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DOI

babette is an R package that combines:

babette logo

Related R packages:

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

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

Package Travis CI logo Codecov logo
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

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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