Hi, Thanks very much for your response.

Unfortunately, using the set.seed() call does not seem to solve my problem.
If I do not use set.seed(), I do indeed get some small differences in
protest() results due to the effect of random starts. But with my sites in a
given order in the input files, and using set.seed(), I get the same results
every time I run protest().

It's only when I change the order of sites in the input files that I get a
big change in results. The differences I see in protest() results after
re-sorting the order of sites in the input file is quite large, larger than
the smaller differences do to random starts I see if I run protest() without
the set.seed. When sites are re-ordered in the input file, the
correlation-like statistic produced by protest() can jump from between 0.28
to 0.52 for a dataset with 38 sites, with a corresponding change in
significance. Without using set.seed the numbers do jump around a bit, but
not to the same extreme degree.

Looking at the NMDS plots to see how ordinations change with the order of
sites in the file, it seems that if I re-order sites, I am simply getting
ordination solutions that are reflections on one another across one of the 3
NMDS axes. These are not real differences in the ordination solutions. Is
there something I am failing to include in the protest() call that should
enable the function to flip one ordination around to maximize it's
similarity to the other ordination (i.e., that should orient the two
ordinations the same way in 3-dimensional space)?

Thanks,

--Christy


On Thu, Dec 2, 2010 at 6:02 AM, Gavin Simpson <gavin.simpson@ucl.ac.uk>wrote:

> On Wed, 2010-12-01 at 14:19 -0600, Christine Dolph wrote:
> > Dear All,
> >
> > I am using a Procrustes analysis to compare two NMDS ordinations for the
> > same set of sites. One ordination is based on fish data, the other is
> based
> > on invertebrate data. Ordinations were derived using metaMDS() from the
> > {vegan} library as follows:
> >
> > fish.mds<-metaMDS(fish.data, distance="bray", k=3, trymax=100,
> > wascores=TRUE, trace=TRUE, zero="add")
> >
> > invert.mds<-metaMDS(bugcal.a, distance="bray", k=3, trymax=100,
> > wascores=TRUE, trace=TRUE, zero="add"),
> >
> >
> > where fish.data and invert.data are site-by-abundance matrices for fish
> and
> > invertebrates, respectively.
> >
> > I have then used protest() to test the significance between the two
> > ordinations:
>
> Simple things first:
>
> You did have a set.seed() call before the protest() call didn't you? In
> fact, I'd probably put set.seed() calls before the two metaMDS() calls
> as well.
>
> The ordering should have no impact at all, but the random starts in
> metaMDS() and the random permutations in protest() will vary from run to
> run unless you set the random seed to some known value.
>
> G
>
> > protest.results<-protest(fish.mds, invert.mds, scale=TRUE,
> symmetric=TRUE,
> > permutations=999)
> >
> > The problem is, the results of the protest analysis seem to be affected
> by
> > the original ordering of sites in the data input files. That is, if I
> > re-sort one of the input files based on some criteria, I sometimes see a
> > change in the strength and significance of the concordance results. In an
> > attempt to figure out what is happening, I have re-ordered each dataset
> in a
> > number of ways, and plotted the resulting ordinations. I have seen that
> > while the ordering of sites in the input file does not change the spatial
> > relationship between them (i.e., does not change the fundamental
> ordination
> > solution), it can change how the sites are oriented with respect to the
> > different NMDS axes. I was of the belief that a difference in orientation
> > with respect to the NMDS axes should not affect the Procrustes comparison
> of
> > two ordinations, as the protest function should be rotating and
> reflecting
> > one matrix with respect to the other to find the closest match between
> them
> > (i.e., it should be accounting for differences in how the two solutions
> are
> > oriented in space). However, I appear to see different results depending
> on
> > how sites are oriented with respect to each NMDS axis.
> >
> > When comparing two ordination solutions with Protest, is it necessary to
> > ensure that the original data input files are ordered in the same way?
> >
> > Thanks in advance for any insight.
> >
> > Sincerely,
> >
> >
> >
>
> --
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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/<http://www.ucl.ac.uk/%7Eucfagls/>
>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
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>
>


-- 
Christy Dolph
Ph.D. Candidate
Water Resources Science
University of Minnesota
200 Hodson Hall, 1980 Folwell Ave
St. Paul, MN 55108
dolph008@umn.edu
612-868-1565

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