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#' Internal function.
#'
#' Internal function to create the \code{branchRateModel} section
#' of the XML as text, for a strict clock model
#' @inheritParams default_params_doc
#' @return a character vector of XML strings
#' @author Richèl J.C. Bilderbeek
#' @export
create_strict_clock_branch_rate_model_xml <- function(# nolint long function name, which is fine for a long function
inference_model
) {
check_true(
is_strict_clock_model(inference_model$clock_model)
)
id <- inference_model$clock_model$id
has_tipdates_filename <- !is_one_na(
inference_model$tipdates_filename
)
has_mrca_prior <- !is_one_na(inference_model$mrca_prior)
has_mrca_prior_distr <- NA
if (has_mrca_prior) {
has_mrca_prior_distr <- is_one_na(
inference_model$mrca_prior$mrca_distr
)
}
do_estimate_clock_rate <- inference_model$clock_model$clock_rate_param$estimate == TRUE # nolint indeed a long line
if (
(!has_tipdates_filename && !has_mrca_prior && !do_estimate_clock_rate) ||
(!has_tipdates_filename && has_mrca_prior && has_mrca_prior_distr &&
!do_estimate_clock_rate
)
) {
xml_begin <- paste0(
"<branchRateModel id=\"StrictClock.c:", id, "\" ",
"spec=\"beast.evolution.branchratemodel.StrictClockModel\">"
)
# initialization may happen here
inference_model$clock_model$clock_rate_param$id <- id
xml_param <- parameter_to_xml(
parameter = inference_model$clock_model$clock_rate_param,
beauti_options = inference_model$beauti_options
)
xml_end <- "</branchRateModel>"
# Layout
c(xml_begin, indent(xml_param), xml_end)
} else {
paste0(
"<branchRateModel id=\"StrictClock.c:", id, "\" ",
"spec=\"beast.evolution.branchratemodel.StrictClockModel\" ",
"clock.rate=\"@clockRate.c:", id, "\"/>" # nolint this is no absolute path
)
}
}
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