#' @title Refreshes the phylogenetic tree dataset
#'
#' @description Internal utility function for refreshing the combined_trees
#' dataset (not exported) This function rapidly updates the combined_trees.rda
#' file once one updates the .tre files.
#'
#' @param data A character vector file containing names of the *.tre files to be
#' combined.
#'
#' @param sample an integer defining the number of trees to create. Passed to
#' mulTree::tree.bind
#'
#' @param root.age a numeric value used to join two trees. Passed to
#' mulTree::tree.bind
#'
#' @return Saves the updated file to ../data/combined_trees.rda for use within
#' the package
#'
#' @author Thomas Guillerme
#'
refresh.combined_tree <- function(data = c("3firstFritzTrees.tre",
"3firstJetzTrees.tre"),
sample = 2,
root.age = 250) {
#Load the two trees (mammals and birds)
mammal_trees <- ape::read.tree(system.file("extdata",
data[1], package = "SIDER"))
bird_trees <- ape::read.tree(system.file("extdata",
data[2], package = "SIDER"))
#Combining the trees
combined_trees <- mulTree::tree.bind(x = mammal_trees,
y = bird_trees,
sample = sample,
root.age = root.age)
#Saving the tree
save(combined_trees, file = "../data/combined_trees.rda", compress = 'xz')
# output notes to screen
cat("combined_trees.rda file successfully updated.\n
Don't forget to update the man page in
\\man\\SIDER.R if necessary.")
}
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