#' Get output log filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_output_log_filename <- function(
folder_name,
model_type
) {
pirouette::check_model_type(model_type)
if (model_type == "generative") {
output_log_filename <- file.path(folder_name, "mbd_gen.log")
}
if (model_type == "candidate") {
output_log_filename <- file.path(folder_name, "mbd_best.log")
}
output_log_filename
}
#' Get output trees filenames
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_output_trees_filenames <- function(
folder_name,
model_type
) {
pirouette::check_model_type(model_type)
if (model_type == "generative") {
output_trees_filenames <- file.path(folder_name, "mbd_gen.trees")
}
if (model_type == "candidate") {
output_trees_filenames <- file.path(folder_name, "mbd_best.trees")
}
output_trees_filenames
}
#' Get input filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_input_filename <- function(
folder_name,
model_type
) {
pirouette::check_model_type(model_type)
if (model_type == "generative") {
input_filename <- file.path(folder_name, "mbd_gen.xml")
}
if (model_type == "candidate") {
input_filename <- file.path(folder_name, "mbd_best.xml")
}
input_filename
}
#' Get output state filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_output_state_filename <- function(
folder_name,
model_type
) {
pirouette::check_model_type(model_type)
if (model_type == "generative") {
output_state_filename <- file.path(folder_name, "mbd_gen.xml.state")
}
if (model_type == "candidate") {
output_state_filename <- file.path(folder_name, "mbd_best.xml.state")
}
output_state_filename
}
#' Get errors filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_errors_filename <- function(
folder_name,
model_type
) {
pirouette::check_model_type(model_type)
if (model_type == "generative") {
errors_filename <- file.path(folder_name, "mbd_nltts_gen.csv")
}
if (model_type == "candidate") {
errors_filename <- file.path(folder_name, "mbd_nltts_best.csv")
}
errors_filename
}
#' Get treelog filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_treelog_filename <- function(
folder_name,
model_type
) {
pirouette::check_model_type(model_type)
if (model_type == "generative") {
treelog_filename <- file.path(folder_name, "mbd_gen.trees")
}
if (model_type == "candidate") {
treelog_filename <- file.path(folder_name, "mbd_best.trees")
}
treelog_filename
}
#' Get tracelog filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_tracelog_filename <- function(
folder_name,
model_type
) {
pirouette::check_model_type(model_type)
if (model_type == "generative") {
tracelog_filename <- file.path(folder_name, "mbd_gen.log")
}
if (model_type == "candidate") {
tracelog_filename <- file.path(folder_name, "mbd_best.log")
}
tracelog_filename
}
#' Get evidence filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_evidence_filename <- function(
folder_name,
tree_type
) {
pirouette::check_tree_type(tree_type)
if (tree_type == "true") {
evidence_filename <- file.path(folder_name, "mbd_marg_lik.csv")
}
if (tree_type == "twin") {
evidence_filename <- file.path(folder_name, "mbd_marg_lik_twin.csv")
}
evidence_filename
}
#' Get alignment filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_alignment_filename <- function(
folder_name,
tree_type
) {
pirouette::check_tree_type(tree_type)
if (tree_type == "true") {
fasta_filename <- file.path(folder_name, "mbd.fasta")
}
if (tree_type == "twin") {
fasta_filename <- file.path(folder_name, "mbd_twin.fasta")
}
fasta_filename
}
#' Get tree filename
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno, Richèl J.C. Bilderbeek
#' @examples
#' get_tree_filename(folder_name = "", tree_type = "true")
#' get_tree_filename(folder_name = "", tree_type = "twin")
#' @export
get_tree_filename <- function(
folder_name,
tree_type
) {
pirouette::check_tree_type(tree_type)
if (tree_type == "true") {
tree_filename <- file.path(folder_name, "mbd.tree")
}
if (tree_type == "twin") {
tree_filename <- file.path(folder_name, "mbd_twin.tree")
}
tree_filename
}
#' Get seed folder name
#' @inheritParams default_params_doc
#' @author Giovanni Laudanno
#' @export
get_seed_folder_name <- function(
project_folder_name,
mbd_params
) {
data_folder_name <- "data"
parsettings_name <- paste0(
mbd_params$lambda,
"-",
mbd_params$mu,
"-",
mbd_params$nu,
"-",
mbd_params$q
)
seed <- mbd_params$seed
seed_folder_name <- file.path(
project_folder_name,
data_folder_name,
parsettings_name,
seed
)
seed_folder_name
}
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