knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
# This is only needed to pass the CRAN Windows build. # # This vignette is tested to clean up nicely on GitHub Actions # and r-hub on Windows # beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()
This vignette briefly demonstrates multiple features of babette
,
without going into much detail.
First, load the library:
library(babette)
This vignette shows how to:
babette
run 'BEAST2'In all cases, this is done for a short MCMC chain length of 10K:
inference_model <- create_test_inference_model()
Also, in all cases, we use the same BEAST2 options:
beast2_options <- create_beast2_options(verbose = TRUE)
babette
run 'BEAST2'For an alignment, we'll use a babette
example alignment.
if (is_beast2_installed()) { out <- bbt_run_from_model( fasta_filename = get_babette_path("anthus_aco_sub.fas"), inference_model = inference_model, beast2_options = beast2_options ) bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) }
if (is_beast2_installed()) { library(ggplot2) p <- ggplot( data = out$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") }
Effective sample sizes, with 20% burn-in removed:
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) }
For a reliable inference, use an ESS of at least 200.
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) }
if (is_beast2_installed()) { plot_densitree(out$anthus_aco_sub_trees, width = 2) }
# 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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