Od: Gian Maria Niccol? Benucci <gian.benucci at gmail.com>
Komu: r-sig-ecology at r-project.org
P?edm?t: Re: [R-sig-eco] how to detect different species among samples
Datum: Mon, 3 Feb 2014 17:50:51 +0100
Hi Martin,
thanks a lot. Also your commands are working... It's very nice to see how
different solutions in R can be found for a single problem.
I just have another question now, but... if I would know which species are
in common (and which not) between two particular selected samples?
Thanks for the brainstorming :)
Gian
On 3 February 2014 17:01, Martin Weiser <weiser2 at natur.cuni.cz> wrote:
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 Niccol? Benucci p??e 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
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
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
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
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
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