How to use bayestraitr

I’ve been using BayesTraits for the last year or so, and had developed some packages to make it easy to create data for BayesTraits and to read in the output - which I’ve put into the R package bayestraitr.

You can check out the code and some more examples on the github page

Here I will walk through how to use it!

Installing

To install this package run this line:

devtools::install_github('SamPassmore/bayestraitr')

and load with

library(bayestraitr)

Reading output files

There are three functions in this package at the moment for reading in BayesTrait *.Log files, *.Schedule files, & *.Stones

log = bt_read.log('./bayestrait_output/Artiodactyl.txt.Log.txt')

Will return a dataframe of the log matrix. The file header are contained as an attribute which can be accessed by using attributes(log)$settings

schedule = bt_read.schedule('./bayestrait_output/Artiodactyl.txt.Schedule.txt')

This returns one data.frame with the contents of the Schedule file.

stones = bt_read.stones('./bayestrait_output/Artiodactyl.txt.Stones.txt')

This returns a list of 2 items. stones_sampling holds the logging for the stones sampling, & marginal_likelihood holds the marginal log-likelihood. The stones file header can be found in the attributes by using the code attributes(stones)$settings

Writing input files

The function bt_write takes various tree types (e.g. phylo & multiphylo) and data.frame input and writes them as input files for BayesTraits.

This function is probably a bit temperamental. Please log any issues you have with it.

library(ape)
tree = read.nexus('bayestraits_output/Artiodactyl.trees')
data = read.csv('bayestraits_output/Artiodactyl.tsv', sep = "\t")
rownames(data) = data$taxa
bt_write(tree = tree, data = data, variables = 'trait1', filename = 'test')