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.zip(r-4.7-any)babette_2.3.4.zip(r-4.6-any)
babette_2.3.4.tar.gz(r-4.7-any)babette_2.3.4.tar.gz(r-4.6-any)
babette_2.3.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
babette/json (API)

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

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:

openjdk

4.05 score 1 packages 74 scripts 543 downloads 1 mentions 16 exports 54 dependencies

Last updated from:85ef7fa83a. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK167
source / vignettesOK269
linux-releaseOK156
windows-develOK100
windows-releaseOK84
wasm-releaseOK136

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:ade4apebeastierbeautierbitbit64clicliprcpp11crayondigestfastmatchgenericsgluehmsigraphjsonlitelatticelifecyclemagrittrMASSMatrixmauricernlmephangornpillarpixmappkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcppRcppArmadilloreadrrJavarlangsegmentedseqinrsessioninfospstringistringrtibbletidyselecttracerertzdbutf8vctrsvroomwithrxml2

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

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

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

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

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

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

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