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README.md

babette

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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

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)

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

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beautier Build Status codecov.io
beastier Build Status codecov.io
mauricer Build Status codecov.io
phangorn Build Status codecov.io
tracerer Build Status codecov.io

Windows

Package Status
babette_on_windows Build status
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tracerer_on_windows Build status

Related packages

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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.

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