babette

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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 :warning: experimental :warning:
• beastier runs BEAST2
• mauricer install BEAST2 packages
• tracerer parses BEAST2 output (.log, .trees, etc) files.

Non-CRAN extensions:

• beastierinstall Install and uninstall BEAST2
• mauricerinstall Install and uninstall BEAST2 packages

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/main/R/rbeauti.R)	[beautier::create_beast2_input_from_model](https://github.com/ropensci/beautier/blob/main/R/create_beast2_input_from_model.R)

Related software:

• BEASTifier: command-line tool to generate BEAST2 XML input files

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.

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.