{"id":32209917,"url":"https://github.com/ropensci/beautier","last_synced_at":"2026-02-21T13:01:59.371Z","repository":{"id":45664209,"uuid":"53443354","full_name":"ropensci/beautier","owner":"ropensci","description":"R package to generate the same BEAST2 XML parameter files as generated by BEAUti 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Status](https://badges.ropensci.org/209_status.svg)](https://github.com/ropensci/software-review/issues/209)\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/beautier)](https://cran.r-project.org/package=beautier)\n[![CRAN total downloads](http://cranlogs.r-pkg.org/badges/grand-total/beautier)]( https://CRAN.R-project.org/package=beautier)\n[![CRAN downloads per months](http://cranlogs.r-pkg.org/badges/beautier)](https://CRAN.R-project.org/package=beautier)\n[![DOI](https://zenodo.org/badge/53443354.svg)](https://zenodo.org/badge/latestdoi/53443354)\n\nBranch   |[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/ropensci/beautier/actions)                                                                                      |[![Codecov logo](man/figures/Codecov.png)](https://about.codecov.io/)\n---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------\n`main`   |[![R-CMD-check](https://github.com/ropensci/beastier/actions/workflows/R-CMD-check.yaml/badge.svg?branch=main)](https://github.com/ropensci/beastier/actions/workflows/R-CMD-check.yaml)   |[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=main)](https://app.codecov.io/github/ropensci/beastier/branch/main)\n`develop`|[![R-CMD-check](https://github.com/ropensci/beastier/actions/workflows/R-CMD-check.yaml/badge.svg?branch=develop)](https://github.com/ropensci/beastier/actions/workflows/R-CMD-check.yaml)|[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=develop)](https://app.codecov.io/github/ropensci/beastier/branch/develop)\n\n\u003c!-- markdownlint-enable MD013 --\u003e\n\n`beautier` is `BEAUti` for R.\n\n![beautier logo](man/figures/beautier_logo.png)\n\nThe purpose of `beautier` is to create\n[a valid BEAST2 XML input file](inst/extdata/2_4.xml)\nfrom a n inference model. In this way, a scientific pipeline using\n`BEAST2` can be fully scripted, instead of using `BEAUti`'s GUI.\n\n`beautier` is part of the\n[`babette`](https://github.com/ropensci/babette) package suite:\n\n* [`beautier`](https://github.com/ropensci/beautier)\n  create a BEAST2 input (`.xml`) file from an inference model.\n* [`tiebeaur`](https://github.com/richelbilderbeek/tiebeaur)\n  creates an inference model from a BEAST2 input (`.xml`) file\n  :warning: experimental :warning:\n* [`beastier`](https://github.com/ropensci/beastier) runs BEAST2\n* [`tracerer`](https://github.com/ropensci/tracerer) allows to\n  works with BEAST2 output (`.log`, `.trees`, etc) files.\n* [`mauricer`](https://github.com/ropensci/mauricer) install BEAST2 packages\n\nRelated R packages:\n\n* [`beautier_on_windows`](https://github.com/richelbilderbeek/beautier_on_windows):\n  verifies `beautier` builds on Windows\n* [`lumier`](https://github.com/ropensci/lumier):\n  Shiny app to help create the function call needed\n\n## Examples\n\nSee [examples](doc/examples.md).\n\n## Installation\n\n`beautier` can be installed:\n\n* Latest CRAN version: CRAN\n* Latest stable version: GitHub, `main` branch\n* Bleeding-edge version: GitHub, `develop` branch\n\n### CRAN\n\nFor the latest CRAN version:\n\n```r\ninstall.packages(\"beautier\")\n```\n\n### GitHub, `main` branch\n\nFor the latest stable version:\n\n```r\nremotes::install_github(\"ropensci/beautier\")\n```\n\n### GitHub, `develop` branch\n\nFor the bleeding-edge version:\n\n```r\nremotes::install_github(\"ropensci/beautier\", ref = \"develop\")\n```\n\n## [FAQ](doc/faq.md)\n\nSee [FAQ](doc/faq.md).\n\n## Supported\n\nThis works, and the interface is unlikely to change.\n\n* 1 DNA alignment\n* Site models:\n    * JC69\n    * HKY\n    * TN93\n    * GTR\n* Clock models:\n    * Strickt\n    * Relaxed log-normal\n* Tree models:\n    * Yule\n    * Birth-Death\n    * Coalescent Bayesian Skyline\n    * Coalescent Constant Population\n    * Coalescent Exponential Population\n* Handle missing data: simply use a dash (´-´) as a sequence\n   in a FASTA file\n\n## Experimental\n\nThis works partially, and the interface may change as well.\n\n### Tip dating\n\nThe tip dates file is a file\nthat needs to not have column, nor row names.\nThe columns need to be tab separated.\n\nSee\n[the example file `G_VII_pre2003_dates_4.txt`](https://github.com/ropensci/beautier/blob/main/inst/extdata/G_VII_pre2003_dates_4.txt)\nfor an example, of which the first rows are shown here:\n\n```text\nKF767106_Indonesia_1976_VII 1976\nKF767104_Indonesia_1988_VII 1988\nKF767105_Indonesia_1988_VII 1988\nAY288998_Indonesia_1990_VII 1990\n```\n\n## Missing features/unsupported\n\n`beautier` cannot do everything `BEAUti` can.\n\nHere are some missing or (yet) unsupported features,\nsome are linked to an Issue:\n\n* [Add offset to a distribution](https://github.com/ropensci/beautier/issues/130)\n* Two or more DNA alignments\n* Two or more site, clock or tree models\n* [Two or more MRCA priors](https://github.com/ropensci/beautier/issues/131)\n* Shared site, clock and/or tree models\n* [Using an amino acid alignment](https://github.com/ropensci/beautier/issues/114)\n* Support for hyper parameters\n* Clock models\n    * Relaxed exponential\n    * Random local\n* Tree priors\n    * Calibrated Yule model\n    * Coalescent Extended Bayesian Skyline\n    * [Birth Death Skyline Serial](https://github.com/ropensci/beautier/issues/133)\n* Initialization (this is a tab that is hidden by default in `BEAUti`)\n\n## There is a feature I miss\n\nSee [CONTRIBUTING](CONTRIBUTING.md), at `Submitting use cases`\n\n## I want to collaborate\n\nSee [CONTRIBUTING](CONTRIBUTING.md), at 'Submitting code'\n\n## I think I have found a bug\n\nSee [CONTRIBUTING](CONTRIBUTING.md), at 'Submitting bugs'\n\n## There's something else I want to say\n\nSure, just add an Issue. Or send an email.\n\n## External links\n\n* [BEAST2 GitHub](https://github.com/CompEvol/beast2)\n\n## Files used by continuous integration scripts\n\n\u003c!-- markdownlint-disable MD013 --\u003e\u003c!-- Tables cannot be split up over lines, hence will break 80 characters per line --\u003e\n\nFilename                                    |Descriptions\n--------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------\n[`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\n[`.spellcheck.yml`](.spellcheck.yml)        |Configuration of the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally\n[`.wordlist.txt`](.wordlist.txt)            |Whitelisted words for the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally\n[`.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.\n[`.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.\n\n\u003c!-- markdownlint-enable MD013 --\u003e\n\n## References\n\n\u003c!-- markdownlint-disable MD013 --\u003e\u003c!-- References are not split up over lines, to keep them copy-pastable, hence will break 80 characters per line --\u003e\n\nArticle about `babette`:\n\n* Bilderbeek, Richèl JC, and Rampal S. Etienne. \"`babette`: BEAUti 2, BEAST 2 and Tracer for R.\" Methods in Ecology and Evolution (2018). \u003chttps://doi.org/10.1111/2041-210X.13032\u003e\n\nFASTA files `anthus_aco.fas` and `anthus_nd2.fas` from:\n\n* Van Els, Paul, and Heraldo V. Norambuena. \"A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data.\" Ibis.\n\nFASTA file `G_VII_pre2003_msa.fas` from:\n\n* 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.\n\n[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)\n\n\u003c!-- markdownlint-enable MD013 --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fropensci%2Fbeautier","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fropensci%2Fbeautier","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fropensci%2Fbeautier/lists"}