#' Creates the XML text for the `logger` tag with ID `treelog`.
#' This section has these elements:
#' ```
#' <logger id="treelog.t:test_output_0" spec="Logger" fileName="my_treelog.trees" logEvery="345000" mode="tree" sanitiseHeaders="true" sort="smart"> # nolint indeed long
#' <log id="TreeWithMetaDataLogger.t:test_output_0" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test_output_0"/> # nolint indeed long
#' </logger>
#' ```
#' @inheritParams default_params_doc
#' @return lines of XML text
#' @author Richèl J.C. Bilderbeek
#' @export
create_treelog_xml <- function(
inference_model
) {
top_line <- paste0(
"<logger id=\"treelog.t:", inference_model$clock_model$id, "\" "
)
if (inference_model$beauti_options$beast2_version == "2.6") {
top_line <- paste0(top_line, "spec=\"Logger\" ")
}
top_line <- paste0(
top_line,
"fileName=\"", inference_model$mcmc$treelog$filename, "\" ",
"logEvery=\"", inference_model$mcmc$treelog$log_every, "\" ",
"mode=\"", inference_model$mcmc$treelog$mode, "\""
)
if (inference_model$mcmc$treelog$sanitise_headers == TRUE) {
top_line <- paste0(top_line, " sanitiseHeaders=\"true\"")
}
if (inference_model$mcmc$treelog$sort != "none") {
top_line <- paste0(
top_line,
"sort=\"", inference_model$mcmc$treelog$sort, "\""
)
}
top_line <- paste0(top_line, ">")
text <- ""
text <- c(text, top_line)
text <- c(
text,
indent(
clock_model_to_xml_treelogger(
inference_model$clock_model
)
)
)
text <- c(text, "</logger>")
text
}
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