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-any)babette_2.3.5.tgz(r-4.4-any)
babette_2.3.5.tar.gz(r-4.6-any)babette_2.3.5.tar.gz(r-4.5-any)
babette_2.3.5.tgz(r-4.4-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 site:https://docs.ropensci.org

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

On CRAN:

Conda:

bayesian-inferencebeast2phylogeneticsopenjdk

8.71 score 45 stars 1 packages 54 scripts 335 downloads 1 mentions 16 exports 56 dependencies

Last updated 19 days agofrom:8de5e01d89 (on main). Checks:7 OK, 2 ERROR, 1 FAIL. Indexed: yes.

TargetResultTotal time
pkgdown docsOK225
source / vignettesOK188
linux-devel-x86_64ERROR141
linux-release-x86_64ERROR150
macos-release-arm64OK76
macos-oldrel-arm64OK95
windows-develOK108
windows-releaseOK133
windows-oldrelOK90
wasm-releaseFAIL118

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:ade4apebeastierbeautierbitbit64clicliprcpp11crayondigestfansifastmatchgenericsgluehmsigraphjsonlitelatticelifecyclemagrittrMASSMatrixmauricernlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtestittibbletidyselecttracerertzdbutf8vctrsvroomwithrxml2

babette demo

Richèl J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon May 19 2025.

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

babette Tutorial

Richèl J.C. Bilderbeek

Rendered fromtutorial.Rmdusingknitr::rmarkdownon May 19 2025.

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

babette: Step by Step

Richèl J.C. Bilderbeek

Rendered fromstep_by_step.Rmdusingknitr::rmarkdownon May 19 2025.

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

Examples

Richèl J.C. Bilderbeek

Rendered fromexamples.Rmdusingknitr::rmarkdownon May 19 2025.

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

Nested Sampling

Richèl J.C. Bilderbeek

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon May 19 2025.

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