#' Internal function
#'
#' Converts a GTR site model to XML,
#' used in the \code{prior} section
#' @inheritParams default_params_doc
#' @return the site model as XML text
#' @examples
#' gtr_site_model_to_xml_prior_distr(
#' site_model = create_gtr_site_model(
#' id = 1,
#' rate_ac_prior_distr = create_uniform_distr(id = 2),
#' rate_ag_prior_distr = create_uniform_distr(id = 3),
#' rate_at_prior_distr = create_uniform_distr(id = 4),
#' rate_cg_prior_distr = create_uniform_distr(id = 5),
#' rate_gt_prior_distr = create_uniform_distr(id = 6)
#' ),
#' beauti_options = create_beauti_options()
#' )
#' @author Richèl J.C. Bilderbeek
#' @export
gtr_site_model_to_xml_prior_distr <- function( # nolint indeed a long internal function name
site_model,
beauti_options
) {
check_true(is_gtr_site_model(site_model))
id <- site_model$id
check_true(is_id(id))
text <- NULL
if (site_model$rate_ac_param$estimate == TRUE) {
text <- c(
text,
paste0(
"<prior id=\"RateACPrior.s:", id, "\" ",
"name=\"distribution\" x=\"@rateAC.s:", id, "\">"
)
)
text <- c(
text,
indent(
distr_to_xml(
site_model$rate_ac_prior_distr,
beauti_options = beauti_options
)
)
)
text <- c(text, paste0("</prior>"))
}
if (site_model$rate_ag_param$estimate == TRUE) {
text <- c(
text,
paste0(
"<prior id=\"RateAGPrior.s:", id, "\" ",
"name=\"distribution\" x=\"@rateAG.s:", id, "\">"
)
)
text <- c(
text,
indent(
distr_to_xml(
site_model$rate_ag_prior_distr,
beauti_options = beauti_options
)
)
)
text <- c(text, paste0("</prior>"))
}
if (site_model$rate_at_param$estimate == TRUE) {
text <- c(
text,
paste0(
"<prior id=\"RateATPrior.s:", id, "\" ",
"name=\"distribution\" x=\"@rateAT.s:", id, "\">"
)
)
text <- c(
text,
indent(
distr_to_xml(
site_model$rate_at_prior_distr,
beauti_options = beauti_options
)
)
)
text <- c(text, paste0("</prior>"))
}
if (site_model$rate_cg_param$estimate == TRUE) {
text <- c(
text,
paste0(
"<prior id=\"RateCGPrior.s:", id, "\" ",
"name=\"distribution\" x=\"@rateCG.s:", id, "\">"
)
)
text <- c(
text,
indent(
distr_to_xml(
site_model$rate_cg_prior_distr,
beauti_options = beauti_options
)
)
)
text <- c(text, paste0("</prior>"))
}
if (site_model$rate_gt_param$estimate == TRUE) {
text <- c(
text,
paste0(
"<prior id=\"RateGTPrior.s:", id, "\" ",
"name=\"distribution\" x=\"@rateGT.s:", id, "\">"
)
)
text <- c(
text,
indent(
distr_to_xml(
site_model$rate_gt_prior_distr,
beauti_options = beauti_options
)
)
)
text <- c(text, paste0("</prior>"))
}
text
}
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