I changed " pruned.tree" to" tree.pruned."
The error still existed.
Elaine
---------- Forwarded message ----------
From: Elaine Kuo <elaine.kuo...@gmail.com>
Date: Fri, Apr 5, 2013 at 6:12 PM
Subject: atomic vector for write.nexus
To: r-sig-phylo@r-project.org
Hello,
This is Elaine.
I am using the command "write.nexus"in package (ape)
to generate a nexus file after pruning a phylogeny tree.
However, an error appeared, saying
Error in obj[[i]]$tip.label : $ operator is invalid for atomic vectors
I searched the archive but found no similar experience in this command.
Please kindly help explain what it means and how to solve it.
code
library(ape)
# read data and tree
birddata <- read.csv("H:/birddata_family_20130405.csv", header = TRUE)
birdtree <- read.nexus("H:/birddata_family_20130405.nexus")
setwd("H:")
species.to.keep <-read.csv("H:/birddata_family_20130405.csv", header =
TRUE)
tree.pruned<-drop.tip(birdtree,birdtree$tip.label[-
na.omit(match(species.to.keep[,1],birdtree$tip.label))])
## prune the data to include only those taxa in the pruned tree
data.pruned <- birddata[tree.pruned$tip.label, ] (Thanks to Klaus and
others)
write.nexus(tree.pruned, "H:/pruneddata_20130405.nexus", translate =
FALSE)
Elaine
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