[Phylobase-commits] r562 - pkg/inst/unitTests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 21 23:00:19 CEST 2009
Author: regetz
Date: 2009-08-21 23:00:18 +0200 (Fri, 21 Aug 2009)
New Revision: 562
Added:
pkg/inst/unitTests/runit.checkdata.R
pkg/inst/unitTests/runit.methods-oldclasses.R
pkg/inst/unitTests/runit.methods-phylo4d.R
pkg/inst/unitTests/runit.pdata.R
pkg/inst/unitTests/runit.phylo4.R
pkg/inst/unitTests/runit.prune.R
pkg/inst/unitTests/runit.readNexus.R
pkg/inst/unitTests/runit.tbind.R
pkg/inst/unitTests/runit.treePlot.R
Log:
added more placeholder unit tests, continuing to mirror pkg/R/.
Added: pkg/inst/unitTests/runit.checkdata.R
===================================================================
--- pkg/inst/unitTests/runit.checkdata.R (rev 0)
+++ pkg/inst/unitTests/runit.checkdata.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,22 @@
+#
+# --- Test checkdata.R ---
+#
+
+checkPhylo4 <- function() {
+}
+
+checkTree <- function() {
+ # function(object,warn="retic",err=NULL)
+}
+
+checkPhylo4Data <- function() {
+}
+
+formatData <- function() {
+ # function(phy, dt, type=c("tip", "internal", "all"),
+ # match.data=TRUE, label.type=c("rownames", "column"),
+ # label.column=1, missing.data=c("fail", "warn", "OK"),
+ # extra.data=c("warn", "OK", "fail"), rownamesAsLabels=FALSE)
+}
+
+
Property changes on: pkg/inst/unitTests/runit.checkdata.R
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Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.methods-oldclasses.R
===================================================================
--- pkg/inst/unitTests/runit.methods-oldclasses.R (rev 0)
+++ pkg/inst/unitTests/runit.methods-oldclasses.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,8 @@
+#
+# --- Test methods-oldclasses.R ---
+#
+
+test.reorder.phylo <- function() {
+ # function(x, order = 'cladewise')
+}
+
Property changes on: pkg/inst/unitTests/runit.methods-oldclasses.R
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Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.methods-phylo4d.R
===================================================================
--- pkg/inst/unitTests/runit.methods-phylo4d.R (rev 0)
+++ pkg/inst/unitTests/runit.methods-phylo4d.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,49 @@
+#
+# --- Test methods-phylo4.R ---
+#
+
+# Create sample tree for testing (ape::phylo object)
+tr <- read.tree(text="(((spA:0.2,(spB:0.1,spC:0.1):0.15):0.5,spD:0.7):0.2,spE:1):0.4;")
+phy <- as(tr, "phylo4")
+## label node ancestr edge.length node.type
+## 6 <NA> 6 NA 0.40 root
+## 7 <NA> 7 6 0.20 internal
+## 8 <NA> 8 7 0.50 internal
+## 9 <NA> 9 8 0.15 internal
+## 1 spA 1 8 0.20 tip
+## 2 spB 2 9 0.10 tip
+## 3 spC 3 9 0.10 tip
+## 4 spD 4 7 0.70 tip
+## 5 spE 5 6 1.00 tip
+phyd <- as(phy, "phylo4d")
+
+test.tdata.phylo4d <- function() {
+ # function(x, type=c("tip", "internal", "allnode"),
+ # label.type=c("row.names","column"), empty.columns=TRUE, ...)
+}
+
+test.Replace.tdata.phylo4d <- function() {
+ # function(object, type = c("tip", "internal", "allnode"), ...,
+ # value)
+}
+
+test.addData.phylo4d <- function() {
+ # function(x, tip.data=NULL, node.data=NULL, all.data=NULL,
+ # pos=c("after", "before"), merge.data=TRUE, match.data=TRUE, ...)
+}
+
+test.addData.phylo4 <- function() {
+ # function(x, tip.data=NULL, node.data=NULL, all.data=NULL,
+ # pos=c("after", "before"), merge.data=TRUE, match.data=TRUE, ...)
+}
+
+test.summary.phylo4d <- function() {
+}
+
+test.hasNodeData.phylo4d <- function() {
+}
+
+test.na.omit.phylo4d <- function() {
+ # function(object, ...)
+}
+
Property changes on: pkg/inst/unitTests/runit.methods-phylo4d.R
___________________________________________________________________
Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.pdata.R
===================================================================
--- pkg/inst/unitTests/runit.pdata.R (rev 0)
+++ pkg/inst/unitTests/runit.pdata.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,21 @@
+#
+# --- Test pdata.R ---
+#
+
+test.pdata <- function() {
+ # function(data,type,comment,metadata)
+}
+
+test.check_pdata <- function() {
+}
+
+test.extract.pdata <- function() {
+ # test "[" and "[["
+}
+
+test.assign.pdata <- function() {
+ # test "[<-" and "[[<-"
+}
+
+test.plot.pdata <- function() {
+}
Property changes on: pkg/inst/unitTests/runit.pdata.R
___________________________________________________________________
Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.phylo4.R
===================================================================
--- pkg/inst/unitTests/runit.phylo4.R (rev 0)
+++ pkg/inst/unitTests/runit.phylo4.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,11 @@
+#
+# --- Test phylo4.R ---
+#
+
+# phylo4.R is mostly used to set generics, so no testing needed
+
+# one non-exported method:
+test..genlab <- function() {
+ # use phylobase:::.genlab
+}
+
Property changes on: pkg/inst/unitTests/runit.phylo4.R
___________________________________________________________________
Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.prune.R
===================================================================
--- pkg/inst/unitTests/runit.prune.R (rev 0)
+++ pkg/inst/unitTests/runit.prune.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,19 @@
+#
+# --- Test prune.R ---
+#
+
+test.DropTip <- function() {
+ # function(phy, tip, ...)
+}
+
+test.prune.phylo4 <- function() {
+ # function(phy, tip, trim.internal = TRUE, subtree = FALSE, ...)
+}
+
+test.prune.phylo4d <- function() {
+ # function(phy, tip, trim.internal = TRUE, subtree = FALSE, ...)
+}
+
+test.prune.phylo <- function() {
+ # function(phy, tip, trim.internal = TRUE, subtree = FALSE, ...)
+}
Property changes on: pkg/inst/unitTests/runit.prune.R
___________________________________________________________________
Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.readNexus.R
===================================================================
--- pkg/inst/unitTests/runit.readNexus.R (rev 0)
+++ pkg/inst/unitTests/runit.readNexus.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,13 @@
+#
+# --- Test readNexus.R ---
+#
+
+test.readNexus <- function() {
+ # function (file, simplify=TRUE, type=c("all", "tree", "data"),
+ # char.all=FALSE, polymorphic.convert=TRUE, levels.uniform=TRUE,
+ # check.node.labels=c("keep", "drop", "asdata"))
+}
+
+test.read.nexustreestring <- function() {
+}
+
Property changes on: pkg/inst/unitTests/runit.readNexus.R
___________________________________________________________________
Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.tbind.R
===================================================================
--- pkg/inst/unitTests/runit.tbind.R (rev 0)
+++ pkg/inst/unitTests/runit.tbind.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,8 @@
+#
+# --- Test tbind.R ---
+#
+
+test.tbind <- function() {
+ # function(...,checkData=TRUE)
+}
+
Property changes on: pkg/inst/unitTests/runit.tbind.R
___________________________________________________________________
Name: svn:eol-style
+ native
Added: pkg/inst/unitTests/runit.treePlot.R
===================================================================
--- pkg/inst/unitTests/runit.treePlot.R (rev 0)
+++ pkg/inst/unitTests/runit.treePlot.R 2009-08-21 21:00:18 UTC (rev 562)
@@ -0,0 +1,30 @@
+#
+# --- Test treePlot.R ---
+#
+
+test.treePlot <- function() {
+}
+
+test.plotOneTree <- function() {
+}
+
+test.phyloXXYY <- function() {
+ # function(phy, tip.order = NULL)
+}
+
+test..bubLegendGrob <- function() {
+}
+
+test.drawDetails.bubLegend <- function() {
+}
+
+test.phylobubbles <- function() {
+}
+
+test.tip.data.plot <- function() {
+}
+
+test.plot.phylo4 <- function() {
+ # signature(x='phylo4', y='missing')
+}
+
Property changes on: pkg/inst/unitTests/runit.treePlot.R
___________________________________________________________________
Name: svn:eol-style
+ native
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