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#' Internal function
#'
#' Internal function to converts a strict clock model
#' to the \code{prior} section of the XML as text
#' @inheritParams default_params_doc
#' @return a character vector of XML strings
#' @author Richèl J.C. Bilderbeek
#' @examples
#' check_empty_beautier_folder()
#' # <distribution id="posterior" spec="util.CompoundDistribution">
#' # <distribution id="prior" spec="util.CompoundDistribution">
#' # HERE, where the ID of the distribution is 'prior'
#' # </distribution>
#' # <distribution id="likelihood" ...>
#' # </distribution>
#' # </distribution>
#' strict_clock_model_to_xml_prior_distr(
#' inference_model = create_inference_model()
#' )
#' check_empty_beautier_folder()
#' @export
strict_clock_model_to_xml_prior_distr <- function( # nolint indeed a long internal function name
inference_model
) {
check_true(is_strict_clock_model(inference_model$clock_model))
text <- NULL
if (inference_model$clock_model$clock_rate_param$estimate == TRUE) {
clock_model <- inference_model$clock_model
# No idea why BEAUti does this, see issue_135 files
if (is_one_double(clock_model$clock_rate_distr$upper)) {
clock_model$clock_rate_distr$upper <- Inf
}
check_true(is_id(clock_model$id))
check_true(is_id(clock_model$clock_rate_distr$id))
opening_tag <- paste0(
"<prior id=\"ClockPrior.c:", clock_model$id, "\" ",
"name=\"distribution\" ",
"x=\"@clockRate.c:", clock_model$id, "\">"
)
distr_xml <- distr_to_xml(
clock_model$clock_rate_distr,
beauti_options = inference_model$beauti_options
)
closing_tag <- "</prior>"
text <- c(
text,
opening_tag,
indent(distr_xml),
closing_tag
)
}
if (!is_one_na(inference_model$tipdates_filename)) {
clock_model <- inference_model$clock_model
id <- clock_model$id
check_true(is_id(id))
text <- c(
text,
paste0(
"<prior id=\"ClockPrior.c:", id, "\" ",
"name=\"distribution\" x=\"@clockRate.c:", id, "\">"
)
)
text <- c(text,
indent(
distr_to_xml(
clock_model$clock_rate_distr,
beauti_options = inference_model$beauti_options
)
)
)
text <- c(text, paste0("</prior>"))
}
text
}
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