Hi all,
Not sure if this is a bug, but I noticed weird behavior when
loading a tree with APE and then converting to phylo4 to do
descendants() -- not all the tips are produced.
Example:
library(ape)
library(phylobase)
trstr =
"((((((((P_hawaiiensis_WaikamoiL1:0.9656850499,P_mauiensis_Eke:0.9656850499):0.7086257935,(P_fauriei2:1.230218511,P_hathewayi_1:1.230218511):0.4440923324):0.1767115552,(P_kaduana_PuuKukuiAS:1.851022399,P_mauiensis_PepeAS:1.851022399):0.0008897862802):0.3347375986,P_kaduana_HawaiiLoa:2.185759997):0.302349378,(P_greenwelliae07:1.131363255,P_greenwelliae907:1.131363255):1.35674612):1.689170274,((((P_mariniana_MauiNui:1.994011054,P_hawaiiensis_Makaopuhi:1.994011054):0.7328279804,P_mariniana_Oahu:2.726839034):0.2574151709,P_mariniana_Kokee2:2.984254205):0.4601084855,P_wawraeDL7428:3.444362691):0.732916959):0.7345185743,(P_grandiflora_Kal2:2.479300491,P_hobdyi_Kuia:2.479300491):2.432497733):0.2873119899,((P_hexandra_K1:2.363984189,P_hexandra_M:2.363984189):0.4630447802,P_hexandra_Oahu:2.826939991):2.372081244);"
# Load tree
tr = read.tree(file="", text=trstr)
tr
# Convert to phylo4
tr4 = as(tr, "phylo4")
# Find root (node 20)
rootnode = nodeId(tr4, type="root")
rootnode
# Only 3 tips! (there should be 19)
tipnames = descendants(phy=tr4, node=rootnode, type="tips")
tipnames
The problem is here in descendants():
if (phy@order == "preorder") {
edge <- phy@edge
}
else {
edge <- reorder(phy, order = "preorder")@edge
}
ancestor <- as.integer(edge[, 1])
descendant <- as.integer(edge[, 2])
isDes <- .Call("descendants", node, ancestor, descendant)
...it works if I force phy@order to "cladewise" or "unknown"
library(ape)
library(phylobase)
trstr =
"((((((((P_hawaiiensis_WaikamoiL1:0.9656850499,P_mauiensis_Eke:0.9656850499):0.7086257935,(P_fauriei2:1.230218511,P_hathewayi_1:1.230218511):0.4440923324):0.1767115552,(P_kaduana_PuuKukuiAS:1.851022399,P_mauiensis_PepeAS:1.851022399):0.0008897862802):0.3347375986,P_kaduana_HawaiiLoa:2.185759997):0.302349378,(P_greenwelliae07:1.131363255,P_greenwelliae907:1.131363255):1.35674612):1.689170274,((((P_mariniana_MauiNui:1.994011054,P_hawaiiensis_Makaopuhi:1.994011054):0.7328279804,P_mariniana_Oahu:2.726839034):0.2574151709,P_mariniana_Kokee2:2.984254205):0.4601084855,P_wawraeDL7428:3.444362691):0.732916959):0.7345185743,(P_grandiflora_Kal2:2.479300491,P_hobdyi_Kuia:2.479300491):2.432497733):0.2873119899,((P_hexandra_K1:2.363984189,P_hexandra_M:2.363984189):0.4630447802,P_hexandra_Oahu:2.826939991):2.372081244);"
# Load tree
tr = read.tree(file="", text=trstr)
tr
# Convert to phylo4
tr4 = as(tr, "phylo4")
# Looks like by default the tree is called "preorder"
tr4@order
# It works if I do this:
tr4@order = "cladewise"
# Find root (node 20)
rootnode = nodeId(tr4, type="root")
rootnode
# Now this works
tipnames = descendants(phy=tr4, node=rootnode, type="tips")
tipnames
# This also works:
# Load tree
tr = read.tree(file="", text=trstr)
tr
# Convert to phylo4
tr4 = as(tr, "phylo4")
# Looks like by default the tree is called "preorder"
tr4@order
# It works if I do this:
tr4@order = "unknown"
# Find root (node 20)
rootnode = nodeId(tr4, type="root")
rootnode
# Now this works
tipnames = descendants(phy=tr4, node=rootnode, type="tips")
tipnames
...so at least there's a workaround...
Cheers,
Nick
--
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Graduate Student Instructor, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page:
http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: [email protected]
Mailing address:
Department of Integrative Biology
1005 Valley Life Sciences Building #3140
Berkeley, CA 94720-3140
-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong.
When people thought the earth was spherical, they were
wrong. But if you think that thinking the earth is spherical
is just as wrong as thinking the earth is flat, then your
view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The
Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
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