[Phylobase-commits] r481 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Aug 18 21:35:30 CEST 2009
Author: regetz
Date: 2009-08-18 21:35:29 +0200 (Tue, 18 Aug 2009)
New Revision: 481
Modified:
pkg/tests/misctests.R
pkg/tests/misctests.Rout.save
Log:
regenerated test output; also removed an extra set.seed(1)
Modified: pkg/tests/misctests.R
===================================================================
--- pkg/tests/misctests.R 2009-08-18 19:28:38 UTC (rev 480)
+++ pkg/tests/misctests.R 2009-08-18 19:35:29 UTC (rev 481)
@@ -35,7 +35,6 @@
labels(p1C) <- tolower(labels(p1C))
## trace("prune",browser,signature="phylo4d")
-set.seed(1)
r1 <- rcoal(5)
## trace("phylo4d", browser, signature = "phylo")
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2009-08-18 19:28:38 UTC (rev 480)
+++ pkg/tests/misctests.Rout.save 2009-08-18 19:35:29 UTC (rev 481)
@@ -63,7 +63,6 @@
"phylo4#ANY#character" would also be valid
>
> ## trace("prune",browser,signature="phylo4d")
-> set.seed(1)
> r1 <- rcoal(5)
>
> ## trace("phylo4d", browser, signature = "phylo")
@@ -110,7 +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: t4
+ The following nodes are not found in the dataset: t2
>
> plot(q2)
> plot(q2,type="cladogram")
@@ -237,64 +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 0.76359346
-16 <NA> 16 15 0.29744 internal -0.79900925
-17 <NA> 17 16 0.04924 internal -1.14765701
-18 <NA> 18 17 0.06859 internal -0.28946157
-19 <NA> 19 18 0.13404 internal -0.29921512
-20 <NA> 20 19 0.10346 internal -0.41151083
-21 <NA> 21 20 0.03550 internal 0.25222345
-22 <NA> 22 21 0.00917 internal -0.89192113
-23 <NA> 23 22 0.07333 internal 0.43568330
-24 <NA> 24 23 0.05500 internal -1.23753842
-25 <NA> 25 19 0.24479 internal -0.22426789
-26 <NA> 26 25 0.05167 internal 0.37739565
-27 <NA> 27 26 0.01500 internal 0.13333636
-1 fuliginosa 1 24 0.05500 tip 0.80418951
-2 fortis 2 24 0.05500 tip -0.05710677
-3 magnirostris 3 23 0.11000 tip 0.50360797
-4 conirostris 4 22 0.18333 tip 1.08576936
-5 scandens 5 21 0.19250 tip -0.69095384
-6 difficilis 6 20 0.22800 tip -1.28459935
-7 pallida 7 25 0.08667 tip 0.04672617
-8 parvulus 8 27 0.02000 tip -0.23570656
-9 psittacula 9 27 0.02000 tip -0.54288826
-10 pauper 10 26 0.03500 tip -0.43331032
-11 Platyspiza 11 18 0.46550 tip -0.64947165
-12 fusca 12 17 0.53409 tip 0.72675075
-13 Pinaroloxias 13 16 0.58333 tip 1.15191175
-14 olivacea 14 15 0.88077 tip 0.99216037
+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
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 0.7635935
-16 <NA> 16 15 0.29744 internal NA -0.7990092
-17 <NA> 17 16 0.04924 internal NA -1.1476570
-18 <NA> 18 17 0.06859 internal NA -0.2894616
-19 <NA> 19 18 0.13404 internal NA -0.2992151
-20 <NA> 20 19 0.10346 internal NA -0.4115108
-21 <NA> 21 20 0.03550 internal NA 0.2522234
-22 <NA> 22 21 0.00917 internal NA -0.8919211
-23 <NA> 23 22 0.07333 internal NA 0.4356833
-24 <NA> 24 23 0.05500 internal NA -1.2375384
-25 <NA> 25 19 0.24479 internal NA -0.2242679
-26 <NA> 26 25 0.05167 internal NA 0.3773956
-27 <NA> 27 26 0.01500 internal NA 0.1333364
-1 fuliginosa 1 24 0.05500 tip 0.80418951 NA
-2 fortis 2 24 0.05500 tip -0.05710677 NA
-3 magnirostris 3 23 0.11000 tip 0.50360797 NA
-4 conirostris 4 22 0.18333 tip 1.08576936 NA
-5 scandens 5 21 0.19250 tip -0.69095384 NA
-6 difficilis 6 20 0.22800 tip -1.28459935 NA
-7 pallida 7 25 0.08667 tip 0.04672617 NA
-8 parvulus 8 27 0.02000 tip -0.23570656 NA
-9 psittacula 9 27 0.02000 tip -0.54288826 NA
-10 pauper 10 26 0.03500 tip -0.43331032 NA
-11 Platyspiza 11 18 0.46550 tip -0.64947165 NA
-12 fusca 12 17 0.53409 tip 0.72675075 NA
-13 Pinaroloxias 13 16 0.58333 tip 1.15191175 NA
-14 olivacea 14 15 0.88077 tip 0.99216037 NA
+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
phyl4d> ### Example with 'all.data'x
phyl4d> nodeLabels(geoTree) <- as.character(nodeId(geoTree))
@@ -335,4 +334,4 @@
>
> proc.time()
user system elapsed
- 3.484 0.088 3.576
+ 2.444 0.065 2.625
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