Updating for merge example

NAMESPACE

@@ -70,6 +70,7 @@ export(setNdsSpn)
 export(setPD)
 export(setTxnyms)
 export(taxaResolve)
+export(twoer)
 export(ultrTree)
 export(unblncdTree)
 export(updateSlts)

R/gen-methods.R

@@ -120,4 +120,35 @@ unblncdTree <- function(n, wndmtrx=FALSE, parallel=FALSE) {
     tree <- addNdmtrx(tree)
   }
   tree
-}
+}
+
+#' @name twoer
+#' @title Generate a tree of two tips
+#' @description Returns a \code{TreeMan} tree with two tips and a root.
+#' @details Useful for building larger trees with \code{addClade()}.
+#' Note, a node matrix cannot be added to a tree of two tips.
+#' @param tids tip IDs
+#' @param spns tip spans
+#' @param rid root ID
+#' @param root_spn root span
+#' @seealso
+#' \code{\link{TreeMan-class}}, \code{\link{randTree}}
+#' @export
+#' @examples
+#' library(treeman)
+#' tree <- twoer()
+twoer <- function(tids=c('t1', 't2'), spns=c(1,1),
+                  rid='root', root_spn=0) {
+  ndlst <- list()
+  ndlst[[rid]] <- list('id'=rid, 'prid'=rid,
+                       'ptid'=tids[1:2], 'spn'=root_spn)
+  ndlst[[tids[1]]] <- list('id'=tids[[1]], 'prid'=rid,
+                           'ptid'=NULL, 'spn'=spns[1])
+  ndlst[[tids[2]]] <- list('id'=tids[[2]], 'prid'=rid,
+                           'ptid'=NULL, 'spn'=spns[2])
+  prinds <- c(1, 1, 1)
+  tinds <- c(2, 3)
+  tree <- new('TreeMan', ndlst=ndlst, root='root', wtxnyms=FALSE,
+              ndmtrx=NULL, prinds=prinds, tinds=tinds)
+  updateSlts(tree)
+}

R/manip-methods.R

@@ -240,7 +240,7 @@ addTip <- function(tree, tid, sid, strt_age=NULL,
 #' @name addClade
 #' @title Add clade to tree
 #' @description Returns a tree with added clade
-#' @details Add a \code{TreeMan} object to an exisiting \code{TreeMan}
+#' @details Add a \code{TreeMan} object to an existing \code{TreeMan}
 #' object by specifying an ID at which to attach. If the id specified
 #' is an internal node, then the original clade descending from that
 #' node will be replaced. Before running, ensure no IDs are shared

R/update-methods.R

@@ -74,6 +74,9 @@ updateSlts <- function(tree) {
 #' tree <- addNdmtrx(tree)
 #' summary(tree)
 addNdmtrx <- function(tree, shared=FALSE, ...) {
+  if(tree@ntips < 3) {
+    stop('Too small for node matrix.')
+  }
   if(!checkTreeMan(tree)) {
     stop('Invalid tree')
   }

other/4_merge.R

@@ -0,0 +1,37 @@
+# LIB
+library(treeman)
+
+# Load BIG trees and get ages
+data(mammals)
+data(birds)
+mml_age <- getAge(mammals)
+brd_age <- getAge(birds)
+
+# Rename internal nodes
+mammals['nds'][1:10]
+birds['nds'][1:10]  # possible node IDs are not unique
+mml_nds <- paste0('mml_', mammals['nds'])
+mml_nds[1:10]
+avs_nds <- paste0('avs_', birds['nds'])
+mammals <- setNdsID(mammals, mammals['nds'], mml_nds)
+birds <- setNdsID(birds, birds['nds'], avs_nds)
+
+# Generate incipient tree
+tree <- twoer()
+
+# Add to mammals and birds to tree
+tree <- setNdsID(tree, c('t1', 't2'), c('Mammalia', 'Aves'))
+# set spans to make tree ultrametric
+tree <- setNdSpn(tree, 'Aves', abs(brd_age - mml_age) + 1)
+# list of form: id=txnym
+txnyms <- list('Aves'='Aves', 'Mammalia'= 'Mammalia',
+               'root'='Amniota')
+tree <- setTxnyms(tree, txnyms)
+tree <- addClade(tree=tree, id='Mammalia', clade=mammals)
+tree <- addClade(tree=tree, id='Aves', clade=birds)
+
+# Complete
+tree[['root']]
+summary(tree)
+# Note, plotting takes time.... have to convert to APE
+plot(as(tree, 'phylo'), show.tip.label=FALSE)

tests/testthat/test-gen-methods.R

@@ -30,4 +30,8 @@ test_that('unblncdTree() works', {
     tree_age <- getAge(tree)
     expect_that(tree['pd'], is_more_than(tree_age))
   }
+})
+test_that('twoer() works', {
+  tree <- twoer()
+  expect_equal(tree['ntips'], 2)
 })