Hi Eugen,
Did you try my suggestion?
In your case, if the species you want to keep are in a row separated
text file, with a header ("species"), first read them in:
> species.to.keep<-read.table(file="species.list.file",header=T)
Now, for "phylo" object tree, type:
> pruned.tree<-drop.tip(tree,tree$tip.label[-match(species.to.keep[,1],
tree$tip.label)])
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
(new) email: liam.rev...@umb.edu
(new) blog: http://phytools.blogspot.com
On 3/4/2011 6:52 AM, Eugen Egorov wrote:
First of all, thank you for helping :)
Well, this didn't work out, although it should work perfectly. When I
type in "nc <- name.check(tree, data)" and then "nc" I get all tree
species (over 3000 species) in the $Tree.not.data part. In the $Data.not
tree part I see 281 numbers from "1" to "281", this is the number of
species in my data file. Seems like R doesnt recognize the species names
in the data file.
The data file is a .csv file and looks like this:
species
Species_1
Speceis_2
Species_3
....
Species_281
so its one column and nothing else. What should I do?
Thanks a lot
----- Original Message ----- From: "Graham Slater" <gsla...@ucla.edu>
To: "Eugen Egorov" <eugen...@online.de>
Cc: <r-sig-phylo@r-project.org>
Sent: Thursday, March 03, 2011 7:54 PM
Subject: Re: [R-sig-phylo] Pruning a tree
drop.tip assumes you have identified the tips that you want to remove,
which you could do using
nc <- name.check(tree, data).
newtree <- drop.tip(tree, nc[[1]])
or
newtree <- drop.tip(tree, nc$Tree.not.data) # note that Tree has a caps
and not using this could cause a weird tree with no tips to be output.
But if your data are simply a list of names (and I assume here you mean
you have a vector of names rather than an actual list) and you don't
know exactly which species are missing then the following might be easier:
missing <- tree$tip.label[is.na(match(tree$tip.label, listofnames))] ##
will use the match() function to identify the tips that are not present
in your list - it essentially is trying to match the tip names from the
tree to your list and if there is no match it reports NA for that tip.
we get the tip names corresponding to those NAs here
newtree <- drop.tip(tree, missing) # this will remove those tips
graham
On Mar 3, 2011, at 9:15 AM, Eugen Egorov wrote:
Hi all,
I have a huge tree and a list with species. Now I want to prune the
tree, so only species appearing in the list are left in the tree. I
tried the geiger package to compare tree species with those in the
list, but that didn't work out, because I recieved a tree with 0 tips
and 1 node after using "drop.tip$tree.not.data". I guess I have to
format the list, but I don't know in which way. Any idea how I do that?
greets
Eugen
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University of California, Los Angeles
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