I have 9 locations with 30 samples from each location. Each sample is a quadrat with species abundance data for multiple species. I want to generate a MDS plot using primer to visualize differences in community composition between the 9 sites.
However I want to use the centroid for each location in my MDS. I think I can calculate the centroid using PCO in Primer but I am not sure how. Does anyone have experience doing this in Primer?
Use PERMANOVA routine to create centroids using the relevant similarity measure - this will create a new matrix that you can then view via nMDS
Use the "distance among Centroids" function in the PERMANOVA menu. Then select the grouping factor. This will generate a distance mathrix, than you can use it to generate a PCO or MDS
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