#' Collect the gamma statistics of the species trees with outgroup
#' @param filename name of the file containing the parameters and results
#' @return a data frame
#' @examples
#' filename <- find_path("toy_example_1.RDa")
#' df <- collect_file_stree_gammas(filename)
#' testit::assert(names(df) == c("sti", "gamma_stat"))
#' testit::assert(nrow(df) == 2)
#' testit::assert(!is.na(df$gamma_stat))
#' @export
#' @author Richel Bilderbeek
collect_file_stree_gammas <- function(filename) {
if (!wiritttes::is_valid_file(filename)) {
stop("invalid file")
}
file <- wiritttes::read_file(filename)
df <- NULL
for (sti in 1:2) {
phylogeny <- NA
g <- NA
tryCatch(
phylogeny <- wiritttes::get_species_tree_by_index(file = file, sti = sti),
error = function(msg) {} # nolint
)
if (class(phylogeny) == "phylo") {
g <- ape::gammaStat(phylogeny)
}
# Remove id column
this_df <- data.frame(
sti = sti,
gamma_stat = g
)
if (is.null(df)) {
df <- this_df
} else {
df <- rbind(df, this_df)
}
}
df
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.