[Phylobase-commits] r565 - in pkg: man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Aug 22 00:10:24 CEST 2009
Author: francois
Date: 2009-08-22 00:10:24 +0200 (Sat, 22 Aug 2009)
New Revision: 565
Modified:
pkg/man/check.phylo4d.Rd
pkg/man/phylo4d.Rd
pkg/tests/misctests.Rout.save
Log:
created some more examples in documentation, removed some obsolete part of doc, updated output of misctests because of the new examples
Modified: pkg/man/check.phylo4d.Rd
===================================================================
--- pkg/man/check.phylo4d.Rd 2009-08-21 22:08:02 UTC (rev 564)
+++ pkg/man/check.phylo4d.Rd 2009-08-21 22:10:24 UTC (rev 565)
@@ -98,13 +98,7 @@
p4d.all2 <- phylo4d(p4, all.data = rbind(dat, nod.dat, match.data=FALSE))
## examples of merge.data
-data(geospiza)
-trGeo <- extractTree(geospiza)
-tDt <- data.frame(a=rnorm(nTips(trGeo)), row.names=nodeId(trGeo, "tip"))
-nDt <- data.frame(a=rnorm(nNodes(trGeo)), row.names=nodeId(trGeo, "internal"))
-(matchData1 <- phylo4d(trGeo, tip.data=tDt, node.data=nDt, merge.data=FALSE))
-(matchData2 <- phylo4d(trGeo, tip.data=tDt, node.data=nDt, merge.data=TRUE))
}
\keyword{misc}
Modified: pkg/man/phylo4d.Rd
===================================================================
--- pkg/man/phylo4d.Rd 2009-08-21 22:08:02 UTC (rev 564)
+++ pkg/man/phylo4d.Rd 2009-08-21 22:10:24 UTC (rev 565)
@@ -42,7 +42,7 @@
tip and node labels?}
\item{merge.data}{if both \code{tip.data} and \code{node.data} are
provided, it determines if they should be merged as a single
- trait. This argument is evaluated only if both \code{tip.data} and
+ trait (if TRUE). This argument is evaluated only if both \code{tip.data} and
\code{node.data} have identical column names.}
\item{check.node.labels}{if \code{x} is of class \code{phylo}, use
either "keep" (the default) to retain internal node labels, "drop"
@@ -118,23 +118,29 @@
exGeo2 <- phylo4d(geoTree, tip.data = geoData, node.data = rNodeData)
-### Example using 'merge.tip.node'
-## some random tip data
-rTipData <- data.frame(randomTrait = rnorm(nTips(geoTree)),
- row.names = labels(geoTree))
+### Example using 'merge.data'
+data(geospiza)
+trGeo <- extractTree(geospiza)
+tDt <- data.frame(a=rnorm(nTips(trGeo)), row.names=nodeId(trGeo, "tip"))
+nDt <- data.frame(a=rnorm(nNodes(trGeo)), row.names=nodeId(trGeo, "internal"))
-(exGeo3 <- phylo4d(geoTree, tip.data = rTipData, node.data = rNodeData))
-(exGeo4 <- phylo4d(geoTree, tip.data = rTipData, node.data = rNodeData,
- merge.data = FALSE))
+(matchData1 <- phylo4d(trGeo, tip.data=tDt, node.data=nDt, merge.data=FALSE))
+(matchData2 <- phylo4d(trGeo, tip.data=tDt, node.data=nDt, merge.data=TRUE))
- ### Example with 'all.data'x
+## Example with 'all.data'
nodeLabels(geoTree) <- as.character(nodeId(geoTree))
rAllData <- data.frame(randomTrait = rnorm(nTips(geoTree) + nNodes(geoTree)),
row.names = labels(geoTree, 'all'))
-
exGeo5 <- phylo4d(geoTree, all.data = rAllData)
+## Examples using 'rownamesAsLabels' and comparing with match.data=FALSE
+tDt <- data.frame(x=letters[1:nTips(trGeo)],
+ row.names=sample(nodeId(trGeo, "tip")))
+tipLabels(trGeo) <- as.character(sample(1:nTips(trGeo)))
+(exGeo6 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=TRUE))
+(exGeo7 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=FALSE))
+(exGeo8 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=FALSE, match.data=FALSE))
}
\keyword{misc}
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2009-08-21 22:08:02 UTC (rev 564)
+++ pkg/tests/misctests.Rout.save 2009-08-21 22:10:24 UTC (rev 565)
@@ -229,26 +229,60 @@
phyl4d> exGeo2 <- phylo4d(geoTree, tip.data = geoData, node.data = rNodeData)
-phyl4d> ### Example using 'merge.tip.node'
-phyl4d> ## some random tip data
-phyl4d> rTipData <- data.frame(randomTrait = rnorm(nTips(geoTree)),
-phyl4d+ row.names = labels(geoTree))
+phyl4d> ### Example using 'merge.data'
+phyl4d> data(geospiza)
-phyl4d> (exGeo3 <- phylo4d(geoTree, tip.data = rTipData, node.data = rNodeData))
- label node ancestor edge.length node.type randomTrait
-15 <NA> 15 NA NA root -0.62645381
-16 <NA> 16 15 0.29744 internal 0.18364332
-17 <NA> 17 16 0.04924 internal -0.83562861
-18 <NA> 18 17 0.06859 internal 1.59528080
-19 <NA> 19 18 0.13404 internal 0.32950777
-20 <NA> 20 19 0.10346 internal -0.82046838
-21 <NA> 21 20 0.03550 internal 0.48742905
-22 <NA> 22 21 0.00917 internal 0.73832471
-23 <NA> 23 22 0.07333 internal 0.57578135
-24 <NA> 24 23 0.05500 internal -0.30538839
-25 <NA> 25 19 0.24479 internal 1.51178117
-26 <NA> 26 25 0.05167 internal 0.38984324
-27 <NA> 27 26 0.01500 internal -0.62124058
+phyl4d> trGeo <- extractTree(geospiza)
+
+phyl4d> tDt <- data.frame(a=rnorm(nTips(trGeo)), row.names=nodeId(trGeo, "tip"))
+
+phyl4d> nDt <- data.frame(a=rnorm(nNodes(trGeo)), row.names=nodeId(trGeo, "internal"))
+
+phyl4d> (matchData1 <- phylo4d(trGeo, tip.data=tDt, node.data=nDt, merge.data=FALSE))
+ label node ancestor edge.length node.type a a.1
+15 <NA> 15 NA NA root NA -1.47075238
+16 <NA> 16 15 0.29744 internal NA -0.47815006
+17 <NA> 17 16 0.04924 internal NA 0.41794156
+18 <NA> 18 17 0.06859 internal NA 1.35867955
+19 <NA> 19 18 0.13404 internal NA -0.10278773
+20 <NA> 20 19 0.10346 internal NA 0.38767161
+21 <NA> 21 20 0.03550 internal NA -0.05380504
+22 <NA> 22 21 0.00917 internal NA -1.37705956
+23 <NA> 23 22 0.07333 internal NA -0.41499456
+24 <NA> 24 23 0.05500 internal NA -0.39428995
+25 <NA> 25 19 0.24479 internal NA -0.05931340
+26 <NA> 26 25 0.05167 internal NA 1.10002537
+27 <NA> 27 26 0.01500 internal NA 0.76317575
+1 fuliginosa 1 24 0.05500 tip -2.21469989 NA
+2 fortis 2 24 0.05500 tip 1.12493092 NA
+3 magnirostris 3 23 0.11000 tip -0.04493361 NA
+4 conirostris 4 22 0.18333 tip -0.01619026 NA
+5 scandens 5 21 0.19250 tip 0.94383621 NA
+6 difficilis 6 20 0.22800 tip 0.82122120 NA
+7 pallida 7 25 0.08667 tip 0.59390132 NA
+8 parvulus 8 27 0.02000 tip 0.91897737 NA
+9 psittacula 9 27 0.02000 tip 0.78213630 NA
+10 pauper 10 26 0.03500 tip 0.07456498 NA
+11 Platyspiza 11 18 0.46550 tip -1.98935170 NA
+12 fusca 12 17 0.53409 tip 0.61982575 NA
+13 Pinaroloxias 13 16 0.58333 tip -0.05612874 NA
+14 olivacea 14 15 0.88077 tip -0.15579551 NA
+
+phyl4d> (matchData2 <- phylo4d(trGeo, tip.data=tDt, node.data=nDt, merge.data=TRUE))
+ label node ancestor edge.length node.type a
+15 <NA> 15 NA NA root -1.47075238
+16 <NA> 16 15 0.29744 internal -0.47815006
+17 <NA> 17 16 0.04924 internal 0.41794156
+18 <NA> 18 17 0.06859 internal 1.35867955
+19 <NA> 19 18 0.13404 internal -0.10278773
+20 <NA> 20 19 0.10346 internal 0.38767161
+21 <NA> 21 20 0.03550 internal -0.05380504
+22 <NA> 22 21 0.00917 internal -1.37705956
+23 <NA> 23 22 0.07333 internal -0.41499456
+24 <NA> 24 23 0.05500 internal -0.39428995
+25 <NA> 25 19 0.24479 internal -0.05931340
+26 <NA> 26 25 0.05167 internal 1.10002537
+27 <NA> 27 26 0.01500 internal 0.76317575
1 fuliginosa 1 24 0.05500 tip -2.21469989
2 fortis 2 24 0.05500 tip 1.12493092
3 magnirostris 3 23 0.11000 tip -0.04493361
@@ -264,44 +298,109 @@
13 Pinaroloxias 13 16 0.58333 tip -0.05612874
14 olivacea 14 15 0.88077 tip -0.15579551
-phyl4d> (exGeo4 <- phylo4d(geoTree, tip.data = rTipData, node.data = rNodeData,
-phyl4d+ merge.data = FALSE))
- label node ancestor edge.length node.type randomTrait randomTrait.1
-15 <NA> 15 NA NA root NA -0.6264538
-16 <NA> 16 15 0.29744 internal NA 0.1836433
-17 <NA> 17 16 0.04924 internal NA -0.8356286
-18 <NA> 18 17 0.06859 internal NA 1.5952808
-19 <NA> 19 18 0.13404 internal NA 0.3295078
-20 <NA> 20 19 0.10346 internal NA -0.8204684
-21 <NA> 21 20 0.03550 internal NA 0.4874291
-22 <NA> 22 21 0.00917 internal NA 0.7383247
-23 <NA> 23 22 0.07333 internal NA 0.5757814
-24 <NA> 24 23 0.05500 internal NA -0.3053884
-25 <NA> 25 19 0.24479 internal NA 1.5117812
-26 <NA> 26 25 0.05167 internal NA 0.3898432
-27 <NA> 27 26 0.01500 internal NA -0.6212406
-1 fuliginosa 1 24 0.05500 tip -2.21469989 NA
-2 fortis 2 24 0.05500 tip 1.12493092 NA
-3 magnirostris 3 23 0.11000 tip -0.04493361 NA
-4 conirostris 4 22 0.18333 tip -0.01619026 NA
-5 scandens 5 21 0.19250 tip 0.94383621 NA
-6 difficilis 6 20 0.22800 tip 0.82122120 NA
-7 pallida 7 25 0.08667 tip 0.59390132 NA
-8 parvulus 8 27 0.02000 tip 0.91897737 NA
-9 psittacula 9 27 0.02000 tip 0.78213630 NA
-10 pauper 10 26 0.03500 tip 0.07456498 NA
-11 Platyspiza 11 18 0.46550 tip -1.98935170 NA
-12 fusca 12 17 0.53409 tip 0.61982575 NA
-13 Pinaroloxias 13 16 0.58333 tip -0.05612874 NA
-14 olivacea 14 15 0.88077 tip -0.15579551 NA
-
-phyl4d> ### Example with 'all.data'x
+phyl4d> ## Example with 'all.data'
phyl4d> nodeLabels(geoTree) <- as.character(nodeId(geoTree))
phyl4d> rAllData <- data.frame(randomTrait = rnorm(nTips(geoTree) + nNodes(geoTree)),
phyl4d+ row.names = labels(geoTree, 'all'))
phyl4d> exGeo5 <- phylo4d(geoTree, all.data = rAllData)
+
+phyl4d> ## Examples using 'rownamesAsLabels' and comparing with match.data=FALSE
+phyl4d> tDt <- data.frame(x=letters[1:nTips(trGeo)],
+phyl4d+ row.names=sample(nodeId(trGeo, "tip")))
+
+phyl4d> tipLabels(trGeo) <- as.character(sample(1:nTips(trGeo)))
+
+phyl4d> (exGeo6 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=TRUE))
+ label node ancestor edge.length node.type x
+15 <NA> 15 NA NA root <NA>
+16 <NA> 16 15 0.29744 internal <NA>
+17 <NA> 17 16 0.04924 internal <NA>
+18 <NA> 18 17 0.06859 internal <NA>
+19 <NA> 19 18 0.13404 internal <NA>
+20 <NA> 20 19 0.10346 internal <NA>
+21 <NA> 21 20 0.03550 internal <NA>
+22 <NA> 22 21 0.00917 internal <NA>
+23 <NA> 23 22 0.07333 internal <NA>
+24 <NA> 24 23 0.05500 internal <NA>
+25 <NA> 25 19 0.24479 internal <NA>
+26 <NA> 26 25 0.05167 internal <NA>
+27 <NA> 27 26 0.01500 internal <NA>
+1 2 1 24 0.05500 tip i
+2 12 2 24 0.05500 tip l
+3 8 3 23 0.11000 tip b
+4 7 4 22 0.18333 tip c
+5 4 5 21 0.19250 tip n
+6 5 6 20 0.22800 tip f
+7 9 7 25 0.08667 tip h
+8 14 8 27 0.02000 tip a
+9 10 9 27 0.02000 tip e
+10 1 10 26 0.03500 tip m
+11 11 11 18 0.46550 tip g
+12 13 12 17 0.53409 tip j
+13 3 13 16 0.58333 tip k
+14 6 14 15 0.88077 tip d
+
+phyl4d> (exGeo7 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=FALSE))
+ label node ancestor edge.length node.type x
+15 <NA> 15 NA NA root <NA>
+16 <NA> 16 15 0.29744 internal <NA>
+17 <NA> 17 16 0.04924 internal <NA>
+18 <NA> 18 17 0.06859 internal <NA>
+19 <NA> 19 18 0.13404 internal <NA>
+20 <NA> 20 19 0.10346 internal <NA>
+21 <NA> 21 20 0.03550 internal <NA>
+22 <NA> 22 21 0.00917 internal <NA>
+23 <NA> 23 22 0.07333 internal <NA>
+24 <NA> 24 23 0.05500 internal <NA>
+25 <NA> 25 19 0.24479 internal <NA>
+26 <NA> 26 25 0.05167 internal <NA>
+27 <NA> 27 26 0.01500 internal <NA>
+1 2 1 24 0.05500 tip m
+2 12 2 24 0.05500 tip i
+3 8 3 23 0.11000 tip k
+4 7 4 22 0.18333 tip n
+5 4 5 21 0.19250 tip f
+6 5 6 20 0.22800 tip d
+7 9 7 25 0.08667 tip c
+8 14 8 27 0.02000 tip b
+9 10 9 27 0.02000 tip h
+10 1 10 26 0.03500 tip e
+11 11 11 18 0.46550 tip g
+12 13 12 17 0.53409 tip l
+13 3 13 16 0.58333 tip j
+14 6 14 15 0.88077 tip a
+
+phyl4d> (exGeo8 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=FALSE, match.data=FALSE))
+ label node ancestor edge.length node.type x
+15 <NA> 15 NA NA root <NA>
+16 <NA> 16 15 0.29744 internal <NA>
+17 <NA> 17 16 0.04924 internal <NA>
+18 <NA> 18 17 0.06859 internal <NA>
+19 <NA> 19 18 0.13404 internal <NA>
+20 <NA> 20 19 0.10346 internal <NA>
+21 <NA> 21 20 0.03550 internal <NA>
+22 <NA> 22 21 0.00917 internal <NA>
+23 <NA> 23 22 0.07333 internal <NA>
+24 <NA> 24 23 0.05500 internal <NA>
+25 <NA> 25 19 0.24479 internal <NA>
+26 <NA> 26 25 0.05167 internal <NA>
+27 <NA> 27 26 0.01500 internal <NA>
+1 2 1 24 0.05500 tip a
+2 12 2 24 0.05500 tip b
+3 8 3 23 0.11000 tip c
+4 7 4 22 0.18333 tip d
+5 4 5 21 0.19250 tip e
+6 5 6 20 0.22800 tip f
+7 9 7 25 0.08667 tip g
+8 14 8 27 0.02000 tip h
+9 10 9 27 0.02000 tip i
+10 1 10 26 0.03500 tip j
+11 11 11 18 0.46550 tip k
+12 13 12 17 0.53409 tip l
+13 3 13 16 0.58333 tip m
+14 6 14 15 0.88077 tip n
> obj1 <- obj2 <- obj3 <- phylo4d(z, data.frame(wing=1:4,color=factor(c("b","w","b","b")), tail=runif(4)*10), match.data=FALSE)
>
> obj2 at tip.data <- as.data.frame(obj2 at tip.data[,1])
@@ -334,4 +433,4 @@
>
> proc.time()
user system elapsed
- 3.396 0.064 3.490
+ 2.584 0.068 2.665
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