[R-sig-eco] how to detect different species among samples

[Martin Weiser]

Hi,
I am not sure that I get what you wanted, but if you are interested in
names, I propose something like this:

is.there <- dune
is.there[is.there > 1] <- 1 #change counts to presence/absence data
number.of.samples <- colSums(is.there)
single.occurrences<-names(dune)[number.of.samples ==1]
multiple.occurrences <- names(dune)[number.of.samples > 1] 

HTH,
Martin

what about:Gian Maria Niccolò Benucci píše v So 01. 02. 2014 v 14:08
+0100:
> Hi Sarah,
> 
> I am sorry, I'll try to be more precise. Given a dataset like...
> 
> > data(dune)
> > dune[1:8, 1:10]
>    Belper Empnig Junbuf Junart Airpra Elepal Rumace Viclat Brarut Ranfla
> 2       3      0      0      0      0      0      0      0      0      0
> 13      0      0      3      0      0      0      0      0      0      2
> 4       2      0      0      0      0      0      0      0      2      0
> 16      0      0      0      3      0      8      0      0      4      2
> 6       0      0      0      0      0      0      6      0      6      0
> 1       0      0      0      0      0      0      0      0      0      0
> 8       0      0      0      4      0      4      0      0      2      2
> 5       2      0      0      0      0      0      5      0      2      0
> 
> In this dataset we can see that the first species, named Belper, is present
> in samples 2, 4 and 5 but is absent in samples 13, 16 and so on... Now my
> question is, how can I extract the names of the species (and even their
> abundances) that are common and the species that are not common between the
> different samples in my dataset?
> 
> Many thanks in advance,
> 
> --
> Gain
> 
> 
> 
> 
> 
> 
> On 1 February 2014 13:42, Sarah Goslee <sarah.goslee at gmail.com> wrote:
> 
> > Hi Gian,
> >
> > I don't understand what you're trying to do. Can you give a simple example
> > of your data and what your results should be?
> >
> > Sarah
> >
> > On Saturday, February 1, 2014, Gian Maria Niccol Benucci <
> > gian.benucci at gmail.com> wrote:
> >
> >> Hi all R-sig-ecologists,
> >>
> >>
> >> Sorry for the very simple and probably stupid question. I was wandering if
> >> exist a simple method or a function in R, to detect which different
> >> species
> >> are present among the samples of a given data community matrix.
> >> Thanks a lot in advance,
> >>
> >> --
> >> Gian
> >>
> >
> >
> > --
> > Sarah Goslee
> > http://www.stringpage.com
> > http://www.sarahgoslee.com
> > http://www.functionaldiversity.org
> >
> 
> 	[[alternative HTML version deleted]]
> 
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