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#' Create a BEAST2 input file
#' @inheritParams default_params_doc
#' @return nothing
#' @examples
#' if (is_on_ci()) {
#'
#' check_empty_beautier_folder()
#'
#' # Get an example FASTA file
#' input_filename <- get_fasta_filename()
#'
#' # The file created by beautier, a BEAST2 input file
#' output_filename <- get_beautier_tempfilename()
#'
#' create_beast2_input_file(
#' input_filename,
#' output_filename
#' )
#' file.remove(output_filename)
#'
#' remove_beautier_folder()
#' check_empty_beautier_folder()
#' }
#' @author Richèl J.C. Bilderbeek
#' @seealso
#' Use \link{create_beast2_input_file_from_model} to do the same with an
#' inference model.
#' See \code{\link{create_site_model}} for examples with
#' different site models. See \code{\link{create_clock_model}} for examples
#' with clock models. See \code{\link{create_tree_prior}} for examples with
#' different tree priors. See \code{\link{create_mcmc}} for examples with
#' a different MCMC setup.
#' @export
create_beast2_input_file <- function(
input_filename,
output_filename,
site_model = create_jc69_site_model(),
clock_model = create_strict_clock_model(),
tree_prior = create_yule_tree_prior(),
mrca_prior = NA,
mcmc = create_mcmc(),
beauti_options = create_beauti_options(),
tipdates_filename = NA
) {
inference_model <- create_inference_model(
site_model = site_model,
clock_model = clock_model,
tree_prior = tree_prior,
mrca_prior = mrca_prior,
mcmc = mcmc,
beauti_options = beauti_options,
tipdates_filename = tipdates_filename
)
create_beast2_input_file_from_model(
input_filename = input_filename,
output_filename = output_filename,
inference_model = inference_model
)
invisible()
}
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