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

[Olmo]

 Hi and sorry, I didn't know how is your data. You could try spp.est
 from fossil package, I hope you find it useful.

 Best luck,
Olmo.

El Sat, 1 Feb 2014 20:07:52 +0100
Gian Maria Niccolò Benucci <gian.benucci at gmail.com> escribió:
> Dear all,
> 
> Thanks for the precious tips you gave...
> Olmo, I would not go for ordination such I have few samples but many
> species as I am working with microbial NGS sequencing data. I have
> not such samples to have a very nice view of alfa and beta diversity
> of my habitats I suppose...
> 
> Stefano, I like your script, I thought something similar to get
> species frequencies:
> 
> species.presence <- apply(dune>0, 2, sum)
> 
> moreover I tried to go for classified community table with vegemite()
> 
> vegemite(varespec, clus, scale = "Hult")
> 
>            1   111  1211221212222
>          431567380922149306254578
>  Cet.niv 21.111.111....11........
>  Cla.ama .1.1...1................
>  Ste.sp  111211111....111.1.111.1
>  Pol.pil ..111..1......111..1....
>  Dip.mon .1...111.1...........1..
>  Cla.phy ..1.....11...1..........
>  Cla.ran 344544332133111223121121
>  Cla.cer 1.........1..........1..
>  Cla.ste 454121215555213111111.1.
>  Cla.arb 322344331111132222121111
>  Vac.uli 11...2.1........1.1..111
> 
> I was wandering if possible to plot abundances instead of coverage
> values usually used in vegetation science... if I omit the scale
> argument the function give me back an error.
> 
> Thanks again,
> 
> Gian
> 
> 
> 
> 
> 
> On 1 February 2014 18:04, Stefano Leonardi
> <stefano.leonardi at gmail.com>wrote:
> 
> > apply( dune[1:8, 1:10],2,sum)
> >
> > or
> >
> > barplot(apply(data.df, 2,sum),las=3 )
> >
> > ;-)
> >
> > Stefano
> >
> >
> > On 01/02/2014 14:08, Gian Maria Niccolò Benucci wrote:
> >
> >> 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 Niccolò 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
> >>
> >>
> >
> > --
> > ======================================================================
> >  Stefano Leonardi
> >  Dipartimento di Bioscienze
> >  Universita` di Parma                E-mail:
> > stefano.leonardi at unipr.it Viale Usberti
> > 11a                             Phone : +39-0521-905659 43124
> > PARMA  (Italy)                          Fax   : +39-0521-905402
> >
> >  Il mio photoblog:
> > http://stefanoleonardi.wordpress.com
> > ======================================================================
> >
> 
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>