babette: Step by Step
Richèl J.C. Bilderbeek
2024-09-25
Source:vignettes/step_by_step.Rmd
step_by_step.Rmd
Introduction
This step-by-step demo shows how to run the babette
pipeline in detail.
First, load babette
:
In all cases, this is done for a short MCMC chain length of 10K:
inference_model <- create_inference_model()
inference_model$mcmc$chain_length <- 10000
inference_model$mcmc$tracelog$filename <- normalizePath(
get_beautier_tempfilename(
pattern = "tracelog_", fileext = ".log"
),
mustWork = FALSE
)
inference_model$mcmc$treelog$filename <- normalizePath(
get_beautier_tempfilename(
pattern = "treelog_",
fileext = ".trees"
),
mustWork = FALSE
)
Create a ‘BEAST2’ input file
This step is commonly done using BEAUti. With babette
,
this can be done as follows:
beast2_input_file <- tempfile(pattern = "beast2_", fileext = ".xml")
create_beast2_input_file_from_model(
input_filename = get_babette_path("anthus_aco.fas"),
inference_model = inference_model,
output_filename = beast2_input_file
)
Display (part of) the ‘BEAST2’ input file
print(head(readLines(beast2_input_file)))
#> [1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><beast beautitemplate='Standard' beautistatus='' namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" required=\"\" version=\"2.4\">"
#> [2] ""
#> [3] ""
#> [4] " <data"
#> [5] "id=\"anthus_aco\""
#> [6] "name=\"alignment\">"
This file can both be loaded by BEAUti and be used by ‘BEAST2’.
The file can be checked if it is indeed a valid input file:
if (is_beast2_installed()) {
is_beast2_input_file(beast2_input_file)
}
Run MCMC
This step is commonly done using ‘BEAST2’ from the command-line or
using its GUI. With babette
, this can be done as
follows:
if (is_beast2_installed()) {
beast2_options <- create_beast2_options(
input_filename = beast2_input_file
)
beastier::check_can_create_file(beast2_options$output_state_filename)
beastier::check_can_create_treelog_file(beast2_options)
run_beast2_from_options(
beast2_options = beast2_options
)
if (!file.exists(beast2_options$output_state_filename)) {
stop("the filename should have been created.")
}
}
Display (part of) the ‘BEAST2’ output files
The .log
file contains the model parameters and
parameter estimates:
if (is_beast2_installed()) {
print(head(readLines(inference_model$mcmc$tracelog$filename)))
print(tail(readLines(inference_model$mcmc$tracelog$filename)))
}
The .trees
file contains the alignment, taxa and
posterior trees:
if (is_beast2_installed()) {
print(head(readLines(inference_model$mcmc$treelog$filename)))
print(tail(readLines(inference_model$mcmc$treelog$filename)))
}
The .xml.state
file contains the final state of the MCMC
run and the MCMC operator acceptances thus far:
Parse output
This step is commonly done using Tracer. With babette
,
this can be done as follows.
Parsing .log
file to obtain the parameter estimates:
if (is_beast2_installed()) {
knitr::kable(
head(parse_beast_tracelog_file(inference_model$mcmc$tracelog$filename))
)
}
Parsing .trees
file to obtain the posterior
phylogenies:
if (is_beast2_installed()) {
plot_densitree(parse_beast_trees(inference_model$mcmc$treelog$filename))
}
Parsing .xml.state
file to obtain the MCMC operator
acceptances:
if (is_beast2_installed()) {
knitr::kable(
head(parse_beast_state_operators(beast2_options$output_state_filename))
)
}