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#' Creates the XML text for the \code{distribution} tag
#' with the \code{treeLikelihood} ID,
#' of a BEAST2 parameter file.
#'
#' Creates the XML text for the \code{distribution} tag
#' with the \code{treeLikelihood} ID,
#' of a BEAST2 parameter file,
#' in an unindented form
#'
#' The \code{distribution} tag (with ID equals \code{treeLikelihood})
#' has these elements:
#'
#' \preformatted{
#' <distribution id="treeLikelihood"[...]>
#' <siteModel[...]>
#' [...]
#' </siteModel>
#' <branchRateModel[...]>
#' [...]
#' </branchRateModel>
#' </distribution>
#' }
#'
#' The \code{siteModel} section
#' is created by \link{create_site_model_xml}.
#' The \code{branchRateModel} section
#' is created by \link{create_branch_rate_model_xml}.
#'
#' Zooming out:
#'
#' \preformatted{
#' <beast[...]>
#' <run[...]>
#' <distribution id="posterior"[...]>
#' <distribution id="likelihood"[...]>
#' [this section]
#' </distribution>
#' </distribution>
#' </run>
#' </beast>
#' }
#'
#' @inheritParams default_params_doc
#' @return lines of XML text
#' @note this function is not intended for regular use, thus its
#' long name length is accepted
#' @author Richèl J.C. Bilderbeek
#' @seealso this function is called by \code{create_beast2_input_distr},
#' together with \code{create_beast2_input_distr_prior}
#' @export
create_tree_likelihood_distr_xml <- function(# nolint long function name indeed
inference_model
) {
text <- NULL
id <- inference_model$site_model$id
brm_line <- ""
text <- c(
text,
paste0(
"<distribution id=\"treeLikelihood.",
id, "\" spec=\"ThreadedTreeLikelihood\" ",
brm_line,
"data=\"@", id,
"\" tree=\"@Tree.t:", id, "\">"
)
)
# Create the '<siteModel' XML section
text <- c(text,
indent(
create_site_model_xml(
inference_model = inference_model
)
)
)
# Create the '<branchRateModel' XML section
text <- c(text,
indent(
create_branch_rate_model_xml(
inference_model = inference_model
)
)
)
# Close of '<distribution id="treeLikelihood.test_output_0"...'
text <- c(text, "</distribution>")
text
}
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