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

[Martin Weiser]

Hi Gian,

there are many ways to do it. In the line with my previous post, you can
do:
new.data <- dune[c(Line.number.where.sampleA.I.am.interested.in.lies,
Line.number.where.sampleB.I.am.interested.in.lies), ]

and proceed with the new.data like with the dune (as I wrote you
already)

another approach:

species.names.from.the.sampleA <-
names(dune)[dune[Line.number.where.sampleA.I.am.interested.in.lies,]>0]
species.names.from.the.sampleB
<-names(dune)[dune[Line.number.where.sampleB.I.am.interested.in.lies,]>0]
multiple.occurrences <-
c(species.names.from.sampleA,species.names.from.sampleB)[duplicated(c(species.names.from.sampleA,species.names.from.sampleB))]
single.occurrences <-
unique(c(species.names.from.sampleA,species.names.from.sampleB))

HTH
Martin





-------- Přeposlaná zpráva --------
> Od: Gian Maria Niccolò Benucci <gian.benucci at gmail.com>
> Komu: r-sig-ecology at r-project.org
> Předmět: 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 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]]
> > >
> > > _______________________________________________
> > > R-sig-ecology mailing list
> > > R-sig-ecology at r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
> >
> >
> >
> 
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