Now convert between multiPhylo and TreeMen

NAMESPACE

@@ -69,6 +69,7 @@ export(writeTrmn)
 exportClasses(Node)
 exportClasses(TreeMan)
 exportClasses(TreeMen)
+exportClasses(multiPhylo)
 exportClasses(phylo)
 exportMethods("[")
 exportMethods("[[")

R/cnvrt-methods.R

@@ -6,11 +6,21 @@
 #' @exportClass phylo
 setOldClass('phylo')
 
+#' multiPhylo class
+#'
+#' @name multiPhylo-class
+#' @aliases multiPhylo
+#'
+#' @exportClass multiPhylo
+setOldClass('multiPhylo')
+
 #' @name TreeMan-to-phylo
 #' @title Convert TreeMan to phylo
 #' @description Return ape's \code{phylo} from a \code{TreeMan}
 #' @seealso 
 #' \code{\link{phylo-to-TreeMan}},
+#' \code{\link{TreeMen-to-multiPhylo}}
+#' \code{\link{multiPhylo-to-TreeMen}}
 #' \code{\link{TreeMan-class}}
 #' @examples 
 #' library(treeman)
@@ -29,6 +39,8 @@ setAs(from="phylo", to="TreeMan", def=function(from, to) {
 #' @description Return a \code{TreeMan} from ape's \code{phylo}
 #' @seealso
 #' \code{\link{TreeMan-to-phylo}},
+#' \code{\link{TreeMen-to-multiPhylo}}
+#' \code{\link{multiPhylo-to-TreeMen}}
 #' \code{\link{TreeMan-class}}
 #' @examples 
 #' library(treeman)
@@ -42,4 +54,42 @@ setAs(from="TreeMan", to="phylo", def=function(from, to) {
   return(tree)
 })
 
-# TODO: multiphylo conversions
+#' @name multiPhylo-to-TreeMen
+#' @title Convert multiPhylo to TreeMen
+#' @description Return a \code{TreeMen} from ape's \code{mutlPhylo}
+#' @seealso
+#' \code{\link{TreeMan-to-phylo}},
+#' \code{\link{phylo-to-TreeMan}},
+#' \code{\link{TreeMen-to-multiPhylo}}
+#' \code{\link{TreeMan-class}}
+#' @examples 
+#' library(treeman)
+#' library(ape)
+#' trees <- c(rtree(10), rtree(10), rtree(10))
+#' trees <- as(trees, 'TreeMen')
+setAs(from="multiPhylo", to="TreeMen", def=function(from, to) {
+  ape::write.tree(from, file='temp.tre')
+  tree <- readTree(file='temp.tre')
+  file.remove('temp.tre')
+  return(tree)
+})
+
+#' @name TreeMen-to-multiPhylo
+#' @title Convert TreeMen to multiPhylo
+#' @description Return ape's \code{multiPhylo} from a \code{TreeMen}
+#' @seealso 
+#' \code{\link{TreeMan-to-phylo}},
+#' \code{\link{phylo-to-TreeMan}},
+#' \code{\link{multiPhylo-to-TreeMen}}
+#' \code{\link{TreeMan-class}}
+#' @examples 
+#' library(treeman)
+#' library(ape)
+#' trees <- cTrees(randTree(10), randTree(10), randTree(10))
+#' trees <- as(trees, 'multiPhylo')
+setAs(from="TreeMen", to="multiPhylo", def=function(from, to) {
+  writeTree(from, file='temp.tre')
+  tree <- ape::read.tree(file='temp.tre')
+  file.remove('temp.tre')
+  return(tree)
+})

tests/testthat/test-cnvrt-methods.R

@@ -7,10 +7,20 @@ context('Testing \'cnvrt-methods\'')
 test_that('TreeMan-to-phylo works', {
   tree <- randTree(100)
   tree <- as(tree, "phylo")
-  expect_equal(class(tree)[1], "phylo")
+  expect_true("phylo" %in% class(tree))
 })
 test_that('phylo-to-TreeMan works', {
   tree <- ape::rtree(100)
   tree <- as(tree, "TreeMan")
   expect_equal(class(tree)[1], "TreeMan")
+})
+test_that('multiPhylo-to-TreeMen works', {
+  trees <- c(ape::rtree(100), ape::rtree(100), ape::rtree(100))
+  trees <- as(trees, "TreeMen")
+  expect_equal(is(trees), "TreeMen")
+})
+test_that('TreeMen-to-multiPhylo works', {
+  trees <- cTrees(randTree(100), randTree(100), randTree(100))
+  trees <- as(trees, "multiPhylo")
+  expect_true("multiPhylo" %in% class(trees))
 })