Hi, maybe my mail was so ambitious... Is there any one that knows how specaccum() function works? And some references to better understand?

Thanks a lot!
I am sorry for my insistence.

EDGAR

Dear all, 
I am trying
to estimate the species richness from two periods of years (1998-1999 and
2005-2008), unfortunately I do not have the same sampling effort. Actually my
data corresponding to observer data from tropical tuna purse seine. I have four
groups of species (e.g. sea turtles, sharks and rays). So, the idea is compare
both periods of years, for instance, in the case of sharks and rays for the
first period I have 191 samples, but in 2005-2008 I only have 29 samples, with 20 and 12 species respectively.
I saw that
using rarefaction curves it is possible to know if I am underestimated the
total richness, and if my number of samples is sufficient. To achieve this it
supposes that I can use individual-based species accumulation curves and
sample-based species accumulation curves respectively. But, due to the sampling
effort difference it must be “rarified” the each database to get the
individual-based rarefaction curve and the corresponding sample-based.
I found specaccum()
and accumresult() functions in the R packages vegan and BiodiversityR to estimate
species accumulation curves (SAC) with some options in the method. 
In the help
of each function says that all methods are based on sampling sites without
replacements and only “rarefaction” method is based on individuals. However,
when I plot the results any method draws in the x-axis the number of the
samples. I think that I am actually estimating the corresponding sample-based
accumulation curve and the rarefied curve. But I cannot arrive to estimate the
individual-based. In the book “A primer of Ecology with R” there is an example
to estimate the individual-based rarefaction curve using the rarefy() function and
then it is possible to plot it, however, there is no function to estimate the
individual-based curve observed. In the help of the accumresult () function there
is an example to estimate the SAC with the “exact” method, so I change it by
the “collector” method (which estimates the observed curve) and the script it
suppose that estimate the individual-based curve, but, if I use the sample
instead the individuals I have the same plot but with different x-axis.
However, Gotelli and Colwell 2001, say that the sample-based curves will be below
of the individual-based curves.
Do you have
any idea if it is possible to estimate the individual-based curves and if I am
well estimating the sample-based curves?
Cheers.
 
EDGAR 

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