https://github.com/richelbilderbeek/pirouette
R package that estimates the error BEAST2 makes from a given phylogeny
https://github.com/richelbilderbeek/pirouette
beast beast2 compare-distributions error-beast2 phylogeny pirouette tree twin-tree
Last synced: over 1 year ago
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R package that estimates the error BEAST2 makes from a given phylogeny
- Host: GitHub
- URL: https://github.com/richelbilderbeek/pirouette
- Owner: richelbilderbeek
- License: gpl-3.0
- Created: 2018-03-19T11:01:37.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-06-10T14:27:30.000Z (about 2 years ago)
- Last Synced: 2025-02-28T03:20:55.792Z (over 1 year ago)
- Topics: beast, beast2, compare-distributions, error-beast2, phylogeny, pirouette, tree, twin-tree
- Language: R
- Homepage:
- Size: 8.75 MB
- Stars: 3
- Watchers: 5
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# pirouette
Branch |[](https://github.com/richelbilderbeek/pirouette/actions) |[](https://www.codecov.io)
---------|------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------
`master` | |[](https://codecov.io/github/richelbilderbeek/pirouette/branch/master)
`develop`||[](https://codecov.io/github/richelbilderbeek/pirouette/branch/develop)
`pirouette` is an R package that estimates the error BEAST2 makes from a given
phylogeny. This phylogeny can be created using any (non-BEAST) speciation model,
for example the Protracted Birth-Death or Multiple-Birth-Death models.
* [Installation](doc/install.md).
* [Examples](https://github.com/richelbilderbeek/pirouette_examples)
* [Interpretation](doc/interpretation.md).
* [Academic article](https://github.com/richelbilderbeek/pirouette_article)
## Common abbreviations
* `nsm`: Nucleotide Substitution Model
* `tral`: TRue ALignment
* `twal`: TWin ALignment
## [FAQ](doc/faq.md)
See the [FAQ](doc/faq.md).
## 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.
## Package dependencies
### `master` branches
Package | |[](https://www.codecov.io)
-------------------------------------------------------|---------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------
[beautier](https://github.com/ropensci/beautier) | |[](https://codecov.io/github/ropensci/beautier/branch/master)
[beastier](https://github.com/ropensci/beastier) | |[](https://codecov.io/github/ropensci/beastier/branch/master)
[mauricer](https://github.com/ropensci/mauricer) | |[](https://codecov.io/github/ropensci/mauricer/branch/master)
[mcbette](https://github.com/ropensci/mcbette) | |[](https://codecov.io/github/ropensci/mcbette/branch/master)
[tracerer](https://github.com/ropensci/tracerer) | |[](https://codecov.io/github/ropensci/tracerer/branch/master)
### `develop` branches
Package | |[](https://www.codecov.io)
-------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------
[beautier](https://github.com/ropensci/beautier) | |[](https://codecov.io/github/ropensci/beautier/branch/develop)
[beastier](https://github.com/ropensci/beastier) | |[](https://codecov.io/github/ropensci/beastier/branch/develop)
[mauricer](https://github.com/ropensci/mauricer) | |[](https://codecov.io/github/ropensci/mauricer/branch/develop)
[mcbette](https://github.com/ropensci/mcbette) | |[](https://codecov.io/github/ropensci/mcbette/branch/develop)
[tracerer](https://github.com/ropensci/tracerer) | |[](https://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)
## External links
* [BEAST2 GitHub](https://github.com/CompEvol/beast2)
## References
* Bilderbeek, RJC, Laudanno, G, Etienne, RS. Quantifying the impact of an inference model in Bayesian phylogenetics. Methods Ecol Evol. 2020; 00: 1– 8. https://doi.org/10.1111/2041-210X.13514