[Phylobase-commits] r593 - pkg/inst/unitTests

[noreply at r-forge.r-project.org]

Author: regetz
Date: 2009-08-26 02:53:54 +0200 (Wed, 26 Aug 2009)
New Revision: 593

Added:
   pkg/inst/unitTests/runit.class-phylo4.R
Log:
created simple tests of phylo4 construction (from matrix and from phylo)


Added: pkg/inst/unitTests/runit.class-phylo4.R
===================================================================
--- pkg/inst/unitTests/runit.class-phylo4.R	                        (rev 0)
+++ pkg/inst/unitTests/runit.class-phylo4.R	2009-08-26 00:53:54 UTC (rev 593)
@@ -0,0 +1,55 @@
+#
+# --- Test class-phylo4.R ---
+#
+
+test.phylo4.matrix <- function() {
+    edge <- structure(c(6L, 7L, 8L, 8L, 9L, 9L, 7L, 6L, 7L, 8L, 1L, 9L,
+      2L, 3L, 4L, 5L), .Dim = c(8, 2))
+    edge.length <- c(0.2, 0.5, 0.2, 0.15, 0.1, 0.1, 0.7, 1)
+    tip.label <- paste("t", 1:5, sep="")
+    node.label <- paste("n", 1:4, sep="")
+    edge.label <- paste("e", 1:8, sep="") 
+    order="preorder"
+    annote <- list(x="annotation")
+    phy <- phylo4(edge, edge.length=edge.length, tip.label=tip.label,
+      node.label=node.label, edge.label=edge.label, order=order,
+      annote=annote)
+
+    # test each slot
+    checkIdentical(edge, unname(edges(phy)))
+    checkIdentical(edge.length, unname(edgeLength(phy)))
+    checkIdentical(4L, nNodes(phy))
+    checkIdentical(tip.label, unname(tipLabels(phy)))
+    checkIdentical(node.label, unname(nodeLabels(phy)))
+    checkIdentical(edge.label, unname(edgeLabels(phy)))
+    checkIdentical(order, edgeOrder(phy))
+    checkIdentical(annote, phy at annote)
+
+    # test improper cases
+    #checkException(phylo4(edge, edge.length=999))  # recycling is allowed?
+    checkException(phylo4(edge, tip.label=999))
+    checkException(phylo4(edge, node.label=999))
+    #checkException(phylo4(edge, edge.label=999))  # recycling is allowed?
+    checkException(phylo4(edge, order="invalid order"))
+    checkException(phylo4(edge, annote="invalid annotation"))
+}
+
+test.phylo4.phylo <- function() {
+    tr <- read.tree(text="(((t1:0.2,(t2:0.1,t3:0.1)n4:0.15)n3:0.5,t4:0.7)n2:0.2,t5:1)n1:0.4;")
+    annote <- list(x="annotation")
+    phy <- phylo4(tr, check.node.labels="keep", annote=annote)
+    checkIdentical(tr$tip.label, unname(tipLabels(phy)))
+    checkIdentical(tr$node.label, unname(nodeLabels(phy)))
+    checkIdentical("unknown", edgeOrder(phy))
+    checkIdentical(annote, phy at annote)
+
+    # test preservation of order attribute
+    phy <- phylo4(reorder(tr, "cladewise"))
+    checkIdentical("preorder", edgeOrder(phy))
+    phy <- phylo4(reorder(tr, "pruningwise"))
+    checkIdentical("pruningwise", edgeOrder(phy))
+
+    # test dropping node labels
+    phy <- phylo4(tr, check.node.labels="drop")
+    checkIdentical(unname(nodeLabels(phy)), rep(NA_character_, nNodes(phy)))
+}


Property changes on: pkg/inst/unitTests/runit.class-phylo4.R
___________________________________________________________________
Name: svn:eol-style
   + native