[R-sig-eco] removing singleton taxa

[Chris Howden]

I'm not sure if I've got the syntax quite right ((m about to rush out the
door), but how about something like.

check <- colSums(df1>0)  ~ gives U a vector of the number of sites with
abundance > 0 for each species
check2 <- [check>1]          ~ gives U a logical vector which is FALSE  if
a species occurs in 0 or 1 site, TRUE otherwise

df2 <- df1[,check2]            ~ subset those columns that are TRUE i.e.
have a species in more than 1 site.



Chris Howden B.Sc. (Hons) GStat.
Founding Partner
Evidence Based Strategic Development, IP Commercialisation and Innovation,
Data Analysis, Modelling and Training
(mobile) 0410 689 945
(fax) +612 4782 9023
chris at trickysolutions.com.au




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-----Original Message-----
From: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Kate Boersma
Sent: Tuesday, 18 December 2012 11:23 AM
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] removing singleton taxa

Hi list. I am new to R and stuck on a very simple problem. Forgive me if
this is not the right forum for my question - feel free to refer me
elsewhere.

I have a community matrix of sites*species, and I want to remove species
that only occur in a single site (singleton taxa). It sounds so simple,
but I have spent hours (no joke) with google and my reference books and am
still stuck.

Here's some example code:
Species1 = sample(0:20, 10, replace=TRUE)
Species2 = sample(0:20, 10, replace=TRUE)
Species3 = c(0,0,0,0,0,0,0,4,0,0)
df1 = data.frame(Species1, Species2, Species3)
df1

I want to remove Species 3. Basically, I want R to count the number of
non-zero cells in a column and remove the column if that number is 1 or 0.

I have tried messing around with rowsums(), length(), table() and
specnumber() in the vegan package and can't figure it out.

Thanks,
Kate

--
Kate Boersma
PhD Candidate
Oregon State University
Department of Zoology
Cordley 3029
Corvallis, OR 97331
kate.boersma at science.oregonstate.edu

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