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beautier is BEAUti for R.

beautier logo

The purpose of beautier is to create a valid BEAST2 XML input file from a n inference model. In this way, a scientific pipeline using BEAST2 can be fully scripted, instead of using BEAUti’s GUI.

beautier is part of the babette package suite:

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

Related R packages:

Examples

See examples.

Installation

beautier can be installed:

  • Latest CRAN version: CRAN
  • Latest stable version: GitHub, master branch
  • Bleeding-edge version: GitHub, develop branch

CRAN

For the latest CRAN version:

install.packages("beautier")

GitHub, master branch

For the latest stable version:

remotes::install_github("ropensci/beautier")

GitHub, develop branch

For the bleeding-edge version:

remotes::install_github("ropensci/beautier", ref = "develop")

FAQ

See FAQ.

Supported

This works, and the interface is unlikely to change.

  • 1 DNA alignment
  • Site models:
    • JC69
    • HKY
    • TN93
    • GTR
  • Clock models:
    • Strickt
    • Relaxed log-normal
  • Tree models:
    • Yule
    • Birth-Death
    • Coalescent Bayesian Skyline
    • Coalescent Constant Population
    • Coalescent Exponential Population
  • Handle missing data: simply use a dash (´-´) as a sequence in a FASTA file

Experimental

This works partially, and the interface may change as well.

Tip dating

The tip dates file is a file that needs to not have column, nor row names. The columns need to be tab separated.

See here for an example, of which the first rows are shown here:

KF767106_Indonesia_1976_VII 1976
KF767104_Indonesia_1988_VII 1988
KF767105_Indonesia_1988_VII 1988
AY288998_Indonesia_1990_VII 1990

In the future, there probably will be a ´to_tipdates_file´ function, to create a temporary tipdates file from a table.

Missing features/unsupported

beautier cannot do everything BEAUti can.

Here are some missing or (yet) unsupported features:

  • Two or more DNA alignments
  • Two or more site, clock or tree models
  • Two or more MRCA priors
  • Shared site, clock and/or tree models
  • Using an amino acid alignment
  • Support for hyper parameters
  • Clock models
    • Relaxed exponential
    • Random local
  • Tree priors
    • Calibrated Yule model
    • Coalescent Extended Bayesian Skyline
  • Initialization (this is a tab that is hidden by default in BEAUti)

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.

References

Article about babette:

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.

FASTA file G_VII_pre2003_msa.fas from:

  • Durr, PA; Wibowo, MH; Tabbu, CR; Asmara, W; Selleck, P; Wang, J; Broz, I; Graham, K.; Dimitrov, K and Afonso, C. (in preparation). Phylodynamics of Genotype VII Newcastle disease virus in Indonesia.