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
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,
--
Gian
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