phytools: expand.clade – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

expand.clade

Expands (or contracts) the tip-spacing of a given clade or clades

Description

The purpose of this function is to compute a custom tip-spacing for users who want to expand or contract the tip-spacing of the descendant taxa from a given node or nodes.

Usage

expand.clade(tree, node, factor=5)
## S3 method for class 'expand.clade'
plot(x, ...)

Arguments

`tree`	tree an object of class `"phylo"` or `"simmap"`.
`node`	node index or vector of node indices.
`factor`	expansion factor for the tip-spacing of the taxa descended from node or nodes in `node`.
`x`	for `plot` method, an object of class `"expand.clade"`.
`...`	optional arguments to be passed to `plotTree` or `plotSimmap`, depending on the class of `x$tree`.

Value

The function returns an object of class "expand.clade" which consists of the (possibly re-ordered) tree and a numerical vector with the calculated tip spacing based on the expansion factor specified by the user. This object can be plotted using the S3 plot method for the object class; or it can be plotted simplying by calling a standard plotting function on the tree & tip spacings.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19