I am using the
vegan package in R to plot non-metric multidimensional scaling (NMDS) ordinations. I am using this package because of its compatibility with common ecological distance measures. When you plot the
metaMDS() ordination, it plots both the samples (as black dots) and the species (as red dots). My question is: How do you interpret this simultaneous view of species and sample points?
My understanding of NMDS:
- you start with a distance matrix of distances between all your points in multi-dimensional space
- The algorithm places your points in fewer dimensional (say 2D) space
- The algorithm moves your points around in 2D space so that the distances between points in 2D space go in the same order (rank) as the distances between points in multi-D space.
BUT there are 2 possible distance matrices you can make with your rows=samples cols=species data:
- distances between samples based on species composition (i.e. distances in species space)
- distances between species based on co-occurrence in samples (i.e. distances in sample space)
metaMDS() calculating BOTH possible distance matrices automatically?
Is the ordination plot an overlay of two sets of arbitrary axes from separate ordinations?
How do you interpret co-localization of species and samples in the ordination plot?
note: I did not include example data because you can see the plots I'm talking about in the package documentation example.