R/tree.roguetaxa.R

In cromanpa94/phruta: Phylogenetic Reconstruction and Time-dating

#' RogueNaRok within phruta
#'
#' Implements the RogueNaRok algorithm for rogue taxon identification
#' within phruta
#'
#' @param folder Name of the folder where the sequences to align are
#'               stored (character).
#' @param ... Arguments passed to \code{"Rogue::RogueTaxa"}.
#'
#' @importFrom Rogue RogueTaxa
#' @importFrom ape read.tree
#' @importFrom utils write.csv
#'
#' @return None
#'
#' @examples
#' \dontrun{
#' sq.retrieve.direct(
#'   clades = c("Felis", "Vulpes", "Phoca"),
#'   species = "Manis_pentadactyla",
#'   genes = c("ADORA3", "CYTB")
#' )
#' sq.curate(
#'   filterTaxonomicCriteria = "Felis|Vulpes|Phoca|Manis",
#'   kingdom = "animals", folder = "0.Sequences"
#' )
#' sq.aln(folder = "1.CuratedSequences")
#' tree.raxml(
#'   folder = "2.Alignments", FilePatterns = "Masked",
#'   raxml_exec = "raxmlHPC", Bootstrap = 100,
#'   outgroup = "Manis_pentadactyla"
#' )
#' tree.roguetaxa(folder = "3.Phylogeny")
#' }
#' @export

tree.roguetaxa <- function(folder = "3.Phylogeny", ...) {

  ##Over-writing?
  if( !isTRUE(pkg.env$.testMode) ) {
    UI <- readline(paste0("This function might overwrite ",
                          "3.1.RogueTaxa", ". Are you sure you want to continue? (y/n)  "))
    if(UI != 'y') stop('Exiting since you did not press y')
  }


  trees <- read.tree(paste0(folder, "/RAxML_bootstrap.phruta"))
  BestTree <- read.tree(paste0(folder, "/RAxML_bipartitions.phruta"))
  RT <- RogueTaxa(trees, bestTree = BestTree, ...)
  unlink("3.1.RogueTaxa", recursive = TRUE)
  dir.create("3.1.RogueTaxa")
  write.csv(RT, "3.1.RogueTaxa/RogueTaxa.csv")
}