#' Create a BEAST2 XML input text
#' @inheritParams default_params_doc
#' @return a character vector of XML strings
#' @seealso
#' Use \link{create_beast2_input_from_model} to create the BEAST2 XML
#' input text from an inference model
#' Use \link{create_beast2_input_file} to also save it to file.
#' @examples
#' if (is_on_ci()) {
#' create_beast2_input(
#' input_filename = get_fasta_filename()
#' )
#' }
#' @seealso \code{\link{create_beast2_input_file}} shows more examples
#' @author Richèl J.C. Bilderbeek
#' @export
create_beast2_input <- function(
input_filename,
tipdates_filename = NA,
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()
) {
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_from_model(
input_filename = input_filename,
inference_model = inference_model
)
}
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