Can someone explain the implications of performing clustering either before or after performing NMDS?
I have some ecological data and I am performing a clustering analysis to identify communities of species which are more prevalent in certain samples.
I have thus far tried two approaches:
1) Perform NMDS on the raw data using vegan function metaMDS() with bray curtis dissimilarity and then cluster the ordination points and visualise.
2) First calculate the bray curtis dissimilarity matrix from the raw data and then perform clustering. Next I perform NMDS on the raw data and then visualise the clustering.
Both of these approaches yield approximately the same clustering however approach (1) performs better in context of silhouette width and gives a slightly better clustering (visually).
What are the implications of clustering before or after ordinations?