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
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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'))

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 44 stars 8.84 score 56 dependencies 1 dependents 1 mentions 53 scripts 416 downloads

Last updated 4 months agofrom:2150931d20 (on master). Checks:OK: 6 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 25 2024
R-4.5-winOKSep 25 2024
R-4.5-linuxERRORSep 25 2024
R-4.4-winOKSep 25 2024
R-4.4-macOKSep 25 2024
R-4.3-winOKSep 25 2024
R-4.3-macOKSep 25 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

Rendered fromdemo.Rmdusingknitr::rmarkdownon Sep 25 2024.

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

babette Tutorial

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Sep 25 2024.

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

babette: Step by Step

Rendered fromstep_by_step.Rmdusingknitr::rmarkdownon Sep 25 2024.

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

Examples

Rendered fromexamples.Rmdusingknitr::rmarkdownon Sep 25 2024.

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

Nested Sampling

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon Sep 25 2024.

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