joey711/phyloseq — Issue #40: reconcile_species() not pruning tree properly (or at all?)
Author: joey711
Created: 2011-10-21 00:20:30+00:00
State: open
Labels: Bug

This was originally detected as a bug in wUniFrac(), which is now closed, because its actually a pruning issue here.

# define the example data, from picante package
data(phylocom)
tree <- phylocom$phylo
OTU <- otuTable(phylocom$sample, speciesAreRows=FALSE)
ex3 <- phyloseq(OTU, tree)

#
reconcile_species(ex3)
otuTree Object

<<< tree >>>
"phylo4"-class phylogenetic tree with
32 tips, and 31 internal nodes.
Tips: sp1 sp2 sp3 ...
Rooted.
<<< tree >>>

OTU Table [6 by 25]:
Samples: clump1, clump2a ... even, random
Species: sp1, sp10 ... sp8, sp9
sp1 sp10 sp11 sp12
clump1 1 0 0 0
clump2a 1 2 2 2
clump2b 1 0 0 0
...