Branch
main
develop

beautier is BEAUti for R.

The purpose of beautier is to create a valid BEAST2 XML input file from a n inference model. 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:

• beautier create a BEAST2 input (.xml) file from an inference model.
• tiebeaur creates an inference model from a BEAST2 input (.xml) file :warning: experimental :warning:
• beastier runs BEAST2
• tracerer allows to works with BEAST2 output (.log, .trees, etc) files.
• mauricer install BEAST2 packages

Related R packages:

• beautier_on_windows: verifies beautier builds on Windows
• lumier: Shiny app to help create the function call needed

See examples.

beautier can be installed:

• Latest CRAN version: CRAN
• Latest stable version: GitHub, main branch
• Bleeding-edge version: GitHub, develop branch

For the latest CRAN version:

install.packages("beautier")

For the latest stable version:

remotes::install_github("ropensci/beautier")

For the bleeding-edge version:

remotes::install_github("ropensci/beautier", ref = "develop")

See FAQ.

This works, and the interface is unlikely to change.

• 1 DNA alignment
• Site models:
  • JC69
  • HKY
  • TN93
  • GTR
• Clock models:
  • Strickt
  • Relaxed log-normal
• Tree models:
  • Yule
  • Birth-Death
  • Coalescent Bayesian Skyline
  • Coalescent Constant Population
  • Coalescent Exponential Population
• Handle missing data: simply use a dash (´-´) as a sequence in a FASTA file

This works partially, and the interface may change as well.

The tip dates file is a file that needs to not have column, nor row names. The columns need to be tab separated.

See the example file G_VII_pre2003_dates_4.txt for an example, of which the first rows are shown here:

KF767106_Indonesia_1976_VII 1976
KF767104_Indonesia_1988_VII 1988
KF767105_Indonesia_1988_VII 1988
AY288998_Indonesia_1990_VII 1990

beautier cannot do everything BEAUti can.

Here are some missing or (yet) unsupported features, some are linked to an Issue:

• Add offset to a distribution
• Two or more DNA alignments
• Two or more site, clock or tree models
• Two or more MRCA priors
• Shared site, clock and/or tree models
• Using an amino acid alignment
• Support for hyper parameters
• Clock models
  • Relaxed exponential
  • Random local
• Tree priors
  • Calibrated Yule model
  • Coalescent Extended Bayesian Skyline
  • Birth Death Skyline Serial
• Initialization (this is a tab that is hidden by default in BEAUti)

See CONTRIBUTING, at Submitting use cases

See CONTRIBUTING, at 'Submitting code'

See CONTRIBUTING, at 'Submitting bugs'

Sure, just add an Issue. Or send an email.

• BEAST2 GitHub

Article about babette:

• Bilderbeek, Richèl JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032

FASTA files anthus_aco.fas and anthus_nd2.fas from:

• Van Els, Paul, and Heraldo V. Norambuena. "A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data." Ibis.

FASTA file G_VII_pre2003_msa.fas from:

• Durr, PA; Wibowo, MH; Tabbu, CR; Asmara, W; Selleck, P; Wang, J; Broz, I; Graham, K.; Dimitrov, K and Afonso, C. (in preparation). Phylodynamics of Genotype VII Newcastle disease virus in Indonesia.