Hi Eugen.
name.check() uses the row names of your data matrix, so that's why it
works now.
The error message that was returned by the -match() method suggests that
you have species in your "to include" file that are not actually in the
tree (thus match() returns one or multiple NAs). I did not anticipate
this. To get around it, just do:
>
pruned.tree<-drop.tip(tree,tree$tip.label[-na.omit(match(species.to.keep[,1],tree$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 1:08 PM, Eugen Egorov wrote:
Well, Liams suggestion produced an error message "only zeros are allowed
to be mixed with negative indices". I just tried a bunch of command
lines from various internet sites and came up with what seems to be a
solution. Here the skript:
tree<-read.tree("tree.tre")
data<-read.csv("data.csv")
data.frame(data[,1])->data1
rownames(data1)<-data[,1]
attach(data1)
name.check(tree, data1) -> overlap
comptree<-drop.tip(tree, overlap$Tree.not.data)
...and this works, but I don't know why exactly...seems like rownames is
an imprtant factor, cause it doesn't work without that command
line...for whatever reason...
Does that make any sense?
----- Original Message ----- From: "Graham Slater" <gsla...@ucla.edu>
To: "Liam J. Revell" <liam.rev...@umb.edu>
Cc: "Eugen Egorov" <eugen...@online.de>; <r-sig-phylo@r-project.org>
Sent: Friday, March 04, 2011 6:33 PM
Subject: Re: [R-sig-phylo] Pruning a tree
Yes, name.check() will only work with a named vector of data or data
frame, so Liam's code should work for you. it also looks like your names
in the vector "species" are different from those of the tip labels, as
you say that nc$Tree.not.data gives you a bunch of numbers but your
vector is made of Species underscore number, e.g. Species_1. If that's
the case, either change your file of species names to be just numbers,
or use the following to change your tree tip labels before using liam's
code.
tree$tip.label <- paste("Species", tree$tip.label, sep = "_")
------------------------------------------------------------
Graham Slater
Department of Ecology and Evolutionary Biology
University of California, Los Angeles
621 Charles E Young Drive South
Los Angeles
CA 90095-1606
(310) 825-4669
gsla...@ucla.edu
www.eeb.ucla.edu/gslater
On Mar 4, 2011, at 7:45 AM, Liam J. Revell wrote:
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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------------------------------------------------------------
Graham Slater Ph. D.
Department of Ecology and Evolutionary Biology
University of California, Los Angeles
610 Charles E. Young Drive South
Los Angeles, CA 90095-1606
(424) 442-4348
gsla...@ucla.edu
www.eeb.ucla.edu/gslater
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