[R-sig-eco] dissimilarity and species turnover

Jari Oksanen jari.oksanen at oulu.fi
Tue Dec 15 18:21:53 CET 2009

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)."

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). 

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
> --
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