[Phylobase-commits] r524 - in pkg: . inst/unitTests

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

Author: regetz
Date: 2009-08-20 01:23:46 +0200 (Thu, 20 Aug 2009)
New Revision: 524

Added:
   pkg/inst/unitTests/runit.phylo4d.R
Removed:
   pkg/RUnit-tests/
Log:
moved Francois' unit tests in with the others


Copied: pkg/inst/unitTests/runit.phylo4d.R (from rev 520, pkg/RUnit-tests/test-phylo4d.R)
===================================================================
--- pkg/inst/unitTests/runit.phylo4d.R	                        (rev 0)
+++ pkg/inst/unitTests/runit.phylo4d.R	2009-08-19 23:23:46 UTC (rev 524)
@@ -0,0 +1,136 @@
+test.Phylo4d.bruteforce <- function() {
+    data(geospiza_raw)
+    ## using the raw data
+    tr <- geospiza_raw$tree
+    tr <- as(tr, "phylo4")
+
+    ## creating some data with rownames matching tip numbers
+    tDt <- data.frame(testData1 = 1:nTips(tr),
+                      testData2 = (1:nTips(tr))*2)
+    tDt <- tDt[sample(1:nrow(tDt)),]
+
+    nDt <- data.frame(testData1 = 1:nNodes(tr))
+    nDt <- nDt[sample(1:nrow(nDt)),]
+
+    aDt <- data.frame(testData1 = 1:(nNodes(tr)+nTips(tr)))
+    aDt <- aDt[sample(1:nrow(aDt)) ,, drop=FALSE]
+
+    ## brute force: no matching; with tip data
+    xx <- phylo4d(tr, tip.data=tDt, match.data=FALSE)
+    checkEquals(xx at tip.data[,1], tDt[,1])
+    checkEquals(tdata(xx)[,1], tDt[,1])
+
+    ## brute force: no matching; with node data
+    yy <- phylo4d(tr, node.data=nDt, match.data=FALSE)
+    checkEquals(yy at node.data[,1], nDt)
+    checkEquals(tdata(yy, "internal")[,1], nDt)
+
+    ## brute force: no matching; with all.data
+    zz <- phylo4d(tr, all.data=aDt, match.data=FALSE)
+    checkEquals(zz at tip.data[,1], aDt[nodeId(tr, "tip"),1])
+    checkEquals(zz at node.data[,1], aDt[nodeId(tr, "internal"),1])
+    checkEquals(tdata(zz, "all")[,1], aDt[,1])
+
+    ## brute force: no matching; with tip & node data
+    ## no merging (data names don't match)
+    xx <- phylo4d(tr, tip.data=tDt, node.data=nDt, match.data=FALSE)
+    checkEquals(xx at tip.data[,1], tDt[,1])
+    checkEquals(xx at node.data[,3], nDt)
+    checkEquals(tdata(xx, "tip")[,1], tDt[,1])
+    checkEquals(tdata(xx, "internal")[,3], nDt)
+
+    ## brute force: no matching; with tip & node data
+    ## merging
+    nDt <- data.frame(nDt)
+    names(nDt) <- names(tDt)[1]
+    xx <- phylo4d(tr, tip.data=tDt[,1,drop=F], node.data=nDt, match.data=FALSE)
+    checkEquals(xx at tip.data[,1], tDt[,1])
+    checkEquals(xx at node.data[,1], nDt[,1])
+    checkEquals(tdata(xx, "tip")[,1], tDt[,1])
+    checkEquals(tdata(xx, "internal")[,1], nDt[,1])
+
+}
+
+test.Phylo4d.withNb <- function() {
+    data(geospiza_raw)
+    ## using the raw data
+    tr <- geospiza_raw$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)))
+}
+
+test.Phylo4d.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)))
+}


Property changes on: pkg/inst/unitTests/runit.phylo4d.R
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Name: svn:mergeinfo
   +