yangxhcaf / rbeast-1

R tools for posterior analyses using BEAST

RBeast

Branch
master
develop

R package for working with BEAST and BEAST2.

Use beautier to create BEAST2 input (.xml) files.

Use beastier to run BEAST2.

Use tracerer to parse BEAST2 output (.log, .trees, etc) files.

Use BEASTmasteR for tip-dating analyses using fossils as dated terminal taxa.

Example

library(RBeast)

# Obtain an example log file its name
filename <- system.file(
  "extdata", "beast2_example_output.log", package = "RBeast"
)

# Parse that log file
beast_log_full <- parse_beast_log(filename)

# Remove the burn-in
beast_log <- remove_burn_ins(
  beast_log_full,
  burn_in_fraction = 0.1
)

# Calculates the effective sample sizes of all parameter estimates
esses <- calc_esses(beast_log, sample_interval = 1000)

Instructions

To install RBeast in R:

install.packages("devtools")
devtools::install_github("beast-dev/RBeast")

Acknowledgements

• This project is supported in part through the National Science Foundation grant DMS 1264153.