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master
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develop
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beautier
is BEAUti
for R.
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 :warning: experimental :warning:beastier
runs BEAST2tracerer
pastes BEAST2 output (.log
, .trees
, etc) files.mauricer
install BEAST2 packagesRelated R packages:
beautier_on_windows
: verifies
beautier
builds on Windowslumier
: Shiny app to help create the function call neededSee examples.
beautier
can be installed:
master
branchdevelop
branchFor the latest CRAN version:
install.packages("beautier")
master
branchFor the latest stable version:
remotes::install_github("ropensci/beautier")
develop
branchFor the bleeding-edge version:
remotes::install_github("ropensci/beautier", ref = "develop")
See FAQ.
This works, and the interface is unlikely to change.
This works partially, and the interface may change as well.
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.
beautier
cannot do everything BEAUti
can.
Here are some missing or (yet) unsupported features, some are linked to an Issue:
BEAUti
)See CONTRIBUTING, at Submitting use cases
See CONTRIBUTING, at 'Submitting code'
See CONTRIBUTING, at 'Submitting bugs'
Sure, just add an Issue. Or send an email.
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.
Article about babette
:
babette
: BEAUti 2, BEAST 2 and Tracer for R." Methods in Ecology and Evolution (2018). https://doi.org/10.1111/2041-210X.13032FASTA files anthus_aco.fas
and anthus_nd2.fas
from:
FASTA file G_VII_pre2003_msa.fas
from:
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