[Phylobase-commits] r501 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 19 09:05:46 CEST 2009
Author: regetz
Date: 2009-08-19 09:05:46 +0200 (Wed, 19 Aug 2009)
New Revision: 501
Modified:
pkg/tests/misctests.R
pkg/tests/misctests.Rout.save
Log:
hard-coded simple test tree into misctests.R instead of using rcoal(5),
to avoid test errors across recent ape versions
Modified: pkg/tests/misctests.R
===================================================================
--- pkg/tests/misctests.R 2009-08-19 01:00:13 UTC (rev 500)
+++ pkg/tests/misctests.R 2009-08-19 07:05:46 UTC (rev 501)
@@ -35,7 +35,7 @@
labels(p1C) <- tolower(labels(p1C))
## trace("prune",browser,signature="phylo4d")
-r1 <- rcoal(5)
+r1 <- read.tree(text="((t4:0.3210275554,(t2:0.2724586465,t3:0.2724586465):0.0485689089):0.1397952619,(t5:0.07551818331,t1:0.07551818331):0.385304634);")
## trace("phylo4d", browser, signature = "phylo")
## untrace("phylo4d", signature = "phylo")
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2009-08-19 01:00:13 UTC (rev 500)
+++ pkg/tests/misctests.Rout.save 2009-08-19 07:05:46 UTC (rev 501)
@@ -63,7 +63,7 @@
"phylo4#ANY#character" would also be valid
>
> ## trace("prune",browser,signature="phylo4d")
-> r1 <- rcoal(5)
+> r1 <- read.tree(text="((t4:0.3210275554,(t2:0.2724586465,t3:0.2724586465):0.0485689089):0.1397952619,(t5:0.07551818331,t1:0.07551818331):0.385304634);")
>
> ## trace("phylo4d", browser, signature = "phylo")
> ## untrace("phylo4d", signature = "phylo")
@@ -80,8 +80,8 @@
mean : 0.2116037
variance : 0.01503145
distribution :
- Min. 1st Qu. Median 3rd Qu. Max. NA's
-0.07552 0.10370 0.23040 0.27250 0.38530 1.00000
+ Min. 1st Qu. Median 3rd Qu. Max.
+0.07552 0.10370 0.23040 0.27250 0.38530
Comparative data:
@@ -109,7 +109,7 @@
> row.names(tipdat2)[1] <- "s1"
> t1 <- try(q1 <- phylo4d(r1,tip.data=tipdat2))
Error in switch(missing.data, warn = warning(msg), fail = stop(msg)) :
- The following nodes are not found in the dataset: t2
+ The following nodes are not found in the dataset: t4
>
> plot(q2)
> plot(q2,type="cladogram")
@@ -131,8 +131,8 @@
mean : 0.1988313
variance : 0.0167175
distribution :
- Min. 1st Qu. Median 3rd Qu. Max. NA's
-0.04857 0.07552 0.20610 0.28460 0.38530 1.00000
+ Min. 1st Qu. Median 3rd Qu. Max.
+0.04857 0.07552 0.20610 0.28460 0.38530
Comparative data:
@@ -236,64 +236,64 @@
phyl4d> (exGeo3 <- phylo4d(geoTree, tip.data = rTipData, node.data = rNodeData))
label node ancestor edge.length node.type randomTrait
-15 <NA> 15 NA NA root 0.73832471
-16 <NA> 16 15 0.29744 internal 0.57578135
-17 <NA> 17 16 0.04924 internal -0.30538839
-18 <NA> 18 17 0.06859 internal 1.51178117
-19 <NA> 19 18 0.13404 internal 0.38984324
-20 <NA> 20 19 0.10346 internal -0.62124058
-21 <NA> 21 20 0.03550 internal -2.21469989
-22 <NA> 22 21 0.00917 internal 1.12493092
-23 <NA> 23 22 0.07333 internal -0.04493361
-24 <NA> 24 23 0.05500 internal -0.01619026
-25 <NA> 25 19 0.24479 internal 0.94383621
-26 <NA> 26 25 0.05167 internal 0.82122120
-27 <NA> 27 26 0.01500 internal 0.59390132
-1 fuliginosa 1 24 0.05500 tip 0.91897737
-2 fortis 2 24 0.05500 tip 0.78213630
-3 magnirostris 3 23 0.11000 tip 0.07456498
-4 conirostris 4 22 0.18333 tip -1.98935170
-5 scandens 5 21 0.19250 tip 0.61982575
-6 difficilis 6 20 0.22800 tip -0.05612874
-7 pallida 7 25 0.08667 tip -0.15579551
-8 parvulus 8 27 0.02000 tip -1.47075238
-9 psittacula 9 27 0.02000 tip -0.47815006
-10 pauper 10 26 0.03500 tip 0.41794156
-11 Platyspiza 11 18 0.46550 tip 1.35867955
-12 fusca 12 17 0.53409 tip -0.10278773
-13 Pinaroloxias 13 16 0.58333 tip 0.38767161
-14 olivacea 14 15 0.88077 tip -0.05380504
+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
+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
+4 conirostris 4 22 0.18333 tip -0.01619026
+5 scandens 5 21 0.19250 tip 0.94383621
+6 difficilis 6 20 0.22800 tip 0.82122120
+7 pallida 7 25 0.08667 tip 0.59390132
+8 parvulus 8 27 0.02000 tip 0.91897737
+9 psittacula 9 27 0.02000 tip 0.78213630
+10 pauper 10 26 0.03500 tip 0.07456498
+11 Platyspiza 11 18 0.46550 tip -1.98935170
+12 fusca 12 17 0.53409 tip 0.61982575
+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 0.73832471
-16 <NA> 16 15 0.29744 internal NA 0.57578135
-17 <NA> 17 16 0.04924 internal NA -0.30538839
-18 <NA> 18 17 0.06859 internal NA 1.51178117
-19 <NA> 19 18 0.13404 internal NA 0.38984324
-20 <NA> 20 19 0.10346 internal NA -0.62124058
-21 <NA> 21 20 0.03550 internal NA -2.21469989
-22 <NA> 22 21 0.00917 internal NA 1.12493092
-23 <NA> 23 22 0.07333 internal NA -0.04493361
-24 <NA> 24 23 0.05500 internal NA -0.01619026
-25 <NA> 25 19 0.24479 internal NA 0.94383621
-26 <NA> 26 25 0.05167 internal NA 0.82122120
-27 <NA> 27 26 0.01500 internal NA 0.59390132
-1 fuliginosa 1 24 0.05500 tip 0.91897737 NA
-2 fortis 2 24 0.05500 tip 0.78213630 NA
-3 magnirostris 3 23 0.11000 tip 0.07456498 NA
-4 conirostris 4 22 0.18333 tip -1.98935170 NA
-5 scandens 5 21 0.19250 tip 0.61982575 NA
-6 difficilis 6 20 0.22800 tip -0.05612874 NA
-7 pallida 7 25 0.08667 tip -0.15579551 NA
-8 parvulus 8 27 0.02000 tip -1.47075238 NA
-9 psittacula 9 27 0.02000 tip -0.47815006 NA
-10 pauper 10 26 0.03500 tip 0.41794156 NA
-11 Platyspiza 11 18 0.46550 tip 1.35867955 NA
-12 fusca 12 17 0.53409 tip -0.10278773 NA
-13 Pinaroloxias 13 16 0.58333 tip 0.38767161 NA
-14 olivacea 14 15 0.88077 tip -0.05380504 NA
+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> nodeLabels(geoTree) <- as.character(nodeId(geoTree))
@@ -334,4 +334,4 @@
>
> proc.time()
user system elapsed
- 2.444 0.065 2.625
+ 2.467 0.066 3.153
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