drop.clade: Drop a clade from a phylogentic tree

In phylepic: Combined Visualisation of Phylogenetic and Epidemiological Data

Drop a clade from a phylogentic tree

Description

drop.clade invokes ape::drop.tip() on all tips descendent from the specified node. This is convenient when used alongside ape::getMRCA() to drop a clade defined by the most recent common ancestor of a set of tips, rather than exhaustively specifying all of its tips.

Usage

drop.clade(phy, node, root.edge = 0, collapse.singles = TRUE)

Arguments

phy	an object of class "phylo".
node	number specifying the parent node of the clade to delete.
root.edge, collapse.singles	passed to ape::drop.tip().

Value

New phylo object with the chosen clade removed

Examples

library("ape")
data(bird.orders)
plot(bird.orders)

# find the common ancestor of some tips
mrca <- ape::getMRCA(bird.orders, c("Passeriformes", "Coliiformes"))

# drop the clade descending from that ancestor
plot(drop.clade(bird.orders, mrca))

phylepic documentation built on June 22, 2024, 9:46 a.m.