alignment_to_beast_posterior: Convert an alignment to a BEAST2 XML input file
In richelbilderbeek/wiritttes: WIRITTE simulation

Description Usage Arguments Value Author(s) Examples

Convert an alignment to a BEAST2 XML input file

1 2	alignment_to_beast_posterior(alignment, nspp, base_filename, crown_age = NA, rng_seed = 42, beast_jar_path = find_beast_jar_path())

`alignment`	The alignment of type DNAbin
`nspp`	The number of states in the MCMC chain BEAST2 will generate, typically one state per one thousand moves
`base_filename`	The base of the filename (the part without the extension). Must not start with '/tmp/' (in '/tmp/' the intermediate files are deleted)
`crown_age`	a positive value if the phylogeny needs a fixed crown age, NA if the crown age needs to be estimated by BEAST2
`rng_seed`	The random number generator seed used by BEAST2
`beast_jar_path`	Where the jar 'beast.jar' can be found

the phylogenies of the BEAST2 posterior

Richel Bilderbeek

  # Prepare the many filenames
  base_filename <- "alignment_to_beast_posterior_example"
  beast_log_filename <- paste0(base_filename, ".log")
  beast_trees_filename <- paste0(base_filename, ".trees")
  beast_state_filename <- paste0(base_filename, ".xml.state")

  # Simulate a random phylogeny its alignment
  alignment <- convert_phylogeny_to_alignment(
    phylogeny = ape::rcoal(5),
    sequence_length = 10,
    mutation_rate = 1
  )

  # See if the BEAST2 .jar file is present
  beast_jar_path <- find_beast_jar_path()
  testit::assert(file.exists(beast_jar_path))

  # Run BEAST2 and extract the phylogenies of its posterior
  posterior <- alignment_to_beast_posterior(
    alignment = alignment,
    nspp = 10,
    crown_age = 5,
    base_filename = base_filename,
    rng_seed = 42,
    beast_jar_path = beast_jar_path
  )

  # Check the posterior
  testit::assert(tracerer::is_posterior(posterior))
  testit::assert(tracerer::is_trees_posterior(posterior$trees))