Looking at presence and absence of algae species above and below a dam, the MDS is perfect with a stress of 0.11, when I did the ANOSIM I expected great results but the Global R is 0.029 and the significance is 36.4%. Why has this happened and can I do any thing about it?
How do I discuss this result?
What do you mean by your MDS is perfect? A stress of 0.11 is fine but it does not mean you have difference between your samples. Do you mean by perfect that your MDS show 2 groups, one with samples below the dam and one above the dam?
How many permutation are available in your ANOSIM, what did you test exactly and how many replicated do you have?
In some situation you can end up having your samples separated by treatments on your MDS and get a non significant difference by ANOSIM, which is explained by the fact you have high similarity percentage between both treatments even if they seems to group differently. This possibility/probability exist.
It would help if you attach your MDS and ANOSIM result to properly help you.
Here's the file. I'm only a student doing a basic assignment, and don't understand the stats I'm doing all that well. The MDS plot shows that the groups are seperate, considering when I compared the two rivers we tested and my MDS was 0.24 stress yet I got a significant anosim.
The nMDS can appear like showing there is 2 separate groups, but the way you read a nMDS, is that 2 samples close to each other show high similarity, and 2 samples far from each other show low similarity. If you look carefully to your nMDS, you will see that L7 and G5 are really close (highly similar), while L6 and L5 are apart showing low similarity. Overall, most of your samples show similarity between group and high variability within, so it is not surprising to have a non significant ANOSIM even if the green look to be on he left and the blue on the right.
Why do you have more green site than blue? Do the numbers correspond to specific location, time..?
As 2D stress of 0.24 only mean that your nMDS is not good to represent your data in 2D. 3D might improve this. It is not surprising that ANOSIM might reveal things you can't see with nMDS, because nMDS loose information by working in 2D, while ANOSIM will work will all the dimension and complexity of your data. You could try other methods than nMDS, such cluster, CAP, PCoA.
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