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#' Convert a CCP tree prior
#' to the XML as part of the \code{state} section
#' @inheritParams default_params_doc
#' @return XML as text
#' @examples
#' check_empty_beautier_folder()
#'
#' # Need an ID and inital value
#' inference_model <- create_inference_model(
#' tree_prior = create_ccp_tree_prior(
#' id = "anthus_nd2_sub",
#' pop_size_distr = create_normal_distr(
#' id = 123,
#' value = 3.14
#' )
#' )
#' )
#'
#' ccp_tree_prior_to_xml_state(inference_model)
#'
#' check_empty_beautier_folder()
#' @export
ccp_tree_prior_to_xml_state <- function(
inference_model
) {
# Do not be smart yet
tree_prior <- inference_model$tree_prior
check_true(is_id(tree_prior$id))
parameter_xml <- paste0(
"<parameter id=\"popSize.t:", tree_prior$id, "\" "
)
if (inference_model$beauti_options$beast2_version == "2.6") {
parameter_xml <- paste0(
parameter_xml, "spec=\"parameter.RealParameter\" "
)
}
if (!is.na(tree_prior$pop_size_distr$lower)) {
parameter_xml <- paste0(
parameter_xml,
paste0("lower=\"", tree_prior$pop_size_distr$lower, "\" ")
)
}
parameter_xml <- paste0(
parameter_xml,
"name=\"stateNode\""
)
if (!is.na(tree_prior$pop_size_distr$upper)) {
parameter_xml <- paste0(
parameter_xml,
" upper=\"", tree_prior$pop_size_distr$upper, "\""
)
}
parameter_xml <- paste0(
parameter_xml,
">",
tree_prior$pop_size_distr$value,
"</parameter>"
)
parameter_xml
}
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