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

Pkgdown:https://docs.ropensci.org

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

3.90 score 1 packages 53 scripts 436 downloads 1 mentions 16 exports 56 dependencies

Last updated 6 months agofrom:85ef7fa83a. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-linuxOKNov 23 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 Nov 23 2024.

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

babette Tutorial

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Last update: 2024-06-26
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babette: Step by Step

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Last update: 2024-06-26
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Examples

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

Nested Sampling

Rendered fromnested_sampling.Rmdusingknitr::rmarkdownon Nov 23 2024.

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