[R-sig-eco] removing singleton taxa

[Peter Solymos]

Kate,

To get what you want the simplest way try:

df1[,colSums(df1>0)>1,drop=FALSE]

Note the drop=FALSE argument, which makes sure that you still get a
matrix if only one species occurs in more than one sites (i.e. no
surprising vector results in the end).

Cheers,

Peter

--
Péter Sólymos, Dept Biol Sci, Univ Alberta, T6G 2E9, Canada AB
solymos at ualberta.ca, Ph 780.492.8534, http://psolymos.github.com
Alberta Biodiversity Monitoring Institute, http://www.abmi.ca
Boreal Avian Modelling Project, http://www.borealbirds.ca


On Mon, Dec 17, 2012 at 5:43 PM, Chris Howden
<chris at trickysolutions.com.au> wrote:
> 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.
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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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