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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