rBt includes several functions to handle phylogenetic data. Specifically, it includes a function read.annot.beast that can read meta-data from BEAST1 or BEAST2 tree files, such as maximum clade credibility (MCC) trees and full posterior trees. This package is being developed with different angles in mind, but it can be used for things like plotting time-trees, and extracting and visualizing phylogenetic data.
Open up an R console:
install.packages("devtools")
library(devtools)
install_github("santiagosnchez/rBt")
- get.tip.spp
- mcc.trees2multi
- mcc2
- order.edges
- read.annot.beast (tested with BEAST1 and BEAST2 trees)
- which.node
- which.tips
- plot.phylo.HPD
- simpleAxisPhylo
- ltt.df.hpd
- RplotEBS
Run the function with ? in front (e.g. ?mcc2) to access the help files, which have examples and more information.
Sánchez-Ramírez, S. (2018) rBt: Handy functions for dealing with BEAST trees in R, GitHub repository: https://github.com/santiagosnchez/rBt