beautier

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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

Examples

See examples.

Installation

beautier can be installed:

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

CRAN

For the latest CRAN version:

install.packages("beautier")

GitHub, main branch

For the latest stable version:

remotes::install_github("ropensci/beautier")

GitHub, develop branch

For the bleeding-edge version:

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

FAQ

See FAQ.

Supported

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

Experimental

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

Tip dating

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

Missing features/unsupported

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)

There is a feature I miss

See CONTRIBUTING, at Submitting use cases

I want to collaborate

See CONTRIBUTING, at 'Submitting code'

I think I have found a bug

See CONTRIBUTING, at 'Submitting bugs'

There's something else I want to say

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

External links

• BEAST2 GitHub

Files used by continuous integration scripts

Filename	Descriptions
mlc_config.json	Configuration of the link checker, use markdown-link-check --config mlc_config.json --quiet docs/**/*.md to do link checking locally
.spellcheck.yml	Configuration of the spell checker, use pyspelling -c .spellcheck.yml to do spellcheck locally
.wordlist.txt	Whitelisted words for the spell checker, use pyspelling -c .spellcheck.yml to do spellcheck locally
.markdownlint.jsonc	Configuration of the Markdown linter, use markdownlint "**/*.md" to do markdown linting locally. The name of this file is a default name.
.markdownlintignore	Files ignored by the Markdown linter, use markdownlint "**/*.md" to do markdown linting locally. The name of this file is a default name.

References

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.