How to subsample a community dataset

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How to subsample a community dataset

Alexandre F. Souza
Hi everyone,

I have two community matrices, one which is presence-absence and the other
which contains abundances of hundreds of species in hundreds of localities.
Because localities had different sizes, I would like to standardize the
number of species per locality before performing beta-diversity
compositional analyses. Are you aware of any packages or functions that
perform this task?

Thank you very much in advance,

Sincerely,

Alexandre

--
Dr. Alexandre F. Souza
Professor Associado
Chefe do Departamento de Ecologia
Universidade Federal do Rio Grande do Norte
CB, Departamento de Ecologia
Campus Universit√°rio - Lagoa Nova
59072-970 - Natal, RN - Brasil
lattes: lattes.cnpq.br/7844758818522706
http://www.esferacientifica.com.br
https://www.youtube.com/user/alexfadigas
http://www.docente.ufrn.br/alexsouza
orcid.org/0000-0001-7468-3631 <http://www.docente.ufrn.br/alexsouza>

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Re: How to subsample a community dataset

trichter
Hi Alexandre,

i am not sure if i understood you correctly, but if you want to  
normalize your samples to a common sample size (e.g., to the lowest  
amount
of observations across all localities), there is vegan's "rrarefy" for  
this purpose:
https://www.rdocumentation.org/packages/vegan/versions/2.4-2/topics/rarefy

Note that this way of subsampling may remove some (rare) species  
entirely, so the presence/absence matrix of a rarefied dataset may  
(slightly) differ
from the one you are working with now.

If you happen to work with microbial data, there are plenty more ways  
to normalize your data set.
Hope this helps, Tim


Zitat von "Alexandre F. Souza" <[hidden email]>:

> Hi everyone,
>
> I have two community matrices, one which is presence-absence and the other
> which contains abundances of hundreds of species in hundreds of localities.
> Because localities had different sizes, I would like to standardize the
> number of species per locality before performing beta-diversity
> compositional analyses. Are you aware of any packages or functions that
> perform this task?
>
> Thank you very much in advance,
>
> Sincerely,
>
> Alexandre



--
Tim Richter-Heitmann
Universität Bremen

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