R/comparetrees.R

In phylotastic/rphylotastic: An R Interface to 'Phylotastic' Web Services

#' Compare two phylogenetic trees
#'
#' @param phylo1 A multiphylo object with two trees to be compared between them or a single phylo object to be compared to phylo2
#' @param phylo2 A phylo object to be compared to phylo1
#' @return A named list with are_same_tree property set to either TRUE or FALSE
#' @examples
#' are_same <- phylo_compare(c(ape::rcoal(5), ape::rcoal(5)))
#' @seealso \url{https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription}


# phylo_compare relied upon a server which is now offline.  The code is commented out below.

# phylo_compare <- function(phylo1, phylo2 = NULL) {
#   url <- paste0(get_base_url(), "md/dp/compare_trees")
#   if(is.list(phylo1) & length(phylo1) == 2){
#     trees <- phylo1
#   } else {
#     if(inherits(phylo1, "phylo") & inherits(phylo2, "phylo")){
#       trees <- list(phylo1, phylo2)
#       # class(trees) <- "multiPhylo"  # this is unnecessary
#     }
#   }
#   if(length(trees)!=2) {
#     stop("Must have two trees as input")
#   }
#   body <- list(tree1_nwk = ape::write.tree(trees[[1]]), tree2_nwk = ape::write.tree(trees[[2]]))
#   response <- httr::POST(url, body = body, encode = "json")
#   result <- httr::content(response,"parsed")

#   return(result$are_same_tree)
# }