[R-sig-eco] dissimilarity and species turnover

[Marcelino de la Cruz]

One recent technique developed by Simon Ferrier 
and mates [Diversity and Distributions,  (2007) 
13 , 252–264] is Generalized Dissimilarity 
Modeling. It looks very appropriated for species 
turnover studies and, probably becasue of its 
short life there are still no "issues" of 
concern, or at least I am unaware of  :)

They have an R implementation too.

 From their abstract:

Generalized dissimilarity modelling (GDM) is a 
statistical technique for analysing
and predicting spatial patterns of turnover in 
community composition (beta diversity)
across large regions. The approach is an 
extension of matrix regression, designed
specifically to accommodate two types of nonlinearity commonly encountered in
large-scaled ecological data sets: (1) the 
curvilinear relationship between increasing
ecological distance, and observed compositional 
dissimilarity, between sites; and
(2) the variation in the rate of compositional 
turnover at different positions along
environmental gradients.


At 18:21 15/12/2009, Jari Oksanen 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).
>
>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]]
> >
> > _______________________________________________
> > R-sig-ecology mailing list
> > R-sig-ecology at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>_______________________________________________
>R-sig-ecology mailing list
>R-sig-ecology at r-project.org
>https://stat.ethz.ch/mailman/listinfo/r-sig-ecology


***************************************
Marcelino de la Cruz Rot
Depto. Biologia Vegetal
EUIT Agricola
Universidad Politecnica de Madrid
28040-Madrid
SPAIN
***************************************