R/parse.slide.clades.R

In danlwarren/RWTY: R We There Yet? Visualizing MCMC Convergence in Phylogenetics

#' Rename clades for easy recall
#'
#' Converts a list of clades (e.g., "1 2 3 4" as a clade) and
#' returns a list of parsed clades, converting numbers to names using a set of trees.
#' Called internally by the slide and cumulative analyses, not user-facing.
#'
#' @param clades A list of clades, as in the first column of a cladetable in an rwty.slide or rwty.cumulative object.
#' @param treelist A list of trees, used for getting tip names.
#'
#' @return output A list of clades with parsed tip names


parse.slide.clades <- function(clades, treelist){
    output <- vector(mode = "character", length = length(clades))
    for(i in 1:length(clades)){
        # Convert factor to set of indices
        nums <- as.numeric(unlist(strsplit(as.character(clades[i]),
                                           split = " ")))
        # Convert indices to tip names
        output[i] <- paste(nums, collapse = ", ")
    }
    output
}