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beastier
is an R package to run BEAST2.
beastier
is part of the babette
package suite:
beautier
creates BEAST2 input (.xml
) files.beastier
runs BEAST2mauricer
: install BEAST2 packagestracerer
pastes BEAST2 output (.log
,.trees
, etc) files.
Related R packages:
beastierinstall
: Install and uninstall BEAST2beastier_on_windows
: Verify thatbeastier
works on the Windows operating systemlumier
: Shiny app to help create the function call needed
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()
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.
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"
)
)
See install.
See FAQ
beastier
cannot do everything BEAST2
can.
- Remove: install BEAST2, use
beastierinstall
- Experimental: Continue a BEAST2 run
- Untested: Setup BEAGLE
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.
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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.