[Phylobase-commits] r453 - in branches/fm-branch: . RUnit-tests tests

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

Author: francois
Date: 2009-08-13 17:11:12 +0200 (Thu, 13 Aug 2009)
New Revision: 453

Added:
   branches/fm-branch/RUnit-tests/
   branches/fm-branch/RUnit-tests/test-phylo4d.R
   branches/fm-branch/tests/RUnit-tests.R
Log:
added RUnit tests on phylo4d constructor -- you need to edit tests/RUnit-tests.R to make it work

Added: branches/fm-branch/RUnit-tests/test-phylo4d.R
===================================================================
--- branches/fm-branch/RUnit-tests/test-phylo4d.R	                        (rev 0)
+++ branches/fm-branch/RUnit-tests/test-phylo4d.R	2009-08-13 15:11:12 UTC (rev 453)
@@ -0,0 +1,136 @@
+testPhylo4d.bruteforce <- function() {
+    data(geospiza_raw)
+    ## using the raw data
+    tr <- geospiza_raw$tree
+    tr <- as(tr, "phylo4")
+
+    ## creating some data with rownames matching tip numbers
+    tDt <- data.frame(testData1 = 1:nTips(tr),
+                      testData2 = (1:nTips(tr))*2)
+    tDt <- tDt[sample(1:nrow(tDt)),]
+
+    nDt <- data.frame(testData1 = 1:nNodes(tr))
+    nDt <- nDt[sample(1:nrow(nDt)),]
+
+    aDt <- data.frame(testData1 = 1:(nNodes(tr)+nTips(tr)))
+    aDt <- aDt[sample(1:nrow(aDt)) ,, drop=FALSE]
+
+    ## brute force: no matching; with tip data
+    xx <- phylo4d(tr, tip.data=tDt, match.data=FALSE)
+    checkEquals(xx at tip.data[,1], tDt[,1])
+    checkEquals(tdata(xx)[,1], tDt[,1])
+
+    ## brute force: no matching; with node data
+    yy <- phylo4d(tr, node.data=nDt, match.data=FALSE)
+    checkEquals(yy at node.data[,1], nDt)
+    checkEquals(tdata(yy, "internal")[,1], nDt)
+
+    ## brute force: no matching; with all.data
+    zz <- phylo4d(tr, all.data=aDt, match.data=FALSE)
+    checkEquals(zz at tip.data[,1], aDt[nodeId(tr, "tip"),1])
+    checkEquals(zz at node.data[,1], aDt[nodeId(tr, "internal"),1])
+    checkEquals(tdata(zz, "all")[,1], aDt[,1])
+
+    ## brute force: no matching; with tip & node data
+    ## no merging (data names don't match)
+    xx <- phylo4d(tr, tip.data=tDt, node.data=nDt, match.data=FALSE)
+    checkEquals(xx at tip.data[,1], tDt[,1])
+    checkEquals(xx at node.data[,3], nDt)
+    checkEquals(tdata(xx, "tip")[,1], tDt[,1])
+    checkEquals(tdata(xx, "internal")[,3], nDt)
+
+    ## brute force: no matching; with tip & node data
+    ## merging
+    nDt <- data.frame(nDt)
+    names(nDt) <- names(tDt)[1]
+    xx <- phylo4d(tr, tip.data=tDt[,1,drop=F], node.data=nDt, match.data=FALSE)
+    checkEquals(xx at tip.data[,1], tDt[,1])
+    checkEquals(xx at node.data[,1], nDt[,1])
+    checkEquals(tdata(xx, "tip")[,1], tDt[,1])
+    checkEquals(tdata(xx, "internal")[,1], nDt[,1])
+
+}
+
+testPhylo4d.withNb <- function() {
+    data(geospiza_raw)
+    ## using the raw data
+    tr <- geospiza_raw$tree
+    tr <- as(tr, "phylo4")
+
+    ## creating some data with rownames matching tip numbers
+    tDt <- data.frame(testData1 = 1:nTips(tr),
+                      testData2 = (1:nTips(tr))*2)
+    tDt <- tDt[sample(1:nrow(tDt)),]
+
+    nDt <- data.frame(testData1 = 1:nNodes(tr))
+    rownames(nDt) <- nodeId(tr, "internal")
+    nDt <- nDt[sample(1:nrow(nDt)) ,, drop=FALSE]
+
+    aDt <- data.frame(testData1 = 1:(nNodes(tr)+nTips(tr)))
+    aDt <- aDt[sample(1:nrow(aDt)) ,, drop=FALSE]
+
+    ## match with node numbers, tip data
+    xx <- phylo4d(tr, tip.data=tDt)
+    checkEquals(xx at tip.data[,1], 1:nTips(tr))
+    checkEquals(tdata(xx, "tip")[,1], 1:nTips(tr))
+
+    ## match with node numbers, node data
+    xx <- phylo4d(tr, node.data=nDt)
+    checkEquals(xx at node.data[,1], 1:nNodes(tr))
+    checkEquals(tdata(xx, "internal")[,1], 1:nNodes(tr))
+
+    ## match with node numbers, tip & node data
+    xx <- phylo4d(tr, tip.data=tDt, node.data=nDt)
+    checkEquals(xx at tip.data[,1], 1:nTips(tr))
+    checkEquals(xx at node.data[,3], 1:nNodes(tr))
+    checkEquals(tdata(xx, "tip")[,1], 1:nTips(tr))
+    checkEquals(tdata(xx, "internal")[,3], 1:nNodes(tr))
+
+    ## match with node numbers, tip & all data
+    xx <- phylo4d(tr, tip.data=tDt, all.data=aDt)
+    checkEquals(xx at tip.data[,1], 1:nTips(tr))
+    checkEquals(xx at node.data[,1], (nTips(tr)+1):(nTips(tr)+nNodes(tr)))
+    checkEquals(tdata(xx, "all")[,1], 1:(nTips(tr)+nNodes(tr)))
+
+    ## match with node numbers, node & all data
+    xx <- phylo4d(tr, node.data=nDt, all.data=aDt)
+    checkEquals(xx at tip.data[,1], 1:nTips(tr))
+    checkEquals(xx at node.data[,2], 1:nNodes(tr))
+    checkEquals(tdata(xx, "all")[,1], 1:(nTips(tr)+nNodes(tr)))
+
+    ## match with node numbers, tip, node & all data
+    xx <- phylo4d(tr, tip.data=tDt, node.data=nDt, all.data=aDt)
+    checkEquals(xx at tip.data[,1], 1:nTips(tr))
+    checkEquals(xx at tip.data[,2], 1:nTips(tr))
+    checkEquals(xx at node.data[,1], (nTips(tr)+1):(nTips(tr)+nNodes(tr)))
+    checkEquals(xx at node.data[,4], 1:nNodes(tr))
+    checkEquals(tdata(xx, "all")[,1], 1:(nTips(tr)+nNodes(tr)))
+}
+
+testPhylo4d.withNames <- function() {
+    data(geospiza_raw)
+    ## using the raw data
+    tr <- geospiza_raw$tree
+    tr <- as(tr, "phylo4")
+
+    ## creating some data with rownames matching tip numbers
+    tDt <- data.frame(testData1 = 1:nTips(tr),
+                      testData2 = (1:nTips(tr))*2)
+    rownames(tDt) <- tipLabels(tr)
+    tDt <- tDt[sample(1:nrow(tDt)),]
+
+    aDt <- data.frame(testData1 = 1:(nNodes(tr)+nTips(tr)))
+    rownames(aDt)[1:nTips(tr)] <- tipLabels(tr)
+    aDt <- aDt[sample(1:nrow(aDt)) ,, drop=FALSE]
+
+    ## match with names, tip data
+    xx <- phylo4d(tr, tip.data=tDt)
+    checkEquals(xx at tip.data[,1], 1:nTips(tr))
+    checkEquals(tdata(xx, "tip")[,1], 1:nTips(tr))
+
+    ## match with names for tips and numbers for nodes with all data
+    xx <- phylo4d(tr, all.data=aDt)
+    checkEquals(xx at tip.data[,1], 1:nTips(tr))
+    checkEquals(xx at node.data[,1], (nTips(tr)+1):(nTips(tr)+nNodes(tr)))
+    checkEquals(tdata(xx, "all")[,1], 1:(nTips(tr)+nNodes(tr)))
+}

Added: branches/fm-branch/tests/RUnit-tests.R
===================================================================
--- branches/fm-branch/tests/RUnit-tests.R	                        (rev 0)
+++ branches/fm-branch/tests/RUnit-tests.R	2009-08-13 15:11:12 UTC (rev 453)
@@ -0,0 +1,7 @@
+require(RUnit)
+## TODO -- find solution to run these tests on R-forge
+
+##testsuite <- defineTestSuite("phylobase", dirs="/home/francois/Work/R-dev/phylobase/branches/fm-branch/RUnit-tests",
+##                             testFileRegexp="^test", testFuncRegexp="^test")
+##testRslt <- runTestSuite(testsuite)
+##printTextProtocol(testRslt)