## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## -----------------------------------------------------------------------------
library(mcbette)
## -----------------------------------------------------------------------------
if (rappdirs::app_dir()$os == "win") {
message("'mcbette' can only run on Linux and MacOS")
} else if (!beastier::is_beast2_installed()) {
message(
"BEAST2 must be installed. ",
"Tip: use 'beastierinstall::install_beast2()'"
)
} else if (!mauricer::is_beast2_ns_pkg_installed()) {
message(
"The BEAST2 'NS' package must be installed. ",
"Tip: use 'mauricerinstall::install_beast2_pkg(\"NS\")'"
)
}
## -----------------------------------------------------------------------------
fasta_filename <- system.file("extdata", "primates.fas", package = "mcbette")
## -----------------------------------------------------------------------------
alignment <- ape::read.FASTA(fasta_filename)
image(alignment)
## -----------------------------------------------------------------------------
inference_model_1 <- beautier::create_ns_inference_model()
inference_model_1$site_model$name
## -----------------------------------------------------------------------------
if (can_run_mcbette()) {
# Create the two inference models
inference_model_1 <- beautier::create_ns_inference_model(
site_model = beautier::create_jc69_site_model()
)
inference_model_2 <- beautier::create_ns_inference_model(
site_model = beautier::create_gtr_site_model()
)
# Shorten the run, by doing a short (dirty, unreliable) MCMC
inference_model_1$mcmc <- beautier::create_test_ns_mcmc()
inference_model_2$mcmc <- beautier::create_test_ns_mcmc()
# Combine the two inference models
inference_models <- c(list(inference_model_1), list(inference_model_2))
# Compare the the two inference models
marg_liks <- est_marg_liks(
fasta_filename = fasta_filename,
inference_models = inference_models
)
knitr::kable(marg_liks)
}
## -----------------------------------------------------------------------------
if (can_run_mcbette()) {
interpret_marg_lik_estimates(marg_liks)
}
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