R/dropTipPartial.R

In motmot: Models of Trait Macroevolution on Trees

#' @title Drop tips from a phylogenetic tree while preserving deleted nodes
#' @description Wrapper for the \code{ape} function \code{drop.tip} that preserves the number of nodes affecting each branch. For use with the \code{psi} and \code{multipsi} models.
#' @param phy Phylogenetic tree in \code{phylo} format
#' @param tip A vector of mode numeric or character specifying the tips to delete, to be passed to \code{drop.tip}
#' @return Phylogenetic tree in \code{phylo} format, with an added element \code{Shid}, a vector of numbers of observed but "missing" speciation events per branch, in the same order as the branches in the \code{phylo} object
#' @references Ingram, T. 2011. Speciation along a depth gradient in a marine adaptive radiation. Proc. R. Soc. B 278: 613-618.
#' @author Travis Ingram
#' @seealso \code{\link{transformPhylo.ML}}
#' @examples
#' ## Read in phylogeny and data from Thomas et al. (2009)
#' data(anolis.tree)
#' data(anolis.data)
#' ## identify tips to drop
#' tips.to.go <- anolis.tree$tip.label[1:30]
#' dropTipPartial(phy=anolis.tree, tip=tips.to.go)
#' @export

dropTipPartial <- function (phy, tip) 
{
    phy1 <- phy
    phy1$edge.length <- phy$edge.length ^ 0
    phy1 <- drop.tip(phy1, tip)
    phy2 <- drop.tip(phy, tip)
    phy2$orig.node <- phy1$edge.length
    phy2
}