doc/faq.md

In richelbilderbeek/rbeast2: Control 'BEAST2'

FAQ

BEAST2

Which version of BEAUti do you use as a guideline?

Run this code:

beastier::get_beast2_version()

Currently, this returns 2.6.4 which means that the BEAUti version 2.6 (the patch version is irrelevant) is ignored.

How to install BEAST2?

See install.md

babette development

What's the road map?

Currently, babette does not have a road map itself, but beautier does:

• beautier road map

How can I indicate a feature that I miss?

Submit an Issue.

How can I submit code?

See CONTRIBUTING, at 'Submitting code'

How can I submit a bug?

See CONTRIBUTING, at 'Submitting bugs'

How can I indicate something else?

Submit an Issue. Or send an email to Richèl Bilderbeek.

What are the babette dependencies?

babette technical questions

How can I inspect a generated BEAST2 .xml file?

The path to the BEAST2 .xml file, which is the file that contains the inference model, can be found in the BEAST2 options. A typical user is unaware these options exists, as these are generated by default.

Here is an example that calls bbt_run_from_model with an explicit BEAST2 options:

# Default BEAST2 options
beast2_options <- create_beast2_options()

# The path where the BEAST2 XML file will be created:
beast2_options$input_filename

bbt_run_from_model(
  fasta_filename = get_babette_path("anthus_aco.fas"),
  beast2_options = beast2_options
)

# Show BEAST2 XML file
readLines(beast2_options$input_filename)

How can I inspect a generated BEAST2 .xml.state file?

The path to the BEAST2 .xml.state file, which is the file that contains the current/final state of the MCMC machinery, can be found in the BEAST2 options. A typical user is unaware these options exists, as these are generated by default.

A typical user is unaware these options exists, as these are generated by default.

Here is an example that calls bbt_run_from_model with an explicit BEAST2 options:

# Default BEAST2 options
beast2_options <- create_beast2_options()

# The path where the final BEAST2 state file will be created:
beast2_options$output_state_filename

bbt_run_from_model(
  fasta_filename = get_babette_path("anthus_aco.fas"),
  beast2_options = beast2_options
)

# Show BEAST2 state file
readLines(beast2_options$output_state_filename)

How can I inspect a generated BEAST2 .trees file?

This .trees file, which holds the estimated trees, is part of the inference_model:

inference_model <- create_test_inference_model()

# Path to .trees file
inference_model$mcmc$treelog$filename

bbt_run_from_model(
  fasta_filename = get_babette_path("anthus_aco.fas"),
  inference_model = inference_model
)

# Show the generated .trees file
readLines(inference_model$mcmc$tracelog$filename)

How can I inspect a generated BEAST2 .log file?

This .log file holds the parameter estimations is part of the inference_model:

inference_model <- create_test_inference_model()

# Path to .log file
inference_model$mcmc$tracelog$filename

bbt_run_from_model(
  fasta_filename = get_babette_path("anthus_aco.fas"),
  inference_model = inference_model
)

# Show the generated .log file
readLines(inference_model$mcmc$tracelog$filename)

Can babette handle missing data in the FASTA files?

Yes. BEAST2 can missing data in the FASTA files (which contain the DNA/RNA or protein sequences) and so does babette.

In your FASTA file, use a dash - (not NA) for the sequences that are missing. This is similar to what the phangorn package does.

If I set a fixed crown age with multiple alignments, only the first alignment has so

Correct. This is a feature of BEAST2. Using the create_mrca prior gives prettier results.

babette in academia

How do I reference to this work?

Bilderbeek, Richèl JC, and Rampal S. Etienne. "babette: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018).

or

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

Are there any related packages?

• lumier: Shiny app to help create the function call needed
• BEASTmasteR: tip-dating analyses using fossils as dated terminal taxa
• RBeast: misc other things

What are the FASTA files?

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.

Thanks to Paul van Els.

babette misc

Why the name?

• ba: BeAutier
• bet: BEasTier
• te: TracErer

Later on, mauricer got added.

Why the logo?

Initially, the logo was a low-tech remake of Babette, a maid in Beauty and the Beast. To prevent problems with Disney, a different logo was picked.

The current logo shows a swan, an animal considered to be graceful. The swan is drawn by Jose Scholte, who kindly allowed her work to be used for free, by attribution.

Error: libjvm.so: cannot open shared object file: No such file or directory

For me, this Stack Overflow post helped me out:

sudo mousepad /etc/ld.so.conf.d/java.conf

In that file put:

/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server

Save, close, restart R studio, fixed!

Else this Stack Overflow post may be helpful:

sudo apt-get install jdk-*
sudo R CMD javareconf
sudo R CMD javareconf -e
export LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH
sudo apt-get install r-cran-rjava

richelbilderbeek/rbeast2 documentation built on Sept. 30, 2023, 9:39 a.m.