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#' Tree distance matrix calculation
#'
#' This function takes a list of trees and returns a distance matrix
#' populated with Robinson-Foulds tree distances between all trees
#' in the list.
#'
#' @param trees a multiPhylo object
#'
#' @return RF A distance matrix of RF distances
#'
#' @keywords treespace, tree distance, robinson-foulds
#'
#' @export tree.dist.matrix
#' @examples
#' \dontrun{
#' data(fungus)
#' tree.dist.matrix(fungus$Fungus.Run1$trees)
#' }
tree.dist.matrix <- function(trees){
if (class(trees) != "multiPhylo")
stop("trees should be an object of class \"multiPhylo\"")
N <- length(trees)
treenames <- 1:N
# use the RF.dist function from Phangorn. Thanks to Klaus Vigo for pointing
# out that we were doing this all wrong before!
# https://github.com/danlwarren/RWTY/issues/47
RF <- as.matrix(RF.dist(trees))
#Row and column names
rownames(RF) <- treenames
colnames(RF) <- treenames
RF
}
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