Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
R
 
 
doc
 
 
 
 
man
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

babette

Peer Review Status CRAN_Status_Badge

Branch GitHub Actions logo Codecov logo
master R-CMD-check codecov.io
develop R-CMD-check codecov.io

DOI

babette is an R package that combines:

  • beautier creates a BEAST2 input (.xml) file from an inference model
  • tiebeaur creates an inference model from a BEAST2 input (.xml) file ⚠️ experimental ⚠️
  • beastier runs BEAST2
  • mauricer install BEAST2 packages
  • tracerer parses BEAST2 output (.log, .trees, etc) files.

babette logo

Non-CRAN extensions:

Related R packages:

  • lumier: Shiny app to help create the function call needed

Related R functions:

Related function babette function
[ips::rbeauti](https://github.com/heibl/ips/blob/master/R/rbeauti.R) [beautier::create_beast2_input_from_model](https://github.com/ropensci/beautier/blob/master/R/create_beast2_input_from_model.R)

Related software:

  • BEASTifier: command-line tool to generate BEAST2 XML input files

Examples

See:

Installation

See doc/install.md (or just click here)

FAQ

See FAQ.

Missing features/unsupported

babette cannot do everything BEAUti and BEAST2 and Tracer can.

See beautier for missing features in creating a BEAST2 input (.xml) file.

See beastier for missing features in running BEAST2

See mauricer for missing features in installing BEAST2 packages.

See tracerer for missing features in parsing BEAST2 output (.log, .trees, etc) files.

There is a feature I miss

See CONTRIBUTING, at Submitting use cases

I want to collaborate

See CONTRIBUTING, at Submitting code

I think I have found a bug

See CONTRIBUTING, at Submitting bugs

There's something else I want to say

Sure, just add an Issue. Or send an email.

Dependencies

Branch GitHub Actions logo master GitHub Actions logo develop Travis CI logo master Travis CI logo develop Codecov logo master Codecov logo develop
beautier R-CMD-check R-CMD-check Build Status Build Status codecov.io codecov.io
beastier R-CMD-check R-CMD-check Build Status Build Status codecov.io codecov.io
mauricer R-CMD-check R-CMD-check Build Status Build Status codecov.io codecov.io
tracerer R-CMD-check R-CMD-check Build Status Build Status codecov.io codecov.io

Windows

Package Status
babette_on_windows Build status
beastier_on_windows Build status
beautier_on_windows Build status
mauricer_on_windows Build status
tracerer_on_windows Build status

Related packages

Package Travis CI logo Codecov logo
lumier Build Status codecov.io

External links

References

Article about babette:

@article{bilderbeek2018babette,
  title={babette: BEAUti 2, BEAST 2 and Tracer for R},
  author={Bilderbeek, Richèl JC and Etienne, Rampal S},
  journal={Methods in Ecology and Evolution},
  year={2018},
  publisher={Wiley Online Library}
}

FASTA files anthus_aco.fas and anthus_nd2.fas from:

  • Van Els, Paul, and Heraldo V. Norambuena. "A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data." Ibis.

ropensci_footer