santiagosnchez / rbt

Handy functions for dealing with BEAST trees in R

rBt

Description

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.

Installation

Open up an R console:

install.packages("devtools")
library(devtools)
install_github("santiagosnchez/rBt")

Some functions

• 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

Examples

Run the function with ? in front (e.g. ?mcc2) to access the help files, which have examples and more information.

Citation

Sánchez-Ramírez, S. (2018) rBt: Handy functions for dealing with BEAST trees in R, GitHub repository: https://github.com/santiagosnchez/rBt

rbt's Issues

plot.phylo.HPD xlim

Hi,

I noticed that plot.phylo.HPD() plots off of the left margin, even on the example tree. I think this is because the xvalues in the tree are positive while the lower xlim values should be negative if the lowest bar extends beyond the tree, but I could be understanding it wrong. In any case, I prevented the margin issue by adding a negative before the min(xxl) in

plot(x, x.lim = c(-min(xxl, na.rm = TRUE), maxxlim), ...)

in line 68 of the script.

Thanks for a very useful package!