[R-sig-eco] rarefied data output

[Jari Oksanen]

On 28/03/2012, at 18:59 PM, cristabel.duran wrote:

> On 03/28/2012 05:36 PM, Jari Oksanen wrote:
>> 
> 
> thank you for your help. I want to know the rarefied richness of single plots. 
> and I  just now rarefied my data within each factor level with rarefy(), and I got what I was looking for.
> 
> I was wondering that the rarefy richness really is much lower than the original:
> original:
> 
>         
> 
>  P1  P5  P9 P11 P17 P23 P30 P33 P36 P38 P41 P50 P54 P56 P59 P62 
>   9  14   2   8  10  11   6   7   6  16  13  10  11  12  10  12
> 
> 
>       
> 
> rarefied:
> 
>         
> 
>       P1       P5       P9      P11      P17      P23      P30      P33      P36 
> 3.313725 2.827956 2.000000 3.293040 2.946823 3.592810 2.263004 3.087552 3.195238 
>      P38      P41      P50      P54      P56      P59      P62 
> 3.659412 3.547713 2.555684 3.376906 3.202633 3.227595 3.428148
> 
> 
>       
> 
> My data is from regeneration of tropical forest, with few species with high abundance and lots of species with few abundance.
> 
> I do doubt of the results, but as I never worked with rarefaction I do not know how interpret such a disparity between non-rarefied and rarefied richness.

Well, the function has been tested and used before...

Study these questions with your data: How many trees did you have originally in each plot? How many trees do you have in your rarefied plots? How many species can you have with that number of trees?

Cheers, Jari Oksanen
-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksanen at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa