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Examples

Richèl J.C. Bilderbeek

2024-10-25

Source: vignettes/examples.Rmd
examples.Rmd

Introduction

This vignette shows some examples how to set up different inference models in babette.

For all examples, do load babette:

All these examples check that BEAST2 is installed at the default location at /github/home/.local/share/beast/lib/launcher.jar. If this is not the case, we will use some fabricated output:

posterior <- create_test_bbt_run_output()
posterior$anthus_aco_sub_trees <- posterior$anthus_aco_trees
names(posterior)
#> [1] "estimates"            "anthus_aco_trees"     "operators"           
#> [4] "output"               "anthus_aco_sub_trees"

All examples read the alignment from a FASTA file (usually my_fasta.fas).

fasta_filename <- get_babette_path("anthus_aco_sub.fas")

Instead of a full run, the MCMC chain length is shortened to 10K states, with a measurement every 1K states:

mcmc <- create_test_mcmc(chain_length = 10000)

We will re-create this MCMC setup, as doing so initializes it with new filenames for temporary files. These temporary files should not exist before a run and should exist after a run. Sure, there is the option to overwrite…

Example #1: all default

Using all default settings, only specify a DNA alignment.

Example #1: all default
Example #1: all default
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    mcmc = mcmc
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}

All other parameters are set to their defaults, as in BEAUti.

plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Example #2: using an MRCA prior to specify a crown age

Example #2: using an MRCA prior to specify a crown age
Example #2: using an MRCA prior to specify a crown age

An alternative is to date the node of the most recent common ancestor of all taxa.

Create the MCMC:

mcmc <- create_test_mcmc(chain_length = 10000)
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    mcmc = mcmc,
    mrca_prior = create_mrca_prior(
      taxa_names = sample(get_taxa_names(fasta_filename), size = 3),
      alignment_id = get_alignment_id(fasta_filename),
      is_monophyletic = TRUE,
      mrca_distr = create_normal_distr(
        mean = 15.0,
        sigma = 0.025
      )
    )
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}

Here we use an MRCA prior with fixed (non-estimated) values of the mean and standard deviation for the common ancestor node’s time.

plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Example #3: JC69 site model

Example #3: JC69 site model
Example #3: JC69 site model
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    site_model = create_jc69_site_model(),
    mcmc = mcmc
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Example #4: Relaxed clock log normal

Example #4: Relaxed clock log normal
Example #4: Relaxed clock log normal
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    clock_model = create_rln_clock_model(),
    mcmc = mcmc
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Example #5: Birth-Death tree prior

Example #5: Birth-Death tree prior
Example #5: Birth-Death tree prior
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    tree_prior = create_bd_tree_prior(),
    mcmc = mcmc
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Example #6: Yule tree prior with a normally distributed birth rate

Example #6: Yule tree prior with a normally distributed birth rate
Example #6: Yule tree prior with a normally distributed birth rate
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = create_normal_distr(
        mean = 1.0,
        sigma = 0.1
      )
    ),
    mcmc = mcmc
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Thanks to Yacine Ben Chehida for this use case

Example #7: HKY site model with a non-zero proportion of invariants

Example #7: HKY site model with a non-zero proportion of invariants
Example #7: HKY site model with a non-zero proportion of invariants
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    site_model = create_hky_site_model(
      gamma_site_model = create_gamma_site_model(prop_invariant = 0.5)
    ),
    mcmc = mcmc
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Thanks to Yacine Ben Chehida for this use case

Example #8: Strict clock with a known clock rate

Example #8: Strict clock with a known clock rate
Example #8: Strict clock with a known clock rate
if (is_beast2_installed()) {
  inference_model <- create_inference_model(
    clock_model = create_strict_clock_model(
      clock_rate_param = 0.5
    ),
    mcmc = mcmc
  )
  beast2_options <- create_beast2_options()
  posterior <- bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
}
plot_densitree(posterior$anthus_aco_sub_trees, width = 2)

Thanks to Paul van Els and Yacine Ben Chehida for this use case.