[R-sig-eco] Rarefaction related queries

[Rajendra Mohan panda]

Dear Jari Oksanen

Thanks a lot for your advise and response to my mail all the time I send to
the forum. I could get the results as per my requirement using 'derarefy'.


With Best Regards
Rajendra M Panda
School of water resources
Indian Institute of Technology Kharagpur

On Wed, Apr 29, 2015 at 8:59 PM, Jari Oksanen <jari.oksanen at oulu.fi> wrote:

>
> On 29/04/2015, at 17:25 PM, Rajendra Mohan panda wrote:
>
> > Dear All
> >
> > I am struggling to rarefy my species data. If I use rarefy function in
> > vegan, I get two columns for all the dataset (312 rows and 6220 columns)
> > even if I change the sample value.
> >
> > If I use rarefaction function of *Jenna Jacobs - email at jennajacobs.org
> > <email at jennajacobs.org>, *I get different rows and columns for the same
> > input data.
> >
> > If I understand properly, the data with sample =5 should yield one-fifth
> of
> > the total rows*columns of input data but that does not come.
> >
> Dear Rajendra Mohan,
>
> I have no idea what you mean with rarefaction. However, rarefy() function
> does what it is documented to do: it gives the rarefied number of species
> for each *row* (sampling unit) of your data. So you should get 312 rarefied
> species richness values for your data. You should only get two columns for
> each sampling unit if you specify se=TRUE in which case you also get what
> they call "standard error" of the rarefied number of species. The function
> assumes your data be counts (of individuals) so that you can meaningfully
> rarefy each sampling unit separately.
>
> It sounds like you did not want to get this, but something completely
> different. It could be useful if you give a hint about your desired outcome.
>
> There are some other functions in vegan that do something else that may be
> closer to what you want to get. Function rrarefy() returns one *random*
> rarefied community of your data -- each call returning a different
> realization of rarefaction. Function drarefy() gives probabilities for each
> species to occur in a rarefied sample of each sampling unit. Functions in
> specaccum() bunch sample subsets of sampling units instead of sampling
> individuals within sampling units. Several other packages have several
> other functions that do the same, almost the same, similar or completely
> different things loosely associated with rarefaction.
>
> Cheers, Jari Oksanen
>
>

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