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-4.5-noble)babette_2.3.4.tar.gz(r-4.4-noble)
babette_2.3.4.tgz(r-4.4-emscripten)babette_2.3.4.tgz(r-4.3-emscripten)
babette.pdf |babette.html✨
babette/json (API)

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

Peer review:

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

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

16 exports 4.20 score 56 dependencies 1 dependents 1 mentions 53 scripts 415 downloads

Last updated 3 months agofrom:85ef7fa83a. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 24 2024
R-4.5-linuxOKSep 24 2024

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 Sep 24 2024.

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

babette Tutorial

Richèl J.C. Bilderbeek

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Sep 24 2024.

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

babette: Step by Step

Richèl J.C. Bilderbeek

Rendered fromstep_by_step.Rmdusingknitr::rmarkdownon Sep 24 2024.

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

Examples

Richèl J.C. Bilderbeek

Rendered fromexamples.Rmdusingknitr::rmarkdownon Sep 24 2024.

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

Nested Sampling

Richèl J.C. Bilderbeek

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon Sep 24 2024.

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