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], Giovanni Laudanno [ctb]

babette_2.3.5.tar.gz
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babette_2.3.5.tgz(r-4.5-emscripten)
babette.pdf |babette.html✨
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

8.58 score 46 stars 1 packages 55 scripts 601 downloads 1 mentions 16 exports 55 dependencies

Last updated from:8de5e01d89 (on main). Checks:2 ERROR, 8 OK. Indexed: yes.

TargetResultTotal timeArtifact
linux-devel-x86_64ERROR151
pkgdown docsOK167
source / vignettesOK318
linux-release-x86_64ERROR154
macos-release-arm64OK89
macos-oldrel-arm64OK90
windows-develOK134
windows-releaseOK102
windows-oldrelOK137
wasm-releaseOK147

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_pathsparse_beast2_outputparse_beast2_output_to_nsplot_densitreeprepare_file_creationupdate_babette

Dependencies:ade4apebeastierbeautierbitbit64clicliprcpp11crayondigestfastmatchgenericsgluehmsigraphjsonlitelatticelifecyclemagrittrMASSMatrixmauricernlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtestittibbletidyselecttracerertzdbutf8vctrsvroomwithrxml2

babette demo

Richèl J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon Oct 31 2025.

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

babette Tutorial

Richèl J.C. Bilderbeek

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Oct 31 2025.

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

babette: Step by Step

Richèl J.C. Bilderbeek

Rendered fromstep_by_step.Rmdusingknitr::rmarkdownon Oct 31 2025.

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

Examples

Richèl J.C. Bilderbeek

Rendered fromexamples.Rmdusingknitr::rmarkdownon Oct 31 2025.

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

Nested Sampling

Richèl J.C. Bilderbeek

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon Oct 31 2025.

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