phytools: orderMappedEdge – R documentation

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orderMappedEdge

Order the columns of mapped.edge to match across trees

Description

This function takes a modified object of class "multiPhylo" with a mapped discrete character (e.g., see read.simmap and sorts the columns of each tree$mapped.edge to have the same state ordering. This is handy if we want to, for instance, run brownie.lite on a set of mapped trees, and then average the fitted parameter values across trees. The function also works for a single tree.

Usage

orderMappedEdge(trees, ordering=NULL)

Arguments

`trees`	object of class `"phylo"` or `"multiPhylo"`.
`ordering`	ordering for the columns of `$mapped.edge`. If `NULL`, then an alphabetical order is assumed. Options are `"alphabetical"`, `"numerical"`, or any specific ordering of the mapped traits (e.g., `c("A","B","C")`.

Value

A modified object of class "phylo" or "multiPhylo".

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