#' Collects the nLTTs of all phylogenies belonging to a
#' parameter file in the melted/uncast/long form
#'
#' @param filename name of the parameter file
#' @param dt the resolution of the nLTT plot,
#' must be in range <0,1>, default is 0.001
#' @return A dataframe of gamma statistics of each phylogeny in time
#' @examples
#' dt <- 0.1
#' filename <- find_path("toy_example_3.RDa")
#' df <- collect_file_nltts(filename)
#' testit::assert(names(df) == c("species_tree_nltts", "posterior_nltts"))
#' testit::assert(names(df$species_tree_nltts)
#' == c("sti", "t", "nltt")
#' )
#' testit::assert(nrow(df$species_tree_nltts) > 2)
#' testit::assert(nrow(df$posterior_nltts) == 80)
#' @export
collect_file_nltts <- function(filename, dt = 0.001) {
if (length(filename) != 1) {
stop(
"there must be exactly one filename supplied"
)
}
if (!wiritttes::is_valid_file(filename = filename)) {
stop(
"invalid file '", filename, "'"
)
}
species_tree_nltts <- wiritttea::collect_file_stree_nltts(
filename = filename, dt = dt
)
posterior_nltts <- wiritttea::collect_file_posterior_nltts(
filename = filename
)
return(
list(
species_tree_nltts = species_tree_nltts,
posterior_nltts = posterior_nltts
)
)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.