#' Creates the \code{init} section of a BEAST2 XML parameter file
#' @inheritParams default_params_doc
#' @return lines of XML text
#' @author Richèl J.C. Bilderbeek
#' @examples
#' check_empty_beautier_folder()
#'
#' inference_model <- init_inference_model(
#' input_filename = get_fasta_filename(),
#' inference_model = create_test_inference_model()
#' )
#' xml <- create_beast2_input_init(
#' inference_model = inference_model
#' )
#'
#' check_empty_beautier_folder()
#' @export
create_beast2_input_init <- function(
inference_model
) {
# Do not be smart yet
ids <- inference_model$site_model$id
check_true(length(ids) == 1)
check_true(are_ids(ids))
text <- NULL
# From https://www.beast2.org/fix-starting-tree/:
#
# if there is an initaliser generated by BEAUti of the form
#
# <init estimate="false" id="RandomTree.t:xxx" initial="@Tree.t:xxx"
# spec="beast.evolution.tree.RandomTree" taxa="@xxx">
# </init>
#
# remove this element from the file, otherwise the tree will be Newick tree
# will be overwritten by a random tree.
#
# In other words: bluntly remove it
n <- length(ids)
for (i in seq(1, n)) {
text <- c(text, "")
text <- c(
text,
indent(rnd_phylo_to_xml_init(inference_model))
)
}
text
}
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