Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

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: 2 months ago
JSON representation

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 (almost 7 years ago)
Default Branch: master
Last Pushed: 2024-06-10T14:27:30.000Z (7 months ago)
Last Synced: 2024-10-10T20:11:16.258Z (3 months 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   |[![GitHub Actions](man/figures/GitHubActions.png)](https://github.com/richelbilderbeek/pirouette/actions)   |[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io)

---------|------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------

`master` |![R-CMD-check](https://github.com/richelbilderbeek/pirouette/workflows/R-CMD-check/badge.svg?branch=master) |[![codecov.io](https://codecov.io/github/richelbilderbeek/pirouette/coverage.svg?branch=master)](https://codecov.io/github/richelbilderbeek/pirouette/branch/master)

`develop`|![R-CMD-check](https://github.com/richelbilderbeek/pirouette/workflows/R-CMD-check/badge.svg?branch=develop)|[![codecov.io](https://codecov.io/github/richelbilderbeek/pirouette/coverage.svg?branch=develop)](https://codecov.io/github/richelbilderbeek/pirouette/branch/develop)

![](pics/pirouette_logo_50.png)

![](pics/errors_125.png)

`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                                                |![GitHub Actions](man/figures/GitHubActions.png)                                                   |[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io)

-------------------------------------------------------|---------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------

[beautier](https://github.com/ropensci/beautier)       |![R-CMD-check](https://github.com/ropensci/beautier/workflows/R-CMD-check/badge.svg?branch=master) |[![codecov.io](https://codecov.io/github/ropensci/beautier/coverage.svg?branch=master)](https://codecov.io/github/ropensci/beautier/branch/master)

[beastier](https://github.com/ropensci/beastier)       |![R-CMD-check](https://github.com/ropensci/beastier/workflows/R-CMD-check/badge.svg?branch=master) |[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=master)](https://codecov.io/github/ropensci/beastier/branch/master)

[mauricer](https://github.com/ropensci/mauricer)       |![R-CMD-check](https://github.com/ropensci/mauricer/workflows/R-CMD-check/badge.svg?branch=master) |[![codecov.io](https://codecov.io/github/ropensci/mauricer/coverage.svg?branch=master)](https://codecov.io/github/ropensci/mauricer/branch/master)

[mcbette](https://github.com/ropensci/mcbette)         |![R-CMD-check](https://github.com/ropensci/mcbette/workflows/R-CMD-check/badge.svg?branch=master)  |[![codecov.io](https://codecov.io/github/ropensci/mcbette/coverage.svg?branch=master)](https://codecov.io/github/ropensci/mcbette/branch/master)

[tracerer](https://github.com/ropensci/tracerer)       |![R-CMD-check](https://github.com/ropensci/tracerer/workflows/R-CMD-check/badge.svg?branch=master) |[![codecov.io](https://codecov.io/github/ropensci/tracerer/coverage.svg?branch=master)](https://codecov.io/github/ropensci/tracerer/branch/master)

### `develop` branches

Package                                                |![GitHub Actions](man/figures/GitHubActions.png)                                                                      |[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io)

-------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------

[beautier](https://github.com/ropensci/beautier)       |![R-CMD-check](https://github.com/ropensci/beautier/workflows/R-CMD-check/badge.svg?branch=develop) |[![codecov.io](https://codecov.io/github/ropensci/beautier/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/beautier/branch/develop)

[beastier](https://github.com/ropensci/beastier)       |![R-CMD-check](https://github.com/ropensci/beastier/workflows/R-CMD-check/badge.svg?branch=develop) |[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/beastier/branch/develop)

[mauricer](https://github.com/ropensci/mauricer)       |![R-CMD-check](https://github.com/ropensci/mauricer/workflows/R-CMD-check/badge.svg?branch=develop) |[![codecov.io](https://codecov.io/github/ropensci/mauricer/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/mauricer/branch/develop)

[mcbette](https://github.com/ropensci/mcbette)         |![R-CMD-check](https://github.com/ropensci/mcbette/workflows/R-CMD-check/badge.svg?branch=develop)  |[![codecov.io](https://codecov.io/github/ropensci/mcbette/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/mcbette/branch/develop)

[tracerer](https://github.com/ropensci/tracerer)       |![R-CMD-check](https://github.com/ropensci/tracerer/workflows/R-CMD-check/badge.svg?branch=develop) |[![codecov.io](https://codecov.io/github/ropensci/tracerer/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/tracerer/branch/develop)

### Windows

Package                                                                       | Status

------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[babette_on_windows](https://github.com/richelbilderbeek/babette_on_windows)  |[![Build status](https://ci.appveyor.com/api/projects/status/jv76errjocm5d5yq/branch/master?svg=true)](https://ci.appveyor.com/project/richelbilderbeek/babette-on-windows/branch/master)

[beastier_on_windows](https://github.com/richelbilderbeek/beastier_on_windows)|[![Build status](https://ci.appveyor.com/api/projects/status/ralex9sdnnxlwbgx/branch/master?svg=true)](https://ci.appveyor.com/project/richelbilderbeek/beastier-on-windows/branch/master)

[beautier_on_windows](https://github.com/richelbilderbeek/beautier_on_windows)|[![Build status](https://ci.appveyor.com/api/projects/status/blvjo5pulbkqxrhb/branch/master?svg=true)](https://ci.appveyor.com/project/richelbilderbeek/beautier-on-windows/branch/master)

[mauricer_on_windows](https://github.com/richelbilderbeek/mauricer_on_windows)|[![Build status](https://ci.appveyor.com/api/projects/status/bc43iwp68xo2dduh/branch/master?svg=true)](https://ci.appveyor.com/project/richelbilderbeek/mauricer-on-windows/branch/master)

[tracerer_on_windows](https://github.com/richelbilderbeek/tracerer_on_windows)|[![Build status](https://ci.appveyor.com/api/projects/status/jyhck66d6yrbr12h/branch/master?svg=true)](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