alignment_to_beast_input_file: Convert an alignment and parameters to a BEAST XML input file
In richelbilderbeek/wiritttes: WIRITTE simulation

Description Usage Arguments Value Author(s) Examples

Convert an alignment and parameters to a BEAST XML input file

1 2	alignment_to_beast_input_file(alignment, nspp, rng_seed = 42, beast_filename, temp_fasta_filename, crown_age = NA)

`alignment`	the DNA alignment of type DNAbin
`nspp`	the number of states in a BEAST2 MCMC chain, typically there is one state per one thousand generations
`rng_seed`	random number generator seed
`beast_filename`	the filename of the XML BEAST2 input file created
`temp_fasta_filename`	the name of a temporary file created
`crown_age`	a postive value should the crown age be fixed at that value, NA if BEAST2 needs to estimate it

Nothing, creates a file called 'beast_filename'

Richel Bilderbeek

  # Simulate a phylogeny
  phylogeny <- ape::rcoal(n = 5)

  # Simulate an alignment from that phylogeny
  alignment <- convert_phylogeny_to_alignment(
    phylogeny = phylogeny,
    sequence_length = 10
  )

  # Create a BEAST2 input file
  beast_xml_input_file <- "alignment_to_beast_input_file_example.xml"
  fasta_filename <- "alignment_to_beast_input_file_examp.fasta"
  alignment_to_beast_input_file(
    alignment = alignment,
    nspp = 10,
    rng_seed = 42,
    beast_filename = beast_xml_input_file,
    temp_fasta_filename = fasta_filename,
    crown_age = NA
  )

  # Check that the BEAST2 input file really exists
  testit::assert(file.exists(beast_xml_input_file))