Package: babette 2.3.4

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_2.3.4.tar.gz
babette_2.3.4.tar.gz(r-4.7-any)babette_2.3.4.tar.gz(r-4.6-any)
babette_2.3.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
babette/json (API)

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

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:

openjdk

4.02 score 1 packages 70 scripts 393 downloads 1 mentions 16 exports 54 dependencies

Last updated from:85ef7fa83a. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK137
source / vignettesOK187
linux-release-x86_64OK135
wasm-releaseOK138

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:ade4apebeastierbeautierbitbit64clicliprcpp11crayondigestfastmatchgenericsgluehmsigraphjsonlitelatticelifecyclemagrittrMASSMatrixmauricernlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtibbletidyselecttracerertzdbutf8vctrsvroomwithrxml2

babette demo

Richèl J.C. Bilderbeek

Rendered fromdemo.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2022-06-21
Started: 2020-01-11

babette Tutorial

Richèl J.C. Bilderbeek

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2024-06-26
Started: 2020-01-11

babette: Step by Step

Richèl J.C. Bilderbeek

Rendered fromstep_by_step.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2024-06-26
Started: 2020-01-11

Examples

Richèl J.C. Bilderbeek

Rendered fromexamples.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2022-06-21
Started: 2020-01-11

Nested Sampling

Richèl J.C. Bilderbeek

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2024-06-26
Started: 2020-01-11