[Phylobase-commits] r672 - pkg/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 29 06:05:18 CEST 2009
Author: pdc
Date: 2009-09-29 06:05:17 +0200 (Tue, 29 Sep 2009)
New Revision: 672
Modified:
pkg/tests/misctests.R
pkg/tests/misctests.Rout.save
pkg/tests/nexusdata.Rout.save
pkg/tests/phylo4dtests.Rout.save
pkg/tests/phylotorture.Rout.save
Log:
Update one test file to have the right edge matrix and the Rout.save files for the remaining tests
Modified: pkg/tests/misctests.R
===================================================================
--- pkg/tests/misctests.R 2009-09-29 03:10:03 UTC (rev 671)
+++ pkg/tests/misctests.R 2009-09-29 04:05:17 UTC (rev 672)
@@ -107,6 +107,6 @@
11, 5,
11, 6,
11, 7,
- NA, 8), ncol=2,byrow=TRUE)
+ 0, 8), ncol=2,byrow=TRUE)
P2 <- phylo4(E)
Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save 2009-09-29 03:10:03 UTC (rev 671)
+++ pkg/tests/misctests.Rout.save 2009-09-29 04:05:17 UTC (rev 672)
@@ -1,5 +1,5 @@
-R version 2.9.1 (2009-06-26)
+R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
@@ -187,7 +187,7 @@
1 Strix_aluco 1 5 4.2 tip 1
2 Asio_otus 2 5 4.2 tip 2
3 Athene_noctua 3 4 7.3 tip 3
-4 <NA> 4 NA NA root NA
+4 <NA> 4 0 NA root NA
5 <NA> 5 4 3.1 internal NA
phyl4d> obj <- phylo4d(as(tree.owls.bis,"phylo4"),data.frame(wing=1:3), match.data=FALSE)
@@ -197,7 +197,7 @@
1 Strix_aluco 1 5 4.2 tip 1
2 Asio_otus 2 5 4.2 tip 2
3 Athene_noctua 3 4 7.3 tip 3
-4 <NA> 4 NA NA root NA
+4 <NA> 4 0 NA root NA
5 <NA> 5 4 3.1 internal NA
phyl4d> print(obj)
@@ -205,7 +205,7 @@
1 Strix_aluco 1 5 4.2 tip 1
2 Asio_otus 2 5 4.2 tip 2
3 Athene_noctua 3 4 7.3 tip 3
-4 <NA> 4 NA NA root NA
+4 <NA> 4 0 NA root NA
5 <NA> 5 4 3.1 internal NA
phyl4d> ####
@@ -257,19 +257,19 @@
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
-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
+15 N15 15 0 NA root NA -1.47075238
+16 N16 16 15 0.29744 internal NA -0.47815006
+17 N17 17 16 0.04924 internal NA 0.41794156
+18 N18 18 17 0.06859 internal NA 1.35867955
+19 N19 19 18 0.13404 internal NA -0.10278773
+20 N20 20 19 0.10346 internal NA 0.38767161
+21 N21 21 20 0.03550 internal NA -0.05380504
+22 N22 22 21 0.00917 internal NA -1.37705956
+23 N23 23 22 0.07333 internal NA -0.41499456
+24 N24 24 23 0.05500 internal NA -0.39428995
+25 N25 25 19 0.24479 internal NA -0.05931340
+26 N26 26 25 0.05167 internal NA 1.10002537
+27 N27 27 26 0.01500 internal NA 0.76317575
phyl4d> (matchData2 <- phylo4d(trGeo, tip.data=tDt, node.data=nDt, merge.data=TRUE))
label node ancestor edge.length node.type a
@@ -287,19 +287,19 @@
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
-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
+15 N15 15 0 NA root -1.47075238
+16 N16 16 15 0.29744 internal -0.47815006
+17 N17 17 16 0.04924 internal 0.41794156
+18 N18 18 17 0.06859 internal 1.35867955
+19 N19 19 18 0.13404 internal -0.10278773
+20 N20 20 19 0.10346 internal 0.38767161
+21 N21 21 20 0.03550 internal -0.05380504
+22 N22 22 21 0.00917 internal -1.37705956
+23 N23 23 22 0.07333 internal -0.41499456
+24 N24 24 23 0.05500 internal -0.39428995
+25 N25 25 19 0.24479 internal -0.05931340
+26 N26 26 25 0.05167 internal 1.10002537
+27 N27 27 26 0.01500 internal 0.76317575
phyl4d> ## Example with 'all.data'
phyl4d> nodeLabels(geoTree) <- as.character(nodeId(geoTree, "internal"))
@@ -331,19 +331,19 @@
12 13 12 17 0.53409 tip j
13 3 13 16 0.58333 tip k
14 6 14 15 0.88077 tip d
-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>
+15 N15 15 0 NA root <NA>
+16 N16 16 15 0.29744 internal <NA>
+17 N17 17 16 0.04924 internal <NA>
+18 N18 18 17 0.06859 internal <NA>
+19 N19 19 18 0.13404 internal <NA>
+20 N20 20 19 0.10346 internal <NA>
+21 N21 21 20 0.03550 internal <NA>
+22 N22 22 21 0.00917 internal <NA>
+23 N23 23 22 0.07333 internal <NA>
+24 N24 24 23 0.05500 internal <NA>
+25 N25 25 19 0.24479 internal <NA>
+26 N26 26 25 0.05167 internal <NA>
+27 N27 27 26 0.01500 internal <NA>
phyl4d> (exGeo7 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=FALSE))
label node ancestor edge.length node.type x
@@ -361,19 +361,19 @@
12 13 12 17 0.53409 tip l
13 3 13 16 0.58333 tip j
14 6 14 15 0.88077 tip a
-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>
+15 N15 15 0 NA root <NA>
+16 N16 16 15 0.29744 internal <NA>
+17 N17 17 16 0.04924 internal <NA>
+18 N18 18 17 0.06859 internal <NA>
+19 N19 19 18 0.13404 internal <NA>
+20 N20 20 19 0.10346 internal <NA>
+21 N21 21 20 0.03550 internal <NA>
+22 N22 22 21 0.00917 internal <NA>
+23 N23 23 22 0.07333 internal <NA>
+24 N24 24 23 0.05500 internal <NA>
+25 N25 25 19 0.24479 internal <NA>
+26 N26 26 25 0.05167 internal <NA>
+27 N27 27 26 0.01500 internal <NA>
phyl4d> (exGeo8 <- phylo4d(trGeo, tip.data=tDt, rownamesAsLabels=FALSE, match.data=FALSE))
label node ancestor edge.length node.type x
@@ -391,19 +391,19 @@
12 13 12 17 0.53409 tip l
13 3 13 16 0.58333 tip m
14 6 14 15 0.88077 tip n
-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>
+15 N15 15 0 NA root <NA>
+16 N16 16 15 0.29744 internal <NA>
+17 N17 17 16 0.04924 internal <NA>
+18 N18 18 17 0.06859 internal <NA>
+19 N19 19 18 0.13404 internal <NA>
+20 N20 20 19 0.10346 internal <NA>
+21 N21 21 20 0.03550 internal <NA>
+22 N22 22 21 0.00917 internal <NA>
+23 N23 23 22 0.07333 internal <NA>
+24 N24 24 23 0.05500 internal <NA>
+25 N25 25 19 0.24479 internal <NA>
+26 N26 26 25 0.05167 internal <NA>
+27 N27 27 26 0.01500 internal <NA>
phyl4d> require(ape) ## for rcoal
@@ -482,10 +482,7 @@
+ 11, 5,
+ 11, 6,
+ 11, 7,
-+ NA, 8), ncol=2,byrow=TRUE)
++ 0, 8), ncol=2,byrow=TRUE)
>
> P2 <- phylo4(E)
>
-> proc.time()
- user system elapsed
- 2.708 0.096 2.950
Modified: pkg/tests/nexusdata.Rout.save
===================================================================
--- pkg/tests/nexusdata.Rout.save 2009-09-29 03:10:03 UTC (rev 671)
+++ pkg/tests/nexusdata.Rout.save 2009-09-29 04:05:17 UTC (rev 672)
@@ -1,5 +1,5 @@
-R version 2.9.1 (2009-06-26)
+R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
@@ -35,6 +35,3 @@
> ## summary(multiLineTrees)
>
>
-> proc.time()
- user system elapsed
- 0.444 0.040 0.481
Modified: pkg/tests/phylo4dtests.Rout.save
===================================================================
--- pkg/tests/phylo4dtests.Rout.save 2009-09-29 03:10:03 UTC (rev 671)
+++ pkg/tests/phylo4dtests.Rout.save 2009-09-29 04:05:17 UTC (rev 672)
@@ -1,5 +1,5 @@
-R version 2.9.1 (2009-06-26)
+R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
@@ -18,8 +18,6 @@
Type 'q()' to quit R.
> library(phylobase)
-Loading required package: grid
-Loading required package: ape
> require(ape)
> tree.phylo <- read.tree(text="(((A,B)C,D),E);") #only one node is labelled
> tree <- as(tree.phylo, "phylo4")
@@ -65,7 +63,7 @@
2 B 2 7 NA tip
3 D 3 6 NA tip
4 E 4 5 NA tip
-5 5 NA NA root
+5 5 0 NA root
6 6 5 NA internal
7 C 7 6 NA internal
> print(treed)
@@ -74,11 +72,8 @@
2 B 2 7 NA tip 2
3 D 3 6 NA tip 4
4 E 4 5 NA tip 3
-5 5 NA NA root NA
+5 5 0 NA root NA
6 6 5 NA internal NA
7 C 7 6 NA internal NA
>
>
-> proc.time()
- user system elapsed
- 1.800 0.044 1.836
Modified: pkg/tests/phylotorture.Rout.save
===================================================================
--- pkg/tests/phylotorture.Rout.save 2009-09-29 03:10:03 UTC (rev 671)
+++ pkg/tests/phylotorture.Rout.save 2009-09-29 04:05:17 UTC (rev 672)
@@ -1,5 +1,5 @@
-R version 2.9.1 (2009-06-26)
+R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
@@ -100,7 +100,7 @@
3 T3 3 8 NA tip
4 T4 4 9 NA tip
5 T5 5 9 NA tip
-6 <NA> 6 NA NA internal
+6 <NA> 6 0 NA internal
7 <NA> 7 6 NA internal
8 <NA> 8 6 NA internal
9 <NA> 9 9 NA internal
@@ -141,7 +141,6 @@
> ## both of the following now fail with
> ## "root node is not at position (nTips+1)
> try(as(broke3,"phylo4") -> tree3) # works with no error message
-Error in .local(x, ...) : root node must be first row of edge matrix
> try(phylo4(broke3$edge)) # works with no error message
label node ancestor edge.length node.type
1 T1 1 6 NA tip
@@ -150,7 +149,7 @@
4 T4 4 9 NA tip
5 T5 5 9 NA tip
6 <NA> 6 7 NA internal
-7 <NA> 7 NA NA internal
+7 <NA> 7 0 NA internal
8 <NA> 8 7 NA internal
9 <NA> 9 8 NA internal
> ## plot(tree3) # would work if we could create it?
@@ -196,6 +195,3 @@
> edge <- matrix(c(3,1,3,2),byrow=TRUE,ncol=2)
> try(p2 <- phylo4(edge), silent=TRUE)
>
-> proc.time()
- user system elapsed
- 1.744 0.044 1.807
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