non-metric MDS comparison - vegan vs. ecodist packages
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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