non-metric MDS comparison - vegan vs. ecodist packages

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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non-metric MDS comparison - vegan vs. ecodist packages

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