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/master/R/rbeauti.R) |
[beautier::create_beast2_input_from_model](https://github.com/ropensci/beautier/blob/master/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.
Dependencies
| Branch | master |
develop |
master |
develop |
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| beautier |  |
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| beastier |  |
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| mauricer |  |
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| tracerer |  |
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Windows
| Package | Status |
|---|---|
| babette_on_windows | |
| beastier_on_windows | |
| beautier_on_windows | |
| mauricer_on_windows | |
| tracerer_on_windows |
Related packages
| Package | |
|---|---|
| lumier |  |
External links
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.
