R/create_true_alignment.R

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

#' Create the true alignment from the true/given phylogeny.
#'
#' We call this the true alignment, as it could thruthfully be found
#' in nature, when assuming the true phylogeny is the true
#' evolutionary history.
#' @inheritParams default_params_doc
#' @return an alignment of type \code{DNAbin}
#' @seealso Use \link{create_tral_file} to save the created alignment
#'   directly to a file
#' @examples
#' # Check cleanup by other functions
#' beastier::check_empty_beaustier_folders()
#'
#' # Create the ancestor's DNA sequence
#' n_base_pairs <- 4
#' root_sequence <- create_blocked_dna(length = n_base_pairs)
#'
#' # How to simulate the alignment
#' alignment_params <- create_alignment_params(
#'   root_sequence = root_sequence
#' )
#'
#' # Create a phylogeny to simulate the DNA sequences on
#' n_taxa <- 5
#' phylogeny <- ape::rcoal(n_taxa)
#'
#' # Simulate the alignment
#' alignment <- create_true_alignment(
#'    true_phylogeny = phylogeny,
#'    alignment_params = alignment_params
#'  )
#' check_alignment(alignment)
#'
#' # Cleanup
#' beastier::remove_beaustier_folders()
#' beastier::check_empty_beaustier_folders()
#' @author Richèl J.C. Bilderbeek, Giovanni Laudanno
#' @export
create_true_alignment <- function(
  true_phylogeny,
  alignment_params
) {
  beautier::check_phylogeny(true_phylogeny)
  pirouette::check_reconstructed_phylogeny(true_phylogeny)
  tryCatch(
    pirouette::check_alignment_params(alignment_params),
    error = function(e) {
      msg <- paste0(
        "'alignment_params' must be a set of alignment parameters. ",
        e$msg
      )
      stop(msg)
    }
  )

  pirouette::sim_true_alignment(
    true_phylogeny = true_phylogeny,
    alignment_params = alignment_params
  )
}