[R-sig-eco] non-metric MDS comparison - vegan vs. ecodist packages

Gavin Simpson gavin.simpson at ucl.ac.uk
Mon Feb 20 20:59:07 CET 2012 

On Mon, 2012-02-20 at 14:30 -0500, Sarah Goslee wrote:
> References are given in the help for nmds. In particular, nmds() uses
> Kruskal's formulation.

And you can read the code. Look at nmds, at the top of the function body
is an inline function sstress() which does the relevant computation,
IIUC.

G

> Sarah
> On Feb 20, 2012 1:48 PM, "Gian Maria Niccol Benucci" <
> gian.benucci at gmail.com> wrote:
> 
> > Dear Gavin and Sarah,
> >
> > I've found how metaMDS() calculate the stress [using monoMDS() of vegan],
> > but I do not find how nmds() of ecodist do it so. Could you please link me
> > the page or where I can find it, maybe it escapes me...
> > Thank you very much for your aid,
> >
> > Gian
> >
> >
> > 2012/2/20 Gavin Simpson <gavin.simpson at ucl.ac.uk>
> >
> > > On Mon, 2012-02-20 at 17:24 +0100, Gian Maria Niccol Benucci wrote:
> > > > Dear Gavin,
> > > >
> > > > Thank you very much. I tried with your advice but the result is almost
> > > > unchanged...
> > >
> > > > Any further advice??
> > >
> > > Yeah, what Sarah said. Read the documentation; the two functions use
> > > different definitions of stress.
> > >
> > > You could always do a procrustes rotation on the two configurations to
> > > see how well they compare.
> > >
> > > G
> > >
> > > > Gian
> > > >
> > > >
> > > >
> > > >
> > > > 2012/2/20 Gavin Simpson <gavin.simpson at ucl.ac.uk>
> > > >
> > > > > On Mon, 2012-02-20 at 16:28 +0100, Gian Maria Niccol Benucci wrote:
> > > > > > Hi r-sig-ecology Members,
> > > > > >
> > > > > > I would please you to examine the differences I found in metaMDS()
> > > and
> > > > > > nmds() outputs and possibly draw some conclusions. As I wrote in
> > past
> > > > > > emails I have 24 samples of ectomycorrhizal fungi grouped into two
> > > > > > different communities (12 natural and 12 cultivated).
> > > > > >
> > > > > > here is the code:
> > > > > >
> > > > > > > metaMDS(data_matrix2, distance="bray", k=2, autotransform=F) ->
> > > metaMDS
> > > > > > > metaMDS
> > > > > >
> > > > > > Call:
> > > > > > metaMDS(comm = data_matrix2, distance = "bray", k = 2,
> > autotransform
> > > = F)
> > > > > >
> > > > > > global Multidimensional Scaling using monoMDS
> > > > > >
> > > > > > Data:     data_matrix2
> > > > > > Distance: bray
> > > > > >
> > > > > > Dimensions: 2
> > > > > > *Stress:     0.04536661 *
> > > > > > Stress type 1, weak ties
> > > > > > No convergent solutions - best solution after 20 tries
> > > > >
> > > > > Perhaps you could try running metaMDS with random starts until it
> > does
> > > > > find convergent solutions?! Why expect metaMDS() to do better in 20
> > > > > tries than nmds() with 100 random tries?
> > > > >
> > > > > add `trymax = 100` and `halfchange = FALSE` to try to make the two
> > > > > functions more comparable.
> > > > >
> > > > > HTH
> > > > >
> > > > > G
> > > > >
> > > > > > Scaling: centring, PC rotation, halfchange scaling
> > > > > > Species: expanded scores based on data_matrix2
> > > > > >
> > > > > > > nmds <- nmds(dist_bray, mindim = 2, maxdim = 2, nits = 100)
> > > > > > Using random start configuration
> > > > > > Using random start configuration
> > > > > > ...
> > > > > > > nmds_min
> > > > > >             X1          X2
> > > > > > 1  -0.66226262  0.16392824
> > > > > > 2 -0.68844987 -0.20891993
> > > > > > 3 -0.47717515  0.55323693
> > > > > > 4 -0.67213392 -0.09195847
> > > > > > 5 0.03305172  0.41844232
> > > > > > 6   0.31992006  0.53887910
> > > > > > 7  -0.61944875  0.34411146
> > > > > > 8 0.07013849  0.65723057
> > > > > > 9 0.53053436  0.37444633
> > > > > > 10  0.26704705  0.39849341
> > > > > > 11 -0.20981416  0.70391983
> > > > > > 12 -0.61620355 -0.43568743
> > > > > > 13 0.14219660 -0.69571194
> > > > > > 14 0.42365981 -0.43308767
> > > > > > 15 0.15840330 -0.12872863
> > > > > > 16 -0.00492407 -0.06889680
> > > > > > 17 -0.20513513 -0.58052156
> > > > > > 18 0.46546214  0.12019775
> > > > > > 19 0.36753709 -0.25048256
> > > > > > 20 -0.09446486 -0.61943616
> > > > > > 21  0.15010553 -0.31995009
> > > > > > 22  0.41540872 -0.29507200
> > > > > > 23  0.42573367 -0.12321584
> > > > > > 24  0.48081354 -0.02121688
> > > > > > > min(nmds$stress)
> > > > > > [*1] 0.2787161*
> > > > > > > nmds$r2[which.min(nmds$stress)]
> > > > > > [1] 0.6338372
> > > > > >
> > > > > > Is it possible I got so different stress values??
> > > > > >
> > > > > > Thanks for replying,
> > > > > >
> > > > > > _______________________________________________
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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/
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> > >  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
> > >  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
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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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