[R-sig-eco] metaMDS: how does stress affect ordination distance?

[Kim Milferstedt]

Hello,

I am using metaMDS in vegan 1.13-1 on R 2.6.1 for ordinating microbial
sequence data.

If've got three general question about nmds using metaMDS:

1) Is it fair to assess the range of the x and y axes in nmds for
comparable data with similar ranges of observed distance?

2) What effect does Kruskal's stress have on the scaling in metaMDS's
analysis?

3) Is Kruskal's stress multiplied by a factor of 100 in metaMDS as well,
as metaMDS relies on isoMDS (see R-mailing list archive under  ``isoMDS
- high stress value and strange configuration'')?

Here's a description of my situation: My sequences come from 12 samples.
Depending on their level of sequence similarity, I group them into 300
to 16 groups (300 unique sequence types to 16 sequence types that allow
sequences to be 20% different). For all the groupings, the overall
observed distance in the data remains quite similar.

I now want to see at what level of similarity, samples start coalescing
in an ordination plot. For this I use metaMDS for various levels of
similarity. I assume that I can see the samples coalesce by observing
the range of the x and y axes shrink in the nmds plot (i.e. the
ordination distance).

As I expected, in general, the range of the x and y axes of the nmds
plot is decreasing the less stringent I group sequences together. But
there's one exception that puzzles me: One plot has vastly different
ranges for the x and y axes than the other plots (200 times wider than
for all the others).

I noticed that for the exceptional grouping, the calculated Kruskal's
stress was about three orders of magnitude smaller than for all the
others, even though the raw data fed into metaMDS looks very much like
its neighboring groupings. What is happening at this one very different
analysis?

I have not posted any sample data as it is a rather large amount of
data. I tried producing a smaller dummy sample but those data did not
reproduce the effect.

Thanks for helping me out!

Kim

-- 
___________________________________________
Kim Milferstedt, PhD
Postdoctoral Researcher
University of Illinois at Urbana-Champaign
Department of Microbiology
C207 CLSL
601 S. Goodwin Avenue MC 110
Urbana, IL 61801

phone: 001-217-244-0721
email: milferst at uiuc.edu