[R-sig-eco] [R] reception of (Vegan) envfit analysis by manuscript reviewers

[Martin Weiser]

Hi Alan,
I think that PCA is even better with envfit than NMDS with envfit. This
is because PCA works in linear euclidean world, so correlation makes
better sense in this case. You are correlating points on lines (envfit)
with points on lines (PCA), rather than points on lines (envfit) with
undetermined something non-regularly stressed (NMDS).
But this is just my feeling, I may be wrong easily, but in that case I
hope someone will correct me.
Best,
Martin Weiser

Alan Haynes píše v Čt 10. 05. 2012 v 13:17 +0200:
> Hi all,
> 
> Im using envfit with some decomposition data currently but with a PCA
> result (via vegan:::rda()). Is envfit still valid for PCA results? I guess
> it doesnt make so very much difference, just the interpretation is slightly
> different.
> Or am I barking up the wrong tree by using this approach?
> 
> Cheers,
> 
> Alan
> 
> --------------------------------------------------
> Email: aghaynes at gmail.com
> Mobile: +41794385586
> Skype: aghaynes
> 
> 
> On 10 May 2012 12:53, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:
> 
> > I've removed R-Help from this now...
> >
> > On Thu, 2012-05-10 at 10:13 +0000, Jari Oksanen wrote:
> > > On 10/05/2012, at 11:45 AM, Gavin Simpson wrote:
> > <snip />
> > > > As you provide little or no context I'll explain what envfit() does
> > etc.
> > > >
> > > > The idea goes back a long way (!) and is in my 1995 edition of Jongman
> > > > et al Data Analysis in Community and Landscape Ecology (Cambridge
> > > > University Press) though most likely was in 1987 version too. See
> > > > Section 5.4 of the Ordination chapter by Ter Braak in that book.
> > > >
> > > > The idea is to find the direction (in the k-dimensional ordination
> > > > space) that has maximal correlation with an external variable.
> > >
> > >
> > > Hello,
> >
> > <snip />
> >
> > > Then about Bray-Curtis. The referee may be correct when writing that
> > > the fitted vectors are not directly related to Bray-Curtis. You fit
> > > the vectors to the NMDS ordination, and that is a non-linear mapping
> > > from Bray-Curtis to the metric ordination space.  There are two points
> > > here: non-linearity and stress. Because of these, it is not strictly
> > > about B-C. Of course, the referee is wrong when writing about NMDS
> > > axes: the fitted vector has nothing to do with axes (unless you rotate
> > > your axis parallel to the fitted vector which you can do). The NMDS is
> > > based on Bray-Curtis, but it is not the same, and the vector fitting
> > > is based on NMDS. So why not write that is about NMDS? Why to insist
> > > on Bray-Curtis which is only in the background?
> >
> > Right, agreed. The analysis is one step removed from the B-C but the
> > point of doing the nMDS was to find a low-d mapping of these B-C
> > distances so in the sense that *if* the mapping is a good one then we
> > can talk about correlations between "distances" between sites and the
> > environmental variables. Whilst it might be strictly more correct to
> > talk about this from the point of view of the nMDS the implication is
> > that for significant envfit()s there is a significant linear correlation
> > between the environmental variable(s) and the approximate ranked
> > distances between samples.
> >
> > I mean, if all we talk about is the nMDS who cares? it is the
> > implications of this for the system under study that are of interest.
> >
> > That said, B-C is just one of many ways to think of distance so to my
> > mind I wouldn't even talk about the B-C distance either; the interest is
> > in differences between sites/samples. The relevance of B-C or some other
> > coefficient only comes in when considering if they are a good descriptor
> > of the "distance" between samples for the variables you are considering.
> >
> > Cheers,
> >
> > G
> >
> > > Cheers, Jari Oksanen
> > >
> >
> > --
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> >  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
> >  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
> >  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
> >  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
> >  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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