matrix(1,nlstate,1,npar);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);      for(j=1; j<=nlstate;j++)
       goto end;        for(theta=1; theta <=npar; theta++)
     }          trgradg[j][theta]=gradg[theta][j];
      
     for(i=(j+1); i>=1;i--){      for(i=1;i<=nlstate;i++)
       cutv(stra,strb,modelsav,'+');        varpl[i][(int)age] =0.;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       /*scanf("%d",i);*/      for(i=1;i<=nlstate;i++)
       if (strchr(strb,'*')) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {      fprintf(ficresvpl,"%.0f ",age );
           cptcovprod--;      for(i=1; i<=nlstate;i++)
           cutv(strb,stre,strd,'V');        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           Tvar[i]=atoi(stre);      fprintf(ficresvpl,"\n");
           cptcovage++;      free_vector(gp,1,nlstate);
             Tage[cptcovage]=i;      free_vector(gm,1,nlstate);
             /*printf("stre=%s ", stre);*/      free_matrix(gradg,1,npar,1,nlstate);
         }      free_matrix(trgradg,1,nlstate,1,npar);
         else if (strcmp(strd,"age")==0) {    } /* End age */
           cptcovprod--;  
           cutv(strb,stre,strc,'V');    free_vector(xp,1,npar);
           Tvar[i]=atoi(stre);    free_matrix(doldm,1,nlstate,1,npar);
           cptcovage++;    free_matrix(dnewm,1,nlstate,1,nlstate);
           Tage[cptcovage]=i;  
         }  }
         else {  
           cutv(strb,stre,strc,'V');  /************ Variance of one-step probabilities  ******************/
           Tvar[i]=ncovcol+k1;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           cutv(strb,strc,strd,'V');  {
           Tprod[k1]=i;    int i, j=0,  i1, k1, l1, t, tj;
           Tvard[k1][1]=atoi(strc);    int k2, l2, j1,  z1;
           Tvard[k1][2]=atoi(stre);    int k=0,l, cptcode;
           Tvar[cptcovn+k2]=Tvard[k1][1];    int first=1, first1;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           for (k=1; k<=lastobs;k++)    double **dnewm,**doldm;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    double *xp;
           k1++;    double *gp, *gm;
           k2=k2+2;    double **gradg, **trgradg;
         }    double **mu;
       }    double age,agelim, cov[NCOVMAX];
       else {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    int theta;
        /*  scanf("%d",i);*/    char fileresprob[FILENAMELENGTH];
       cutv(strd,strc,strb,'V');    char fileresprobcov[FILENAMELENGTH];
       Tvar[i]=atoi(strc);    char fileresprobcor[FILENAMELENGTH];
       }  
       strcpy(modelsav,stra);      double ***varpij;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/    strcpy(fileresprob,"prob"); 
     }    strcat(fileresprob,fileres);
 }    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   printf("cptcovprod=%d ", cptcovprod);    }
   scanf("%d ",i);*/    strcpy(fileresprobcov,"probcov"); 
     fclose(fic);    strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     /*  if(mle==1){*/      printf("Problem with resultfile: %s\n", fileresprobcov);
     if (weightopt != 1) { /* Maximisation without weights*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       for(i=1;i<=n;i++) weight[i]=1.0;    }
     }    strcpy(fileresprobcor,"probcor"); 
     /*-calculation of age at interview from date of interview and age at death -*/    strcat(fileresprobcor,fileres);
     agev=matrix(1,maxwav,1,imx);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
     for (i=1; i<=imx; i++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       for(m=2; (m<= maxwav); m++) {    }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
          anint[m][i]=9999;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
          s[m][i]=-1;    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);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     }    
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     for (i=1; i<=imx; i++)  {    fprintf(ficresprob,"# Age");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       for(m=1; (m<= maxwav); m++){    fprintf(ficresprobcov,"# Age");
         if(s[m][i] >0){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           if (s[m][i] >= nlstate+1) {    fprintf(ficresprobcov,"# Age");
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];    for(i=1; i<=nlstate;i++)
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      for(j=1; j<=(nlstate+ndeath);j++){
            else {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
               if (andc[i]!=9999){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
               agev[m][i]=-1;      }  
               }   /* fprintf(ficresprob,"\n");
             }    fprintf(ficresprobcov,"\n");
           }    fprintf(ficresprobcor,"\n");
           else if(s[m][i] !=9){ /* Should no more exist */   */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   xp=vector(1,npar);
             if(mint[m][i]==99 || anint[m][i]==9999)    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               agev[m][i]=1;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             else if(agev[m][i] <agemin){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
               agemin=agev[m][i];    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    first=1;
             }    fprintf(ficgp,"\n# Routine varprob");
             else if(agev[m][i] >agemax){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
               agemax=agev[m][i];    fprintf(fichtm,"\n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
             /*   agev[m][i] = age[i]+2*m;*/    file %s<br>\n",optionfilehtmcov);
           }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
           else { /* =9 */  and drawn. It helps understanding how is the covariance between two incidences.\
             agev[m][i]=1;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
             s[m][i]=-1;    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
           }  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
         }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
         else /*= 0 Unknown */  standard deviations wide on each axis. <br>\
           agev[m][i]=1;   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
      To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     }  
     for (i=1; i<=imx; i++)  {    cov[1]=1;
       for(m=1; (m<= maxwav); m++){    tj=cptcoveff;
         if (s[m][i] > (nlstate+ndeath)) {    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           printf("Error: Wrong value in nlstate or ndeath\n");      j1=0;
           goto end;    for(t=1; t<=tj;t++){
         }      for(i1=1; i1<=ncodemax[t];i1++){ 
       }        j1++;
     }        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
     free_vector(severity,1,maxwav);          fprintf(ficresprobcov, "\n#********** Variable "); 
     free_imatrix(outcome,1,maxwav+1,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(moisnais,1,n);          fprintf(ficresprobcov, "**********\n#\n");
     free_vector(annais,1,n);          
     /* free_matrix(mint,1,maxwav,1,n);          fprintf(ficgp, "\n#********** Variable "); 
        free_matrix(anint,1,maxwav,1,n);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(moisdc,1,n);          fprintf(ficgp, "**********\n#\n");
     free_vector(andc,1,n);          
           
              fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     wav=ivector(1,imx);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          
              fprintf(ficresprobcor, "\n#********** Variable ");    
     /* Concatenates waves */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          fprintf(ficresprobcor, "**********\n#");    
         }
         
       Tcode=ivector(1,100);        for (age=bage; age<=fage; age ++){ 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          cov[2]=age;
       ncodemax[1]=1;          for (k=1; k<=cptcovn;k++) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                }
    codtab=imatrix(1,100,1,10);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    h=0;          for (k=1; k<=cptcovprod;k++)
    m=pow(2,cptcoveff);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            
    for(k=1;k<=cptcoveff; k++){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
      for(i=1; i <=(m/pow(2,k));i++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
        for(j=1; j <= ncodemax[k]; j++){          gp=vector(1,(nlstate)*(nlstate+ndeath));
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          gm=vector(1,(nlstate)*(nlstate+ndeath));
            h++;      
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;          for(theta=1; theta <=npar; theta++){
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            for(i=1; i<=npar; i++)
          }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
        }            
      }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
    }            
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            k=0;
       codtab[1][2]=1;codtab[2][2]=2; */            for(i=1; i<= (nlstate); i++){
    /* for(i=1; i <=m ;i++){              for(j=1; j<=(nlstate+ndeath);j++){
       for(k=1; k <=cptcovn; k++){                k=k+1;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                gp[k]=pmmij[i][j];
       }              }
       printf("\n");            }
       }            
       scanf("%d",i);*/            for(i=1; i<=npar; i++)
                  xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    /* Calculates basic frequencies. Computes observed prevalence at single age      
        and prints on file fileres'p'. */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
                for(i=1; i<=(nlstate); i++){
                  for(j=1; j<=(nlstate+ndeath);j++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                k=k+1;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                gm[k]=pmmij[i][j];
     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(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     /* For Powell, parameters are in a vector p[] starting at p[1]              gradg[theta][i]=(gp[i]-gm[i])/(double)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) */  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     if(mle==1){            for(theta=1; theta <=npar; theta++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              trgradg[j][theta]=gradg[theta][j];
     }          
              matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     /*--------- results files --------------*/          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     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);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    jk=1;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          pmij(pmmij,cov,ncovmodel,x,nlstate);
    for(i=1,jk=1; i <=nlstate; i++){          
      for(k=1; k <=(nlstate+ndeath); k++){          k=0;
        if (k != i)          for(i=1; i<=(nlstate); i++){
          {            for(j=1; j<=(nlstate+ndeath);j++){
            printf("%d%d ",i,k);              k=k+1;
            fprintf(ficres,"%1d%1d ",i,k);              mu[k][(int) age]=pmmij[i][j];
            for(j=1; j <=ncovmodel; j++){            }
              printf("%f ",p[jk]);          }
              fprintf(ficres,"%f ",p[jk]);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
              jk++;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
            }              varpij[i][j][(int)age] = doldm[i][j];
            printf("\n");  
            fprintf(ficres,"\n");          /*printf("\n%d ",(int)age);
          }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  if(mle==1){            }*/
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */          fprintf(ficresprob,"\n%d ",(int)age);
     hesscov(matcov, p, npar, delti, ftolhess, func);          fprintf(ficresprobcov,"\n%d ",(int)age);
  }          fprintf(ficresprobcor,"\n%d ",(int)age);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
      for(i=1,jk=1; i <=nlstate; i++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       for(j=1; j <=nlstate+ndeath; j++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         if (j!=i) {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
           fprintf(ficres,"%1d%1d",i,j);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           printf("%1d%1d",i,j);          }
           for(k=1; k<=ncovmodel;k++){          i=0;
             printf(" %.5e",delti[jk]);          for (k=1; k<=(nlstate);k++){
             fprintf(ficres," %.5e",delti[jk]);            for (l=1; l<=(nlstate+ndeath);l++){ 
             jk++;              i=i++;
           }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           printf("\n");              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
           fprintf(ficres,"\n");              for (j=1; j<=i;j++){
         }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
      }              }
                }
     k=1;          }/* end of loop for state */
     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");        } /* end of loop for age */
     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");  
     for(i=1;i<=npar;i++){        /* Confidence intervalle of pij  */
       /*  if (k>nlstate) k=1;        /*
       i1=(i-1)/(ncovmodel*nlstate)+1;          fprintf(ficgp,"\nset noparametric;unset label");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fprintf(ficres,"%3d",i);          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);
       printf("%3d",i);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       for(j=1; j<=i;j++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         fprintf(ficres," %.5e",matcov[i][j]);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         printf(" %.5e",matcov[i][j]);        */
       }  
       fprintf(ficres,"\n");        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       printf("\n");        first1=1;
       k++;        for (k2=1; k2<=(nlstate);k2++){
     }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
                if(l2==k2) continue;
     while((c=getc(ficpar))=='#' && c!= EOF){            j=(k2-1)*(nlstate+ndeath)+l2;
       ungetc(c,ficpar);            for (k1=1; k1<=(nlstate);k1++){
       fgets(line, MAXLINE, ficpar);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       puts(line);                if(l1==k1) continue;
       fputs(line,ficparo);                i=(k1-1)*(nlstate+ndeath)+l1;
     }                if(i<=j) continue;
     ungetc(c,ficpar);                for (age=bage; age<=fage; age ++){ 
     estepm=0;                  if ((int)age %5==0){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     if (estepm==0 || estepm < stepm) estepm=stepm;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     if (fage <= 2) {                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       bage = ageminpar;                    mu1=mu[i][(int) age]/stepm*YEARM ;
       fage = agemaxpar;                    mu2=mu[j][(int) age]/stepm*YEARM;
     }                    c12=cv12/sqrt(v1*v2);
                        /* Computing eigen value of matrix of covariance */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    /* Eigen vectors */
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     while((c=getc(ficpar))=='#' && c!= EOF){                    /*v21=sqrt(1.-v11*v11); *//* error */
     ungetc(c,ficpar);                    v21=(lc1-v1)/cv12*v11;
     fgets(line, MAXLINE, ficpar);                    v12=-v21;
     puts(line);                    v22=v11;
     fputs(line,ficparo);                    tnalp=v21/v11;
   }                    if(first1==1){
   ungetc(c,ficpar);                      first1=0;
                        printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                    }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    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);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    /*printf(fignu*/
                          /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   while((c=getc(ficpar))=='#' && c!= EOF){                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     ungetc(c,ficpar);                    if(first==1){
     fgets(line, MAXLINE, ficpar);                      first=0;
     puts(line);                      fprintf(ficgp,"\nset parametric;unset label");
     fputs(line,ficparo);                      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");
   ungetc(c,ficpar);                      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,\
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                              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);
   fscanf(ficpar,"pop_based=%d\n",&popbased);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   fprintf(ficparo,"pop_based=%d\n",popbased);                        fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fprintf(ficres,"pop_based=%d\n",popbased);                        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);
   while((c=getc(ficpar))=='#' && c!= EOF){                      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",\
     ungetc(c,ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fgets(line, MAXLINE, ficpar);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     puts(line);                    }else{
     fputs(line,ficparo);                      first=0;
   }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   ungetc(c,ficpar);                      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);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);                      fprintf(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",\
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
 while((c=getc(ficpar))=='#' && c!= EOF){                } /* end loop age */
     ungetc(c,ficpar);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     fgets(line, MAXLINE, ficpar);                first=1;
     puts(line);              } /*l12 */
     fputs(line,ficparo);            } /* k12 */
   }          } /*l1 */
   ungetc(c,ficpar);        }/* k1 */
       } /* loop covariates */
   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);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fclose(ficresprob);
     fclose(ficresprobcov);
 /*------------ gnuplot -------------*/    fclose(ficresprobcor);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    fflush(ficgp);
      fflush(fichtmcov);
 /*------------ free_vector  -------------*/  }
  chdir(path);  
    
  free_ivector(wav,1,imx);  /******************* Printing html file ***********/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                      int lastpass, int stepm, int weightopt, char model[],\
  free_ivector(num,1,n);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
  free_vector(agedc,1,n);                    int popforecast, int estepm ,\
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                    double jprev1, double mprev1,double anprev1, \
  fclose(ficparo);                    double jprev2, double mprev2,double anprev2){
  fclose(ficres);    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
 /*--------- index.htm --------*/  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   /*   } */
    
   /*--------------- Prevalence limit --------------*/     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 \
   strcpy(filerespl,"pl");   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
   strcat(filerespl,fileres);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   - Life expectancies by age and initial health status (estepm=%2d months): \
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;     <a href=\"%s\">%s</a> <br>\n</li>", \
   }             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   fprintf(ficrespl,"#Prevalence limit\n");             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
   fprintf(ficrespl,"#Age ");             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    
   prlim=matrix(1,nlstate,1,nlstate);   m=cptcoveff;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   jj1=0;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   for(k1=1; k1<=m;k1++){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */     for(i1=1; i1<=ncodemax[k1];i1++){
   k=0;       jj1++;
   agebase=ageminpar;       if (cptcovn > 0) {
   agelim=agemaxpar;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   ftolpl=1.e-10;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   i1=cptcoveff;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   if (cptcovn < 1){i1=1;}         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   for(cptcov=1;cptcov<=i1;cptcov++){       /* Pij */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       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> \
         k=k+1;  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/       /* Quasi-incidences */
         fprintf(ficrespl,"\n#******");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
         for(j=1;j<=cptcoveff;j++)   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
         fprintf(ficrespl,"******\n");         /* Stable prevalence in each health state */
                 for(cpt=1; cpt<nlstate;cpt++){
         for (age=agebase; age<=agelim; age++){           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
           fprintf(ficrespl,"%.0f",age );         }
           for(i=1; i<=nlstate;i++)       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficrespl," %.5f", prlim[i][i]);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
           fprintf(ficrespl,"\n");  <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>\
   fclose(ficrespl);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
   /*------------- h Pij x at various ages ------------*/   }/* End k1 */
     fprintf(fichtm,"</ul>");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   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\
   printf("Computing pij: result on file '%s' \n", filerespij);   - 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\
   stepsize=(int) (stepm+YEARM-1)/YEARM;   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   /*if (stepm<=24) stepsize=2;*/   - 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\
   agelim=AGESUP;   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   hstepm=stepsize*YEARM; /* Every year of age */           rfileres,rfileres,\
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
             subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
   k=0;           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
   for(cptcov=1;cptcov<=i1;cptcov++){           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
       k=k+1;           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)  /*  if(popforecast==1) fprintf(fichtm,"\n */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
         fprintf(ficrespij,"******\n");  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
          /*      <br>",fileres,fileres,fileres,fileres); */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  /*  else  */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /*    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); */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;   m=cptcoveff;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)   jj1=0;
             for(j=1; j<=nlstate+ndeath;j++)   for(k1=1; k1<=m;k1++){
               fprintf(ficrespij," %1d-%1d",i,j);     for(i1=1; i1<=ncodemax[k1];i1++){
           fprintf(ficrespij,"\n");       jj1++;
           for (h=0; h<=nhstepm; h++){       if (cptcovn > 0) {
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
             for(i=1; i<=nlstate;i++)         for (cpt=1; cpt<=cptcoveff;cpt++) 
               for(j=1; j<=nlstate+ndeath;j++)           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             fprintf(ficrespij,"\n");       }
           }       for(cpt=1; cpt<=nlstate;cpt++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
           fprintf(ficrespij,"\n");  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 */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   fprintf(fichtm,"</ul>");
    fflush(fichtm);
   fclose(ficrespij);  }
   
   /******************* Gnuplot file **************/
   /*---------- Forecasting ------------------*/  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    char dirfileres[132],optfileres[132];
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     free_matrix(mint,1,maxwav,1,n);    int ng;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     free_vector(weight,1,n);}  /*     printf("Problem with file %s",optionfilegnuplot); */
   else{  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
     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);  
   }    /*#ifdef windows */
      fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   /*---------- Health expectancies and variances ------------*/    m=pow(2,cptcoveff);
   
   strcpy(filerest,"t");    strcpy(dirfileres,optionfilefiname);
   strcat(filerest,fileres);    strcpy(optfileres,"vpl");
   if((ficrest=fopen(filerest,"w"))==NULL) {   /* 1eme*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    for (cpt=1; cpt<= nlstate ; cpt ++) {
   }     for (k1=1; k1<= m ; k1 ++) {
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       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\
   strcpy(filerese,"e");  set ylabel \"Probability\" \n\
   strcat(filerese,fileres);  set ter png small\n\
   if((ficreseij=fopen(filerese,"w"))==NULL) {  set size 0.65,0.65\n\
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  strcpy(fileresv,"v");         else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcat(fileresv,fileres);       }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       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);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
   k=0;       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   for(cptcov=1;cptcov<=i1;cptcov++){       for (i=1; i<= nlstate ; i ++) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       k=k+1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficrest,"\n#****** ");       }  
       for(j=1;j<=cptcoveff;j++)       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     }
       fprintf(ficrest,"******\n");    }
     /*2 eme*/
       fprintf(ficreseij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    for (k1=1; k1<= m ; k1 ++) { 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficreseij,"******\n");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       fprintf(ficresvij,"\n#****** ");      for (i=1; i<= nlstate+1 ; i ++) {
       for(j=1;j<=cptcoveff;j++)        k=2*i;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficresvij,"******\n");        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       oldm=oldms;savm=savms;        }   
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);          if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       oldm=oldms;savm=savms;        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
          }   
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        fprintf(ficgp,"\" t\"\" w l 0,");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficrest,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       epj=vector(1,nlstate+1);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(age=bage; age <=fage ;age++){        }   
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         if (popbased==1) {        else fprintf(ficgp,"\" t\"\" w l 0,");
           for(i=1; i<=nlstate;i++)      }
             prlim[i][i]=probs[(int)age][i][k];    }
         }    
            /*3eme*/
         fprintf(ficrest," %4.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    for (k1=1; k1<= m ; k1 ++) { 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        k=2+nlstate*(2*cpt-2);
           }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
           epj[nlstate+1] +=epj[j];        fprintf(ficgp,"set ter png small\n\
         }  set size 0.65,0.65\n\
         for(i=1, vepp=0.;i <=nlstate;i++)  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
           for(j=1;j <=nlstate;j++)        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             vepp += vareij[i][j][(int)age];          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         for(j=1;j <=nlstate;j++){          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         fprintf(ficrest,"\n");          
       }        */
     }        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);
           
   fclose(ficreseij);        } 
   fclose(ficresvij);      }
   fclose(ficrest);    }
   fclose(ficpar);    
   free_vector(epj,1,nlstate+1);    /* CV preval stable (period) */
      for (k1=1; k1<= m ; k1 ++) { 
   /*------- Variance limit prevalence------*/        for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
   strcpy(fileresvpl,"vpl");        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   strcat(fileresvpl,fileres);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  set ter png small\nset size 0.65,0.65\n\
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  unset log y\n\
     exit(0);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   }        
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
   k=0;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   for(cptcov=1;cptcov<=i1;cptcov++){        
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        l=3+(nlstate+ndeath)*cpt;
       k=k+1;        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
       fprintf(ficresvpl,"\n#****** ");        for (i=1; i< nlstate ; i ++) {
       for(j=1;j<=cptcoveff;j++)          l=3+(nlstate+ndeath)*cpt;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"+$%d",l+i+1);
       fprintf(ficresvpl,"******\n");        }
              fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       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);    
     }    /* proba elementaires */
  }    for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
   fclose(ficresvpl);        if (k != i) {
           for(j=1; j <=ncovmodel; j++){
   /*---------- End : free ----------------*/            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            jk++; 
              fprintf(ficgp,"\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
        }
       }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       for(jk=1; jk <=m; jk++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
           if (ng==2)
   free_matrix(matcov,1,npar,1,npar);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   free_vector(delti,1,npar);         else
   free_matrix(agev,1,maxwav,1,imx);           fprintf(ficgp,"\nset title \"Probability\"\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
   if(erreur >0)         for(k2=1; k2<=nlstate; k2++) {
     printf("End of Imach with error or warning %d\n",erreur);           k3=i;
   else   printf("End of Imach\n");           for(k=1; k<=(nlstate+ndeath); k++) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */             if (k != k2){
                 if(ng==2)
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   /*printf("Total time was %d uSec.\n", total_usecs);*/               else
   /*------ End -----------*/                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
  end:                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
 #ifdef windows                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   /* chdir(pathcd);*/                   ij++;
 #endif                 }
  /*system("wgnuplot graph.plt");*/                 else
  /*system("../gp37mgw/wgnuplot graph.plt");*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  /*system("cd ../gp37mgw");*/               }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/               fprintf(ficgp,")/(1");
  strcpy(plotcmd,GNUPLOTPROGRAM);               
  strcat(plotcmd," ");               for(k1=1; k1 <=nlstate; k1++){   
  strcat(plotcmd,optionfilegnuplot);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  system(plotcmd);                 ij=1;
                  for(j=3; j <=ncovmodel; j++){
 #ifdef windows                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   while (z[0] != 'q') {                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     /* chdir(path); */                     ij++;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                   }
     scanf("%s",z);                   else
     if (z[0] == 'c') system("./imach");                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     else if (z[0] == 'e') system(optionfilehtm);                 }
     else if (z[0] == 'g') system(plotcmd);                 fprintf(ficgp,")");
     else if (z[0] == 'q') exit(0);               }
   }               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 #endif               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);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     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("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (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 */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* 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("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime 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.1.93


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