Package: babette 2.3.5

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], Tanmay Dimri [ctb], Giovanni Laudanno [ctb]

babette_2.3.5.tar.gz
babette_2.3.5.zip(r-4.7)babette_2.3.5.zip(r-4.6)babette_2.3.5.zip(r-4.5)
babette_2.3.5.tgz(r-4.6-any)babette_2.3.5.tgz(r-4.5-any)
babette_2.3.5.tar.gz(r-4.7-any)babette_2.3.5.tar.gz(r-4.6-any)
babette_2.3.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
babette/json (API)

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

Reviews:rOpenSci Software Review #209

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:

bayesian-inferencebeast2phylogeneticsopenjdk

8.93 score 46 stars 1 packages 70 scripts 395 downloads 1 mentions 18 exports 54 dependencies

Last updated from:ea644a8a68 (on main). Checks:2 ERROR, 8 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR176
pkgdown docsOK225
source / vignettesOK208
linux-release-x86_64ERROR160
macos-release-arm64OK129
macos-oldrel-arm64OK103
windows-develOK84
windows-releaseOK90
windows-oldrelOK88
wasm-releaseOK163

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_pathsis_dropbox_pathparse_beast2_outputparse_beast2_output_to_nsplot_densitreeprepare_file_creationupdate_babettewarn_if_dropbox

Dependencies:ade4apebeastierbeautierbitbit64clicliprcpp11crayondigestfastmatchgenericsgluehmsigraphjsonlitelatticelifecyclemagrittrMASSMatrixmauricernlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtibbletidyselecttracerertzdbutf8vctrsvroomwithrxml2

babette Tutorial
Introduction | fasta_filename | inference_model and mcmc | site_model | clock_model | tree_prior | mrca_prior
Rendered fromtutorial.Rmdusingknitr::rmarkdown

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

babette: Step by Step
Introduction | Create a 'BEAST2' input file | Display (part of) the 'BEAST2' input file | Run MCMC | Display (part of) the 'BEAST2' output files | Parse output
Rendered fromstep_by_step.Rmdusingknitr::rmarkdown

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

Nested Sampling
Introduction | Setup | Experiment | Do the run | References
Rendered fromnested_sampling.Rmdusingknitr::rmarkdown

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

babette demo
Introduction | Let babette run 'BEAST2' | Plot the posterior estimates | Show the effective sample sizes (ESS) | Show the summary statistics | Plot the posterior phylogenies
Rendered fromdemo.Rmdusingknitr::rmarkdown

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

Examples
Introduction | Example #1: all default | Example #2: using an MRCA prior to specify a crown age | Example #3: JC69 site model | Example #4: Relaxed clock log normal | Example #5: Birth-Death tree prior | Example #6: Yule tree prior with a normally distributed birth rate | Example #7: HKY site model with a non-zero proportion of invariants | Example #8: Strict clock with a known clock rate
Rendered fromexamples.Rmdusingknitr::rmarkdown

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