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@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@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@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@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>>
>
> --
> ======================================================================
>  Stefano Leonardi
>  Dipartimento di Bioscienze
>  Universita` di Parma                E-mail: stefano.leonardi@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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