knitr::opts_chunk$set( collapse = TRUE, comment = "" ) beautier::remove_beautier_folder() beautier::check_empty_beautier_folder()
The purpose of beautier
is to create a valid BEAST2
XML input file
from its function argument. 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 (website at https://github.com/ropensci/babette).
babette
allows to use BEAST2 (and its tools) from R.
First, beautier
is loaded:
library(beautier)
A BEAST2 XML input file needs an alignment (as BEAST2 infers
phylogenies and parameters on DNA sequences). This demonstration uses
a testing FASTA file used by beautier
:
fasta_filename <- get_beautier_path("test_output_0.fas")
We can display the alignment in the file:
image(ape::read.FASTA(fasta_filename))
Specify the filename for our XML file, here I use a temporary filename, so there is no need to clean up afterwards:
output_filename <- get_beautier_tempfilename() output_filename
Now we can create our XML file. We do not specify any inference model, and just use the BEAUti default settings:
create_beast2_input_file(
fasta_filename,
output_filename
)
The file indeed is a BEAST2 input file:
readLines(output_filename)
This XML input file can be read by BEAST2.
You can use beastier
to run BEAST2 from R, see https://github.com/ropensci/beastier.
You can use babette
to do a BEAST2 inference directly,
see https://github.com/ropensci/babette.
file.remove(output_filename) beautier::remove_beautier_folder() beautier::check_empty_beautier_folder()
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