[R-sig-eco] Bray-Curtis for more than pairwise overlap

[Jarrett Byrnes]

Jari,

Thanks, I'll look at those.  To answer your questions below

1) I'm looking at negative values as I'm not comparing dissimilarity in composition, but dissimilarity in species effects.  Sometimes they are negative.  I suppose I could add a constant to bring the lowest value to 0, but that seems incorrect.

2) I have actually written new R code, so, I'm sure its slower, but, I needed to do so in order to handle these cases.  I'll take a look at the methods you implemented to see if they'll work and/or compare to the multi-case derivation I've come up with.

-Jarrett

On May 4, 2012, at 10:15 PM, Jari Oksanen wrote:

> Jarrett,
> 
> I really do not understand what you try to do and what properties you expect your measure to have. However,  Baselga (Global Ecol Biogeog 19, 134-143; 2010) has proposed multiple site Sørensen (= Bray-Curtis for presence/absence) and Jaccard indices, and they are implemented as functions nestedbetasor() and nestedbetajac() in vegan (recent version).
Great, I'll look at these.

> 
> On 05/05/2012, at 00:48 AM, Jarrett Byrnes wrote:
> 
>> As implemented in the literature, Bray-Curtis dissimilarity measures are used to look at pairwise comparisons.  So, how dissimilar are 2 plots in their composition, for example.
>> 
>> I'm wondering if anyone has run across or implemented a method to look at BC dissimilarity or otherwise that has two different twists to it
>> 	1) Negative values are possible.
> 
> What do these negative values mean? Do they mean that compared groups are more similar than absolutely identical?
> 
> Methods that expect to have dissimilarities as input will not usually accept negative dissimilarities (but these can appear in results when analysing non-Euclidean indices, but that's another issue).
> 
>> 	2) The index is for an n-wise measure of dissimilarity.  For example, instead of asking how dissimilar 2 plots are, what is the dissimilarity between 3 plots.
>> 
>> I've been trying to play with vegdist to see if I can implement this, and have been rolling my own functions that work well with just presence-abscence data.  But I'm unclear of how to do so for continuous data.  Thanks!
>> 
> 
> In vegdist, the actual BC is calculated in C code. Do you mean that you have written new C code for this special variant or are you deriving your index from pairwise dissimilarities?
> 
> Cheers, Jari Oksanen
> -- 
> Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
> 
> 
> 
>