beautier

Branch
`master`
`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 ⚠️ experimental ⚠️
beastier runs BEAST2
tracerer pastes 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, master branch
Bleeding-edge version: GitHub, develop branch

CRAN

For the latest CRAN version:

install.packages("beautier")

GitHub, `master` 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 here 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

In the future, there probably will be a ´to_tipdates_file´ function, to create a temporary tipdates file from a table.

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.

ropensci/beautier