extractTree: Get tree from tree+data object

In phylobase: Base Package for Phylogenetic Structures and Comparative Data

Get tree from tree+data object

Description

Extracts a phylo4 tree object from a phylo4d tree+data object.

Usage

extractTree(from)

Arguments

from	a phylo4d object, containing a phylogenetic tree plus associated phenotypic data. Created by the phylo4d() function.

Details

extractTree extracts just the phylogeny from a tree+data object. The phylogeny contains the topology (how the nodes are linked together), the branch lengths (if any), and any tip and/or node labels. This may be useful for extracting a tree from a phylo4d object, and associating with another phenotypic dataset, or to convert the tree to another format.

Author(s)

Ben Bolker

See Also

phylo4-methods, phylo4d-methods, coerce-methods for translation functions.

Examples

tree.phylo <- ape::read.tree(text = "((a,b),c);")
tree <- as(tree.phylo, "phylo4")
plot(tree)
tip.data <- data.frame(size = c(1, 2, 3), row.names = c("a", "b", "c"))
(treedata <- phylo4d(tree, tip.data))
plot(treedata)
(tree1 <- extractTree(treedata))
plot(tree1)

phylobase documentation built on May 29, 2024, 11:24 a.m.