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.
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.
Because ropensci
does not have AppVeyor.
To do check for Windows,
is created. That repo only checks the master
branch of beautier
.
What's the road map?
See road map.
Submit an Issue.
See CONTRIBUTING, at 'Submitting code'
See CONTRIBUTING, at 'Submitting bugs'
Submit an Issue. Or send an email to Richèl Bilderbeek.
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}
}
- 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
The butterfly symbolizes beauty. Then it was combined with an R logo.
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.
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](The Tidyverse Style Guide))
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.
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
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 $*
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