Functions for importing and creating BayesTraits files into R.
If you have any troubles with this package - please log an issue and I will get to it ASAP!
(or if you can fix it yourself, please feel free!)
To install this package run this line:
devtools::install_github('SamPassmore/bayestraitr')
and load with
library(bayestraitr)
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
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')