rOpenSci: The babette package

Branch
master
develop		.

babette is an R package that combines:

• beautier creates a BEAST2 input (.xml) file from an inference model
• tiebeaur creates an inference model from a BEAST2 input (.xml) file ⚠️ experimental ⚠️
• beastier runs BEAST2
• mauricer install BEAST2 packages
• tracerer parses BEAST2 output (.log, .trees, etc) files.

Related R packages:

• lumier: Shiny app to help create the function call needed

Related R functions:

Related function	babette function
[ips::rbeauti](https://github.com/heibl/ips/blob/master/R/rbeauti.R)	[beautier::create_beast2_input_from_model](https://github.com/ropensci/beautier/blob/master/R/create_beast2_input_from_model.R)

Examples

See:

• lumier: R Shiny app to help create the R function call needed
• examples: examples tested by Travis CI and AppVeyor
• article, in ‘Methods in Ecology and Evolution’
• Methods.blog post: The babette R Package: How to Sooth the Phylogenetic BEAST2
• rOpenSci blog post: Call BEAST2 for Bayesian evolutionary analysis from R
• pre-print article, in bioRxiv
• ‘babette’ YouTube channel

Installation

See doc/install.md (or just click here)

FAQ

See FAQ.

Missing features/unsupported

babette cannot do everything BEAUti and BEAST2 and Tracer can.

See beautier for missing features in creating a BEAST2 input (.xml) file.

See beastier for missing features in running BEAST2

See mauricer for missing features in installing BEAST2 packages.

See tracerer for missing features in parsing BEAST2 output (.log, .trees, etc) files.

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.

Dependencies

Package
beautier
beastier
mauricer
phangorn
tracerer

Windows

Package	Status
babette_on_windows
beastier_on_windows
beautier_on_windows
mauricer_on_windows
tracerer_on_windows

Related packages

Package
lumier

External links

• BEAST2 GitHub

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

@article{bilderbeek2018babette,
  title={babette: BEAUti 2, BEAST 2 and Tracer for R},
  author={Bilderbeek, Richèl JC and Etienne, Rampal S},
  journal={Methods in Ecology and Evolution},
  year={2018},
  publisher={Wiley Online Library}
}

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.