In richelbilderbeek/beastier: Call 'BEAST2'

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
beastier::remove_beaustier_folders()

Introduction

This vignette demonstrates how to use beastier.

First, load the library:

library(beastier)

Also, we'll load the testthat library, to verify the statements in this vignette:

library(testthat)

To run BEAST2, we need to create a BEAST2 options structure`. We will use a supplied BEAST2 XML file. For the rest, we'll use the default options:

beast2_options <- create_beast2_options(
  input_filename = get_beastier_path("2_4.xml")
)
names(beast2_options)

Before running BEAST2, the BEAST2 input file must exist, and we expect no output file to be created just yet:

expect_true(file.exists(beast2_options$input_filename))
expect_false(file.exists(beast2_options$output_state_filename))

We can run beastier now, if BEAST2 is installed. Because BEAST2 needs to be installed by the user, this vignette checks if it is installed in every step:

if (is_beast2_installed()) {
  output <- run_beast2_from_options(beast2_options)
}

If beastier has run BEAST2, the BEAST2 output can be shown:

if (is_beast2_installed()) {
  print(output)
}

If beastier has run BEAST2, the MCMC's final state will be saved to a file:

if (is_beast2_installed()) {
  expect_true(file.exists(beast2_options$output_state_filename))
  file.remove(beast2_options$output_state_filename)
}
beastier::remove_beaustier_folders()

This final state can be used to continue the run.

richelbilderbeek/beastier documentation built on Nov. 8, 2023, 9:29 p.m.