In ropensci/beautier: 'BEAUti' from R

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = ""
)
beautier::remove_beautier_folder()
beautier::check_empty_beautier_folder()

Introduction

The purpose of beautier is to create a valid BEAST2 XML input file from its function argument. In this way, a scientific pipeline using BEAST2 can be fully scripted, instead of using BEAUti's GUI.

beautier is part of the babette package suite (website at https://github.com/ropensci/babette). babette allows to use BEAST2 (and its tools) from R.

Getting started

For all examples, do load beautier:

library(beautier)

Each example shows a picture of a BEAUti dialog to achieve the same. BEAUti is part of the BEAST2 tool suite and it's a GUI to create BEAST2 input files. beautier is an R package to supplement BEAUti, by providing to do the same from an R script.

Each example reads the alignment from a FASTA file called anthus_aco_sub.fas, which is part of the files supplied with beautier:

input_filename <- get_beautier_path("anthus_aco_sub.fas")

In this vignette, the generated BEAST2 XML is shown. Use create_beast2_input_file to save the resulting XML directly to file instead.

Example #1: all default

Using all default settings, only specify a DNA alignment.

create_beast2_input(
  input_filename
)

All other parameters are set to their defaults, as in BEAUti.

Example #2: JC69 site model

create_beast2_input(
  input_filename,
  site_model = create_jc69_site_model()
)

Example #3: Relaxed clock log normal

create_beast2_input(
  input_filename,
  clock_model = create_rln_clock_model()
)

Example #4: Birth-Death tree prior

create_beast2_input(
  input_filename,
  tree_prior = create_bd_tree_prior()
)

Example #5: Yule tree prior with a normally distributed birth rate

create_beast2_input(
  input_filename,
  tree_prior = create_yule_tree_prior(
    birth_rate_distr = create_normal_distr()
  )
)

Thanks to Yacine Ben Chehida for this use case

Example #6: HKY site model with a non-zero proportion of invariants

create_beast2_input(
  input_filename,
  site_model = create_hky_site_model(
    gamma_site_model = create_gamma_site_model(prop_invariant = 0.5)
  )
)

Thanks to Yacine Ben Chehida for this use case

Example #7: Strict clock with a known clock rate

create_beast2_input(
  input_filename,
  clock_model = create_strict_clock_model(
    clock_rate_param = 0.5
  )
)

Thanks to Paul van Els and Yacine Ben Chehida for this use case.

Example #8: Use MRCA prior

create_beast2_input(
  input_filename,
  mrca_prior = create_mrca_prior()
)

Example #9: Use MRCA prior to specify a close-to-fixed crown age

With an MRCA prior, it is possible to specify a close-to-fixed crown age:

crown_age <- 15

create_beast2_input(
  input_filename,
  mrca_prior = create_mrca_prior(
    is_monophyletic = TRUE,
    mrca_distr = create_normal_distr(
      mean = crown_age,
      sigma = 0.001
    )
  )
)

Cleanup

beautier::remove_beautier_folder()
beautier::check_empty_beautier_folder()

ropensci/beautier documentation built on April 2, 2024, 5:01 a.m.