#' Converts a site model to XML,
#' used in the \code{state} section
#' @inheritParams default_params_doc
#' @return the site model as XML text
#' @author Richèl J.C. Bilderbeek
#' @export
hky_site_model_to_xml_state <- function(
site_model,
beauti_options = create_beauti_options()
) {
check_true(is_site_model(site_model))
check_beauti_options(beauti_options)
id <- site_model$id
check_true(is_id(id))
text <- NULL
check_true(is_hky_site_model(site_model))
check_true("freq_param" %in% names(site_model))
check_true("kappa_param" %in% names(site_model))
if (is_one_na(site_model$freq_param$id)) {
site_model$freq_param$id <- id
}
if (is_one_na(site_model$kappa_param$id)) {
site_model$kappa_param$id <- id
}
text <- c(
text,
parameter_to_xml(
site_model$kappa_param,
beauti_options = beauti_options
)
)
text <- c(
text,
freq_param_to_xml(
site_model$freq_param,
beauti_options = beauti_options
)
)
text <- c(
text,
gamma_site_model_to_xml_state(site_model$gamma_site_model, id)
)
text
}
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