doc/faq.md

In richelbilderbeek/beastscriptr: 'BEAUti' from R

FAQ

Shouldn't the slogan be 'beautier: BEAUti 2 for R'?

That slogan would indeed be more precise. That extra precision would come at the cost of readability (the extra '2'). As there is no BEAUti 1, there is no possible confusion and that extra number does not add extra information.

Which version of BEAUti do you use as a guideline?

The first BEAST2 XML files created by beautier followed BEAST2 v2.4. beautier follows the BEAST2 versions, which is now at v2.6.0.

The BEAST2 version actually used by babette can be found in the beastier::install_beast2 function.

Why does AppVeyor only check the main branch?

Because ropensci does not have AppVeyor.

To do check for Windows, the beautier_on_windows repo is created. That repo only checks the main branch of beautier.

What's the road map?

See 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.

How do I reference to this work?

Cite:

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, Richèl 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
• BEASTifier: generate BEAST input files from a NEXUS file, similar to beautier
• RBeast: misc other things

What is the idea behind the logo?

The butterfly symbolizes beauty. Then it was combined with an R logo.

What are the FASTA files?

Filename |Reference -----------------------|------------ anthus_aco.fas |[1] anthus_nd2.fas |[1] G_VII_pre2003_msa.fas|[2] Others |Artificial

• [1] Van Els, Paul, and Heraldo V. Norambuena. "A revision of species limits in Neotropical pipits Anthus based on multilocus genetic and vocal data." Ibis.
• [2] 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.

Thanks to Peter A. Durr and Paul van Els for supplying the FASTA files.

Why are the functions prefixed with create_?

Or, why is this chosen:

out <- create_beast2_input(
  "alignment.fas",
  tree_prior = create_yule_tree_prior(
    birth_rate_distr = create_exp_distr()    
  )
)

over this:

out <- create_beast2_input(
  "alignment.fas",
  tree_prior = yule_tree_prior(
    birth_rate_distr = exp_distr()    
  )
)

Answer: because function names should start with a verb (see e.g. https://style.tidyverse.org/functions.html#naming)

Why the name?

beautier is 'BEAUti for R'.

Additionally, it is a joke that suggests beautier would have more beauty than BEAUti. This suggestion benefits the image of author of beautier, who, however, thinks that both tools are equally valuable and beautiful.

Why the logo?

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

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

BEAUti problems

Not enough memory

./beauti

Can't start up: not enough memory

On Artful Aardvark, remove -Xms256m -Xmx4g from the bin/beauti file's last line. Change:

"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx4g -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beauti.BeautiLauncher -capture $*

to

"$JAVA" -Dlauncher.wait.for.exit=true -Djava.library.path="$BEAST_LIB" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beauti.BeautiLauncher -capture $*

BEAUti requires Java version at least 8

Do:

sudo update-alternatives --config java

Pick /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java:

There are 5 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-9-openjdk-amd64/bin/java       1091      auto mode
  1            /usr/bin/gij-4.8                                 1048      manual mode
  2            /usr/bin/gij-5                                   1050      manual mode
  3            /usr/bin/gij-6                                   1060      manual mode
* 4            /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java   1081      manual mode
  5            /usr/lib/jvm/java-9-openjdk-amd64/bin/java       1091      manual mode

richelbilderbeek/beastscriptr documentation built on Feb. 26, 2025, 5:31 a.m.