Hi List,

I’m using  the vegan function specaccum to produce a rarefaction curve. In
the function’s help it says: “Function ‘specaccum’ finds species
accumulation curves or the number of species for a certain number of sampled
sites or individuals”. Well, I would like to finds this curve for
individuals, but when I compute it the function (using the ‘rarefaction’
method) gives me Sites, Richness and Standand Deviation as values. When I
plot it, y axis is the richness (ok with that) and x axis is Sites (here is
the question), how could I make it calculate and plot the accumulating
individuals number?

Well, one problem may be the fact that my data frame has species as columns
and Sites as rows (and abundance data frame)… May you help me?

 

Ps.: The ‘rarefaction’ method option brings this details: “All these methods
are based on sampling sites without replacement. In contrast, the ‘method =
"rarefaction"’ finds the expected species richness and its standard
deviation by sampling individuals instead of sites”. Exactly what I really
want, but not what I get!

 

Here is the command line used.

plot(specaccum(Spp[,-227],'rarefaction'),col='black',lwd=2,ci.lty=0,ci.type=
'poly',ci.col='lightgray',ylab='Riqueza',ylim=c(0,250),yaxp=c(0,250,10),bty=
'n',main='Fauna Viva - Bacia de Campos - Março 2009')

 

Thank you very much.

Regards.

 

-------------------------------------------------------------

MSc.  <mailto:r.aluizio@gmail.com> Rodrigo Aluizio

Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000




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