How to make nmds plot in r?
3 answer(s)
Answer # 1 #
I use NMDS a lot in ecology work. After running metaMDS() always check the stress value—below 0.2 is usually acceptable below 0.1 is great. You can also overlay species or environmental vectors using envfit() to make the plot more meaningful.
Answer # 2 #
If you’re new to ordination methods the official vegan documentation is actually very readable and has examples you can copy and tweak: https://cran.r-project.org/package=vegan
Answer # 3 #
NMDS plots are commonly done using the vegan package in R. First you install and load the package then use the metaMDS() function on your distance matrix or community data. Once the model runs you can plot it using plot() or ordiplot(). NMDS is sensitive to data scaling so that step matters.