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babette demo

Richèl J.C. Bilderbeek

2024-06-24

Introduction

This vignette briefly demonstrates multiple features of babette, without going into much detail.

First, load the library:

library(babette)

This vignette shows how to:

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)

Let 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
  )
}

Plot the posterior estimates

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")
}

Show the effective sample sizes (ESS)

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.

Show the summary statistics

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)
}

Plot the posterior phylogenies

if (is_beast2_installed()) {
  plot_densitree(out$anthus_aco_sub_trees, width = 2)
}

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.