[Phylobase-commits] r776 - pkg/inst/unitTests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 1 22:09:42 CEST 2010
Author: francois
Date: 2010-04-01 22:09:41 +0200 (Thu, 01 Apr 2010)
New Revision: 776
Removed:
pkg/inst/unitTests/runit.labelsReplaceMethod.R
Log:
fixes bug 669, all tests for labels replace methods are now in runit.methods-phylo4.R
Deleted: pkg/inst/unitTests/runit.labelsReplaceMethod.R
===================================================================
--- pkg/inst/unitTests/runit.labelsReplaceMethod.R 2010-04-01 20:02:26 UTC (rev 775)
+++ pkg/inst/unitTests/runit.labelsReplaceMethod.R 2010-04-01 20:09:41 UTC (rev 776)
@@ -1,255 +0,0 @@
-data(geospiza)
-
-p4 <- extractTree(geospiza)
-p4d <- geospiza
-
-test.labelsTipsPhylo4 <- function() {
- tLbl <- paste("t", 1:nTips(p4), sep="")
- nmTLbl <- tLbl
- names(nmTLbl) <- nodeId(p4, "tip")
- tLbl <- sample(tLbl)
- nmTLbl <- sample(nmTLbl)
-
- ## case all options by default and unnamed vector
- p4c <- p4
- tipLabels(p4c) <- tLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4c)) %in% nodeId(p4c, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4c)), tLbl)
-
- ## case all options by default and named vector
- p4c <- p4
- tipLabels(p4c) <- nmTLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4c)) %in% nodeId(p4c, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4c)), unname(nmTLbl))
-
- ## case type defined
- p4c <- p4
- tipLabels(p4c) <- tLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4c)) %in% nodeId(p4c, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4c)), tLbl)
-
- ## case type defined and use.names=TRUE but no names
- p4c <- p4
- tipLabels(p4c, use.names=TRUE) <- tLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4c)) %in% nodeId(p4c, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4c)), tLbl)
-
- ## case type defined and use.names=TRUE with names
- p4c <- p4
- tipLabels(p4c, use.names=TRUE) <- nmTLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4c)) %in% nodeId(p4c, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(tipLabels(p4c), nmTLbl[order(as.numeric(names(nmTLbl)))])
-}
-
-test.labelsNodePhylo4 <- function() {
-
- ndLbl <- paste("n", 1:nNodes(p4), sep="")
- nmNdLbl <- ndLbl
- names(nmNdLbl) <- nodeId(p4, "internal")
-
- ndLbl <- sample(ndLbl)
- nmNdLbl <- sample(nmNdLbl)
-
- ## case type defined
- p4c <- p4
- nodeLabels(p4c) <- ndLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(nodeLabels(p4c)) %in% nodeId(p4c, "all")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(nodeLabels(p4c)), ndLbl)
-
- ## case type defined and use.names=TRUE but no names
- p4c <- p4
- nodeLabels(p4c, use.names=TRUE) <- ndLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(nodeLabels(p4c)) %in% nodeId(p4c, "all")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(nodeLabels(p4c)), ndLbl)
-
- ## case type defined and use.names=TRUE with names
- p4c <- p4
- nodeLabels(p4c, use.names=TRUE) <- nmNdLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(nodeLabels(p4c)) %in% nodeId(p4c, "all")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(nodeLabels(p4c), nmNdLbl[order(as.numeric(names(nmNdLbl)))])
-
-}
-
-test.labelsTipsPhylo4d <- function() {
- tLbl <- paste("t", 1:nTips(p4d), sep="")
- nmTLbl <- tLbl
- names(nmTLbl) <- nodeId(p4d, "tip")
- tLbl <- sample(tLbl)
- nmTLbl <- sample(nmTLbl)
-
- ## case all options by default and unnamed vector
- p4dc <- p4d
- tipLabels(p4dc) <- tLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4dc)) %in% nodeId(p4dc, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4dc)), tLbl)
-
- ## case all options by default and named vector
- p4dc <- p4d
- tipLabels(p4dc) <- nmTLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4dc)) %in% nodeId(p4dc, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4dc)), unname(nmTLbl))
-
- ## case type defined
- p4dc <- p4d
- tipLabels(p4dc) <- tLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4dc)) %in% nodeId(p4dc, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4dc)), tLbl)
-
- ## case type defined and use.names=TRUE but no names
- p4dc <- p4d
- tipLabels(p4dc, use.names=TRUE) <- tLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4dc)) %in% nodeId(p4dc, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(tipLabels(p4dc)), tLbl)
-
- ## case type defined and use.names=TRUE with names
- p4dc <- p4d
- tipLabels(p4dc, use.names=TRUE) <- nmTLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(tipLabels(p4dc)) %in% nodeId(p4dc, "tip")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(tipLabels(p4dc), nmTLbl[order(as.numeric(names(nmTLbl)))])
-}
-
-test.labelsNodePhylo4d <- function() {
-
- ndLbl <- paste("n", 1:nNodes(p4d), sep="")
- nmNdLbl <- ndLbl
- names(nmNdLbl) <- nodeId(p4d, "internal")
-
- ndLbl <- sample(ndLbl)
- nmNdLbl <- sample(nmNdLbl)
-
- ## case type defined
- p4dc <- p4d
- nodeLabels(p4dc) <- ndLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(nodeLabels(p4dc)) %in% nodeId(p4dc, "internal")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(nodeLabels(p4dc)), ndLbl)
-
- ## case type defined and use.names=TRUE but no names
- p4dc <- p4d
- nodeLabels(p4dc, use.names=TRUE) <- ndLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(nodeLabels(p4dc)) %in% nodeId(p4dc, "internal")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(unname(nodeLabels(p4dc)), ndLbl)
-
- ## case type defined and use.names=TRUE with names
- p4dc <- p4d
- nodeLabels(p4dc, use.names=TRUE) <- nmNdLbl
- ## check the internal names are there and match tips
- checkTrue(all(names(nodeLabels(p4dc)) %in% nodeId(p4dc, "internal")))
- ## check that the labels are correct: here use.names=FALSE
- ## so the order should be the same as in the shuffled vector
- ## of name labels
- checkEquals(nodeLabels(p4dc), nmNdLbl[order(as.numeric(names(nmNdLbl)))])
-
-}
-
-test.labelsAllPhylo4 <- function() {
-
- allLbl <- paste("n", 1:(nTips(p4)+nNodes(p4)), sep="")
- nmAllLbl <- allLbl
- names(nmAllLbl) <- nodeId(p4, "all")
-
- allLbl <- sample(allLbl)
- nmAllLbl <- sample(nmAllLbl)
-
- p4c <- p4
- labels(p4c, "all") <- allLbl
- checkTrue(all(names(labels(p4c)) %in% nodeId(p4c, "all")))
- checkEquals(unname(labels(p4c)), allLbl)
-
- p4c <- p4
- labels(p4c, "all") <- nmAllLbl
- checkTrue(all(names(labels(p4c)) %in% nodeId(p4c, "all")))
- checkEquals(unname(labels(p4c)), unname(nmAllLbl))
-
- p4c <- p4
- tmpNm <- nmAllLbl[order(as.numeric(names(nmAllLbl)))]
- labels(p4c, "all", use.names=TRUE) <- nmAllLbl
- checkTrue(all(names(labels(p4c)) %in% nodeId(p4c, "all")))
- checkEquals(labels(p4c), tmpNm[names(tmpNm) %in% nodeId(p4c, "all")])
-}
-
-test.labelsAllPhylo4d <- function() {
-
- allLbl <- paste("n", 1:(nTips(p4d)+nNodes(p4d)), sep="")
- nmAllLbl <- allLbl
- names(nmAllLbl) <- nodeId(p4d, "all")
-
- allLbl <- sample(allLbl)
- nmAllLbl <- sample(nmAllLbl)
-
- p4dc <- p4d
- labels(p4dc, "all") <- allLbl
- checkTrue(all(names(labels(p4dc)) %in% nodeId(p4dc, "all")))
- checkEquals(unname(labels(p4dc)), allLbl)
-
- p4dc <- p4d
- labels(p4dc, "all") <- nmAllLbl
- checkTrue(all(names(labels(p4dc)) %in% nodeId(p4dc, "all")))
- checkEquals(unname(labels(p4dc)), unname(nmAllLbl))
-
-
- p4dc <- p4d
- tmpNm <- nmAllLbl[order(as.numeric(names(nmAllLbl)))]
- labels(p4dc, "all", use.names=TRUE) <- nmAllLbl
- checkTrue(all(names(labels(p4dc)) %in% nodeId(p4dc, "all")))
- checkEquals(labels(p4dc), tmpNm[names(tmpNm) %in% nodeId(p4dc, "all")])
-}
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