https://github.com/ropensci/beautier
R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
https://github.com/ropensci/beautier
bayesian beast beast2 beauti phylogenetic-inference phylogenetics r r-package rstats
Last synced: 5 months ago
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R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
- Host: GitHub
- URL: https://github.com/ropensci/beautier
- Owner: ropensci
- License: gpl-3.0
- Created: 2016-03-08T20:35:37.000Z (over 10 years ago)
- Default Branch: main
- Last Pushed: 2025-12-08T19:16:09.000Z (8 months ago)
- Last Synced: 2026-01-27T14:51:54.337Z (6 months ago)
- Topics: bayesian, beast, beast2, beauti, phylogenetic-inference, phylogenetics, r, r-package, rstats
- Language: R
- Homepage: https://docs.ropensci.org/beautier
- Size: 11 MB
- Stars: 13
- Watchers: 1
- Forks: 4
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Codemeta: codemeta.json
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README
# beautier
[](https://github.com/ropensci/software-review/issues/209)
[](https://cran.r-project.org/package=beautier)
[]( https://CRAN.R-project.org/package=beautier)
[](https://CRAN.R-project.org/package=beautier)
[](https://zenodo.org/badge/latestdoi/53443354)
Branch |[](https://github.com/ropensci/beautier/actions) |[](https://about.codecov.io/)
---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------
`main` |[](https://github.com/ropensci/beastier/actions/workflows/R-CMD-check.yaml) |[](https://app.codecov.io/github/ropensci/beastier/branch/main)
`develop`|[](https://github.com/ropensci/beastier/actions/workflows/R-CMD-check.yaml)|[](https://app.codecov.io/github/ropensci/beastier/branch/develop)
`beautier` is `BEAUti` for R.
The purpose of `beautier` is to create
[a valid BEAST2 XML input file](inst/extdata/2_4.xml)
from a n inference model. In this way, a scientific pipeline using
`BEAST2` can be fully scripted, instead of using `BEAUti`'s GUI.
`beautier` is part of the
[`babette`](https://github.com/ropensci/babette) package suite:
* [`beautier`](https://github.com/ropensci/beautier)
create 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
* [`tracerer`](https://github.com/ropensci/tracerer) allows to
works with BEAST2 output (`.log`, `.trees`, etc) files.
* [`mauricer`](https://github.com/ropensci/mauricer) install BEAST2 packages
Related R packages:
* [`beautier_on_windows`](https://github.com/richelbilderbeek/beautier_on_windows):
verifies `beautier` builds on Windows
* [`lumier`](https://github.com/ropensci/lumier):
Shiny app to help create the function call needed
## Examples
See [examples](doc/examples.md).
## Installation
`beautier` can be installed:
* Latest CRAN version: CRAN
* Latest stable version: GitHub, `main` branch
* Bleeding-edge version: GitHub, `develop` branch
### CRAN
For the latest CRAN version:
```r
install.packages("beautier")
```
### GitHub, `main` branch
For the latest stable version:
```r
remotes::install_github("ropensci/beautier")
```
### GitHub, `develop` branch
For the bleeding-edge version:
```r
remotes::install_github("ropensci/beautier", ref = "develop")
```
## [FAQ](doc/faq.md)
See [FAQ](doc/faq.md).
## Supported
This works, and the interface is unlikely to change.
* 1 DNA alignment
* Site models:
* JC69
* HKY
* TN93
* GTR
* Clock models:
* Strickt
* Relaxed log-normal
* Tree models:
* Yule
* Birth-Death
* Coalescent Bayesian Skyline
* Coalescent Constant Population
* Coalescent Exponential Population
* Handle missing data: simply use a dash (´-´) as a sequence
in a FASTA file
## Experimental
This works partially, and the interface may change as well.
### Tip dating
The tip dates file is a file
that needs to not have column, nor row names.
The columns need to be tab separated.
See
[the example file `G_VII_pre2003_dates_4.txt`](https://github.com/ropensci/beautier/blob/main/inst/extdata/G_VII_pre2003_dates_4.txt)
for an example, of which the first rows are shown here:
```text
KF767106_Indonesia_1976_VII 1976
KF767104_Indonesia_1988_VII 1988
KF767105_Indonesia_1988_VII 1988
AY288998_Indonesia_1990_VII 1990
```
## Missing features/unsupported
`beautier` cannot do everything `BEAUti` can.
Here are some missing or (yet) unsupported features,
some are linked to an Issue:
* [Add offset to a distribution](https://github.com/ropensci/beautier/issues/130)
* Two or more DNA alignments
* Two or more site, clock or tree models
* [Two or more MRCA priors](https://github.com/ropensci/beautier/issues/131)
* Shared site, clock and/or tree models
* [Using an amino acid alignment](https://github.com/ropensci/beautier/issues/114)
* Support for hyper parameters
* Clock models
* Relaxed exponential
* Random local
* Tree priors
* Calibrated Yule model
* Coalescent Extended Bayesian Skyline
* [Birth Death Skyline Serial](https://github.com/ropensci/beautier/issues/133)
* Initialization (this is a tab that is hidden by default in `BEAUti`)
## 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.
## External links
* [BEAST2 GitHub](https://github.com/CompEvol/beast2)
## Files used by continuous integration scripts
Filename |Descriptions
--------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------
[`mlc_config.json`](mlc_config.json) |Configuration of the link checker, use `markdown-link-check --config mlc_config.json --quiet docs/**/*.md` to do link checking locally
[`.spellcheck.yml`](.spellcheck.yml) |Configuration of the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally
[`.wordlist.txt`](.wordlist.txt) |Whitelisted words for the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally
[`.markdownlint.jsonc`](.markdownlint.jsonc)|Configuration of the Markdown linter, use `markdownlint "**/*.md"` to do markdown linting locally. The name of this file is a default name.
[`.markdownlintignore`](.markdownlintignore)|Files ignored by the Markdown linter, use `markdownlint "**/*.md"` to do markdown linting locally. The name of this file is a default name.
## 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).
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.
FASTA file `G_VII_pre2003_msa.fas` from:
* Durr, PA; Wibowo, MH; Tabbu, CR; Asmara, W; Selleck, P; Wang, J; Broz, I; Graham, K.; Dimitrov, K and Afonso, C. (in preparation). Phylodynamics of Genotype VII Newcastle disease virus in Indonesia.
[](https://ropensci.org)