Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----check_empty_cache_at_start, include = FALSE------------------------------
# This is only needed to pass the CRAN Windows build.
#
# This vignette is tested to clean up nicely on GitHub Actions
# and r-hub on Windows
#
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
## ----load_babette, results='hide', warning=FALSE, error=FALSE, message=FALSE----
library(babette)
## -----------------------------------------------------------------------------
inference_model <- create_test_inference_model()
## -----------------------------------------------------------------------------
beast2_options <- create_beast2_options(verbose = TRUE)
## -----------------------------------------------------------------------------
if (is_beast2_installed()) {
out <- bbt_run_from_model(
fasta_filename = get_babette_path("anthus_aco_sub.fas"),
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## -----------------------------------------------------------------------------
if (is_beast2_installed()) {
library(ggplot2)
p <- ggplot(
data = out$estimates,
aes(x = Sample)
)
p + geom_line(aes(y = TreeHeight), color = "green")
p + geom_line(aes(y = YuleModel), color = "red")
p + geom_line(aes(y = birthRate), color = "blue")
}
## -----------------------------------------------------------------------------
if (is_beast2_installed()) {
traces <- remove_burn_ins(
traces = out$estimates,
burn_in_fraction = 0.2
)
esses <- t(
calc_esses(
traces,
sample_interval = inference_model$mcmc$tracelog$log_every
)
)
colnames(esses) <- "ESS"
knitr::kable(esses)
}
## -----------------------------------------------------------------------------
if (is_beast2_installed()) {
sum_stats <- t(
calc_summary_stats(
traces$posterior,
sample_interval = inference_model$mcmc$tracelog$log_every
)
)
colnames(sum_stats) <- "Statistic"
knitr::kable(sum_stats)
}
## ----fig.width=7, fig.height=7------------------------------------------------
if (is_beast2_installed()) {
plot_densitree(out$anthus_aco_sub_trees, width = 2)
}
## ----check_empty_cache_at_end, include = FALSE--------------------------------
# This is only needed to pass the CRAN Windows build.
#
# This vignette is tested to clean up nicely on GitHub Actions
# and r-hub on Windows
#
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
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