Package: babette 2.3.3

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_2.3.3.tar.gz
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babette.pdf |babette.html
babette/json (API)
NEWS

# Install babette in R:
install.packages('babette', repos = c('https://ropensci.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

On CRAN:

bayesian-inferencebeast2phylogenetics

16 exports 42 stars 3.21 score 56 dependencies 1 dependents 117 downloads

Last updated 9 days agofrom:56a4b25ca4e85ebc3dd353611d8d99947226a050 (via master)

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

Rendered fromdemo.Rmdusingknitr::rmarkdownon Jun 10 2024.

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

babette Tutorial

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Jun 10 2024.

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

babette: Step by Step

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

Examples

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

Nested Sampling

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon Jun 10 2024.

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