ropensci/beastier - Githubissues

# beastier

Branch
`master`
`develop`

beastier is an R package to run BEAST2.

beastier logo

beastier is part of the babette package suite:

beautier creates BEAST2 input (.xml) files.
beastier runs BEAST2
mauricer: install BEAST2 packages
tracerer pastes BEAST2 output (.log, .trees, etc) files.

Related R packages:

beastierinstall: Install and uninstall BEAST2
beastier_on_windows: Verify that beastier works on the Windows operating system
lumier: Shiny app to help create the function call needed

Install BEAST2

Due to CRAN policy, beastier cannot install BEAST2. As a workaround, the non-CRAN beastierinstall can be used.

To install BEAST2:

remotes::install_github("richelbilderbeek/beastierinstall")
beastierinstall::install_beast2()

Example for `v2.1`

Run BEAST2:

output_state_filename <- "out.state"

run_beast2(
  input_filename = get_beastier_path("2_4.xml"),
  output_state_filename = output_state_filename
)

This will create the files as specified in the 2_4.xml BEAST2 input file.

Example for `v2.0.25`

output_log_filename <- "out.log"
output_trees_filename <- "out.trees"
output_state_filename <- "out.state"

run_beast2(
  input_filename = get_beastier_path("2_4.xml"),
  output_log_filename = output_log_filename,
  output_trees_filenames = output_trees_filename,
  output_state_filename = output_state_filename
)

Note that in this version, the filenames for the .log and .trees files could be specified. This is unneeded: the 2_4.xml BEAST2 input file specifies where these files will be stored:

<?xml [...]?><beast [...]>

[...]

<run [...]>

    [...]

    <logger id="tracelog" fileName="test_output_0.log" [...]>
        [...]
    </logger>

    [...]

    <logger id="treelog.t:[...]" fileName="$(tree).trees" [...]>
        [...]
    </logger>
</run>
</beast>

When using beautier, this can be specified in create_mcmc:

create_mcmc(
  tracelog = create_tracelog(
    filename = "my_trace.log"
  ),
  treeslog = create_treeslog(
    filename = "my_trees.trees"
  )
)

Install

See install.

FAQ

See FAQ

Missing features/unsupported

beastier cannot do everything BEAST2 can.

Remove: install BEAST2, use beastierinstall
Experimental: Continue a BEAST2 run
Untested: Setup BEAGLE

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.

External links

BEAST2 GitHub

Dependencies

Branch
`beautier` `master`
`beautier` `develop`
`beastierinstall` `master`
`beastierinstall` `develop`

Branch
`beastier_on_windows` `master`
`beastier_on_windows` `develop`

Files used by continuous integration scripts

Filename	Descriptions
mlc_config.json	Configuration of the link checker, use `markdown-link-check --config mlc_config.json --quiet docs/*/.md` to do link checking locally
.spellcheck.yml	Configuration of the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally
.wordlist.txt	Whitelisted words for the spell checker, use `pyspelling -c .spellcheck.yml` to do spellcheck locally
.markdownlint.jsonc	Configuration of the markdown linter, use `markdownlint "*/.md"` to do markdown linting locally. The name of this file is a default name.
.markdownlintignore	Files ignored by the markdown linter, use `markdownlint "*/.md"` to do markdown linting locally. The name of this file is a default name.

References

Article about babette:

Bilderbeek, Richèl JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032

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.