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https://github.com/ropensci/babette
babette is an R package to work with BEAST2
https://github.com/ropensci/babette
bayesian-inference beast2 phylogenetics r r-package rstats
Last synced: 3 months ago
JSON representation
babette is an R package to work with BEAST2
- Host: GitHub
- URL: https://github.com/ropensci/babette
- Owner: ropensci
- License: gpl-3.0
- Created: 2018-01-23T13:45:12.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2024-06-27T08:43:11.000Z (4 months ago)
- Last Synced: 2024-07-27T16:47:28.276Z (3 months ago)
- Topics: bayesian-inference, beast2, phylogenetics, r, r-package, rstats
- Language: R
- Homepage: https://docs.ropensci.org/babette
- Size: 10.2 MB
- Stars: 42
- Watchers: 7
- Forks: 6
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Codemeta: codemeta.json
Awesome Lists containing this project
- jimsghstars - ropensci/babette - babette is an R package to work with BEAST2 (R)
README
# babette
[](https://github.com/ropensci/software-review/issues/209)
[](https://cran.r-project.org/package=babette)
[]( https://CRAN.R-project.org/package=babette)
[](https://CRAN.R-project.org/package=babette)
Branch |[](https://github.com/ropensci/babette/actions)|[](https://about.codecov.io/)
---------|----------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------
`master` | |[](https://app.codecov.io/github/ropensci/babette/branch/master)
`develop`| |[](https://app.codecov.io/github/ropensci/babette/branch/develop)
[](https://zenodo.org/badge/latestdoi/118616108)
`babette` is an R package that combines:
* [beautier](https://github.com/ropensci/beautier) creates a BEAST2 input (`.xml`) file from an inference model
* [tiebeaur](https://github.com/richelbilderbeek/tiebeaur) creates an inference model from a BEAST2 input (`.xml`) file :warning: experimental :warning:
* [beastier](https://github.com/ropensci/beastier) runs BEAST2
* [mauricer](https://github.com/ropensci/mauricer) install BEAST2 packages
* [tracerer](https://github.com/ropensci/tracerer) parses BEAST2 output (`.log`, `.trees`, etc) files.
Non-CRAN extensions:
* [beastierinstall](https://github.com/richelbilderbeek/beastierinstall) Install and uninstall BEAST2
* [mauricerinstall](https://github.com/richelbilderbeek/mauricerinstall) Install and uninstall BEAST2 packages
Related R packages:
* [lumier](https://github.com/ropensci/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](https://github.com/josephwb/BEASTifier): command-line tool to generate BEAST2 XML input files
## Examples
See:
* [lumier](https://github.com/ropensci/lumier): R Shiny app to help create the R function call needed
* [examples](https://github.com/richelbilderbeek/babette_examples): examples tested by Travis CI and AppVeyor
* [article](https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13032), in 'Methods in Ecology and Evolution'
* [Methods.blog post: The babette R Package: How to Sooth the Phylogenetic BEAST2](https://methodsblog.com/2018/06/25/babette-beast2/)
* [rOpenSci blog post: Call BEAST2 for Bayesian evolutionary analysis from R](https://ropensci.org/blog/2020/01/28/babette/)
* [pre-print article](https://doi.org/10.1101/271866), in bioRxiv
* ['babette' YouTube channel](https://www.youtube.com/watch?v=nA-0-Fc95xY&list=PLu8_ZyzXyRDFIRx-kdDI5Q6xVr-HnY7TB)
## Installation
See [doc/install.md](doc/install.md) (or just click [here](doc/install.md))
## FAQ
See [FAQ](doc/faq.md).
## Missing features/unsupported
`babette` cannot do everything `BEAUti` and `BEAST2` and `Tracer` can.
See [beautier](https://github.com/ropensci/beautier)
for missing features in creating a BEAST2 input (`.xml`) file.
See [beastier](https://github.com/ropensci/beastier) for missing
features in running BEAST2
See [mauricer](https://github.com/ropensci/mauricer) for missing
features in installing BEAST2 packages.
See [tracerer](https://github.com/ropensci/tracerer)
for missing features in parsing BEAST2 output (`.log`, `.trees`, etc) files.
## There is a feature I miss
See [CONTRIBUTING](CONTRIBUTING.md), at `Submitting use cases`
## I want to collaborate
See [CONTRIBUTING](CONTRIBUTING.md), at `Submitting code`
## I think I have found a bug
See [CONTRIBUTING](CONTRIBUTING.md), at `Submitting bugs`
## There's something else I want to say
Sure, just add an Issue. Or send an email.
## Dependencies
Branch |[](https://github.com/ropensci/babette/actions) `master`|[](https://github.com/ropensci/babette/actions) `develop`|[](https://about.codecov.io/) `master` |[](https://about.codecov.io/) `develop`
------------------------------------------------|-------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------
[beautier](https://github.com/ropensci/beautier)| | |[](https://app.codecov.io/github/ropensci/beautier/branch/master)|[](https://app.codecov.io/github/ropensci/beautier/branch/develop)
[beastier](https://github.com/ropensci/beastier)| | |[](https://app.codecov.io/github/ropensci/beastier/branch/master)|[](https://app.codecov.io/github/ropensci/beastier/branch/develop)
[mauricer](https://github.com/ropensci/mauricer)| | |[](https://app.codecov.io/github/ropensci/mauricer/branch/master)|[](https://app.codecov.io/github/ropensci/mauricer/branch/develop)
[tracerer](https://github.com/ropensci/tracerer)| | |[](https://app.codecov.io/github/ropensci/tracerer/branch/master)|[](https://app.codecov.io/github/ropensci/tracerer/branch/develop)
## Windows
Package | Status
------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
[babette_on_windows](https://github.com/richelbilderbeek/babette_on_windows) |[](https://ci.appveyor.com/project/richelbilderbeek/babette-on-windows/branch/master)
[beastier_on_windows](https://github.com/richelbilderbeek/beastier_on_windows)|[](https://ci.appveyor.com/project/richelbilderbeek/beastier-on-windows/branch/master)
[beautier_on_windows](https://github.com/richelbilderbeek/beautier_on_windows)|[](https://ci.appveyor.com/project/richelbilderbeek/beautier-on-windows/branch/master)
[mauricer_on_windows](https://github.com/richelbilderbeek/mauricer_on_windows)|[](https://ci.appveyor.com/project/richelbilderbeek/mauricer-on-windows/branch/master)
[tracerer_on_windows](https://github.com/richelbilderbeek/tracerer_on_windows)|[](https://ci.appveyor.com/project/richelbilderbeek/tracerer-on-windows/branch/master)
## Related packages
Package |[](https://about.codecov.io/)
--------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------
[lumier](https://github.com/ropensci/lumier)|[](https://app.codecov.io/github/ropensci/lumier/branch/master)
## External links
* [BEAST2 GitHub](https://github.com/CompEvol/beast2)
## 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.
[](https://ropensci.org)