Package: babette 2.3.5

Richèl J.C. Bilderbeek

babette: Control 'BEAST2'

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.

Authors:Richèl J.C. Bilderbeek [aut, cre], Joëlle Barido-Sottani [rev], David Winter [rev], Jason Griffiths [ctb], Olivier Roy [ctb], Tanmay Dimri [ctb], Giovanni Laudanno [ctb]

babette_2.3.5.tar.gz
babette_2.3.5.zip(r-4.7)babette_2.3.5.zip(r-4.6)babette_2.3.5.zip(r-4.5)
babette_2.3.5.tgz(r-4.6-any)babette_2.3.5.tgz(r-4.5-any)
babette_2.3.5.tar.gz(r-4.7-any)babette_2.3.5.tar.gz(r-4.6-any)
babette_2.3.5.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
babette/json (API)
NEWS

# Install 'babette' in R:
install.packages('babette', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #209

Bug tracker:https://github.com/ropensci/babette/issues

Pkgdown/docs site:https://docs.ropensci.org

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

Conda:

bayesian-inferencebeast2phylogeneticsopenjdk

9.00 score 46 stars 1 packages 65 scripts 342 downloads 18 exports 54 dependencies

Last updated from:ea644a8a68 (on main). Checks:2 ERROR, 8 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR148
pkgdown docsOK180
source / vignettesOK202
linux-release-x86_64ERROR156
macos-release-arm64OK108
macos-oldrel-arm64OK134
windows-develOK92
windows-releaseOK94
windows-oldrelOK105
wasm-releaseOK187

Exports:bbt_continuebbt_delete_temp_filesbbt_runbbt_run_from_modelbbt_self_testcheck_beast2_pkgscreate_test_bbt_run_outputcreate_test_ns_outputget_alignment_ids_from_xmlget_babette_pathget_babette_pathsis_dropbox_pathparse_beast2_outputparse_beast2_output_to_nsplot_densitreeprepare_file_creationupdate_babettewarn_if_dropbox

Dependencies:ade4apebeastierbeautierbitbit64clicliprcpp11crayondigestfastmatchgenericsgluehmsigraphjsonlitelatticelifecyclemagrittrMASSMatrixmauricernlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtibbletidyselecttracerertzdbutf8vctrsvroomwithrxml2

babette demo

Richèl J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-06-20
Started: 2018-01-30

babette Tutorial

Richèl J.C. Bilderbeek

Rendered fromtutorial.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2023-12-27
Started: 2018-07-07

babette: Step by Step

Richèl J.C. Bilderbeek

Rendered fromstep_by_step.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2023-12-27
Started: 2018-05-07

Examples

Richèl J.C. Bilderbeek

Rendered fromexamples.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2022-06-20
Started: 2018-02-07

Nested Sampling

Richèl J.C. Bilderbeek

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon May 13 2026.

Last update: 2023-12-27
Started: 2018-09-12