get_posterior_tree: Extract a BEAST2 posterior tree from a file
In richelbilderbeek/wiritttes: WIRITTE simulation

Description Usage Arguments Value Author(s) Examples

Extract a BEAST2 posterior tree from a file

1	get_posterior_tree(file, sti, ai, pi, si)

`file`	A loaded parameter file
`sti`	the species tree index, a value from 1 to and including 2
`ai`	the alignment index, the ai-th alignment of that species tree, a value from 1 to and including the number of alignments per species tree
`pi`	the posterior index, the pi-th posterior of that alignment, a value from 1 to and including the number of posteriors per alignment
`si`	the posterior state index, the si-th state in the posterior, a value from 1 to and including the number of posterior states per posterior

the posterior

Richel Bilderbeek

  # Read a file with one or more posteriors
  file <- read_file(find_path("toy_example_1.RDa"))
  # Pick the indices of the posterior to extract
  sti  <- 1 # Species tree index
  ai   <- 1 # Alignment index
  pi   <- 1 # Posterior index
  si   <- 1 # Posterior state index
  # Extract the posterior
  tree <- get_posterior_tree(file = file, sti = sti, ai = 1, pi = 1, si = 1)
  # Check that it is indeed a phylogeny
  testit::assert(ribir::is_phylogeny(tree))