[R-sig-eco] dissimilarity and species turnover

[Michael Denslow]

Hi Everyone,

On Tue, Dec 15, 2009 at 12:21 PM, Jari Oksanen <jari.oksanen at oulu.fi> wrote:
> On 15/12/09 18:54 PM, "Amanda Stanley" <amanda at appliedeco.org> wrote:
>
>> Robert,
>> check out package ncf by Ottar Bjornstad
>> http://cran.r-project.org/web/packages/ncf/index.html.
>> The spline correlogram function might be what you need.  From the
>> documentation:
>>
>> "The spline (cross-)correlogram differes from the spatial correlogram (and
>> Mantel correlogram) in
>> that it estimated spatial dependence as a continous functions of distance
>> (rather than binning into
>> distance classes)."
>>
> Howdy,
>
> Actually, the binning is not *the* problem (and basic Mantel test does not
> use binning at all: it is only for the correlograms). The problem is
> partitioning *distances* into *additive* components like is implicitly done
> when you have something like partial Mantel tests.
>
> What you can do for a starter is to go the October archive of R-sig-eco
> which has two threads on the very same issues ("using two distance metrices
> in formula", "Mantel test with skew-symmetric matrices?") The staring
> questions were not exactly identical to this question, but the discussion
> soon radiated to relevant issues. I'd recommend you check Sarah Goslee's
> comments at the minimum. If you want to go deeper here (and you should if
> you are serious), dig up the late 2008 issue of the Ecology with the
> Legendre & mates vs. Tuomisto discussion -- somewhere around pages 3230 to
> 3256 of vol 89).

I think that the discussion that Jari is referring to is posted here:
http://www.bio.umontreal.ca/legendre/reprints/Beta_diversity_comments_2008.pdf

It is definitely worth reading!

Michael

>
> That's for the starter.
>
> Cheers, Jari Oksanen
>
>> I've been exploring using this approach for a similar problem. I'd be
>> curious to know the opinions of this group if it appropriately deals with
>> the issues surrounding Mantel tests.
>>
>> --Amanda Stanley
>>
>> ***
>> Amanda G. Stanley, Ph.D.
>> Project Director
>>
>> Institute for Applied Ecology
>> P.O. Box 2855
>> Corvallis, OR 97339-2855
>> (Phone)541-753-3099 x133
>> (Fax)541-753-3098
>>
>> amanda at appliedeco.org
>> www.appliedeco.org
>>
>> From: Robert Ptacnik <ptacnik at icbm.de>
>> To: r-sig-ecology at r-project.org
>> Date: Mon, 14 Dec 2009 17:26:39 +0100
>> Subject: [R-sig-eco] dissimilarity and species turnover
>> Hi,
>> mantel statistics has repeatedly been criticized. I wonder if there is an
>> (approved) alternative for my problem:
>> I aim to test whether one parameter (productivity, P) affects turnover (t)
>> among ecological communities in time (T) or space (S).  (ÄT and ÄS will be
>> used as a co-variables).
>> To avoid confusion - I do NOT aim to test whether P affects composition as
>> such (which could be tested by an ordination method), but whether the degree
>> of similarity among samples scales with P.
>>  My approach so far was to calculate a dissimilarity matrix from my
>> community data, distance matrices for the relevant environmental data (ÄT,
>> ÄS, ÄP) and a mean (P) matrix, giving the mean(P) for each pair of
>> observations.
>> The I performed mantel tests whether t correlates with mean(P), taking other
>> variables into account (partialing out). However, mantel and especially
>> partialing out are often criticized (e.g. see documentation in vegan).
>> any views?
>> thanks!
>> Robert
>>
>>
>> Robert Ptacnik, PhD
>>
>> ICBM, Univ. of Oldenburg
>> Schleusenstrasse 1, DE-26382 Wilhelmshaven
>> http://www.icbm.de/planktologie/en/
>>
>> ptacnik at icbm.de
>>
>> --
>>
>> [[alternative HTML version deleted]]
>>
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-- 
Michael Denslow

Graduate Student & Adjunct Instructor
I.W. Carpenter Jr. Herbarium [BOON]
Department of Biology
Appalachian State University
Boone, North Carolina U.S.A.
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