\name{KLD.matrix}
\alias{KLD.matrix}
\alias{KLD.matrix,matrix-method}
\alias{KLD.matrix,list-method}
\alias{KLD.matrix,ExpressionSet-method}
\title{Continuous version of Kullback-Leibler Distance (KLD)}
\description{
Calculate KLD by estimating by smoothing 
 \eqn{\log(f(x)/g(x))*f(x)}{\log(f(x)/g(x))*f(x)} and then integrating.
}
\usage{
KLD.matrix(x, \dots) 
}
\arguments{
  \item{x}{n by p matrix or ExpressionSet; if x is an ExpressionSet, then the function works against its 'exprs' slot.}
  \item{\dots}{arguments passed to \code{KLD.matrix}:
  \item{method}{use \code{locfit} or \code{density} to estimate integrand; default is c("locfit", "density")(i.e. both methods).}
  \item{supp}{upper and lower limits of the integral; default is c(-3, 3).}
  \item{subdivisions}{subdivisions for the integration; default is 1000.}
  \item{diag}{if TRUE, then the diagonal of the distance matrix will be displayed; default is FALSE.}
  \item{upper}{if TRUE, then the upper triangle of the distance matrix will be displayed; default is FALSE.}
  \item{sample}{for ExpressionSet methods: if TRUE, then distances are computed between samples,
  otherwise, they are computed between genes.}
}
}
\details{
  The pairwise distances between the rows of \code{x} are computed.

  The list method is meant for use when samples sizes are unequal.
}
\value{
An object of class \code{dist} with the pairwise, between rows, 
Kullback-Leibler distances.
}
\author{Beiying Ding, Vincent Carey}
\seealso{ \code{\link{cor.dist}}, \code{\link{spearman.dist}}, 
  \code{\link{tau.dist}}, \code{\link{dist}}, 
  \code{\link{KLdist.matrix}}, \code{\link{mutualInfo}}}
\examples{
 x <- matrix(rnorm(100), nrow = 5)
 KLD.matrix(x, method = "locfit", supp = range(x))
}
\keyword{manip}