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beastier demo

Richèl J.C. Bilderbeek

2024-10-06

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)
#> [1] "input_filename"        "output_state_filename" "rng_seed"             
#> [4] "n_threads"             "use_beagle"            "overwrite"            
#> [7] "beast2_path"           "verbose"

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.