#' See if a file its two species trees have different branch lengths
#' @param file The file, as read from wiritttes::read_file
#' @return TRUE if the two species have different branch lengths, else FALSE
#' # Create a parameter file
#' filename <- "add_species_trees_example.RDa"
#' save_parameters_to_file(
#' rng_seed = 42,
#' sirg = 0.5,
#' siri = 0.5,
#' scr = 0.5,
#' erg = 0.5,
#' eri = 0.5,
#' age = 5,
#' mutation_rate = 0.1,
#' n_alignments = 1,
#' sequence_length = 10,
#' nspp = 10,
#' n_beast_runs = 1,
#' filename = filename
#' )
#'
#' # Simulate an incipient species tree
#' add_pbd_output(filename)
#'
#' # Add the species trees
#' add_species_trees(filename = filename)
#' testit::assert(has_species_trees(read_file(filename)))
#'
#' testit::assert(have_same_strees(read_file(filename)))
#'
#' @author Richel Bilderbeek
#' @export
have_same_strees <- function(file) {
if (!wiritttes::has_species_trees(file)) {
stop("File lacks species trees. ",
"These can be added by running wiritttes::add_species_trees")
}
brts_1 <- sort(ape::branching.times(
wiritttes::get_species_tree_youngest(file)))
brts_2 <- sort(
ape::branching.times(wiritttes::get_species_tree_oldest(file)))
return(identical(brts_1, brts_2))
}
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