Output from vegan metaMDS won't run in 'fortify' function

Question

I am trying to retrieve the coordinates for each species in my NMDS using the fortify function, but receive:

Error: data must be a data frame, or other object coercible by fortify(), not an S3 object with class metaMDS/monoMDS.

I have tried converting the NMDS output to a dataframe but this did not work. My sample data and my code are below:

spp1 <- c(5, 0, 3, 1, 2) 

spp2 <- c(0, 12, 1, 8, 1) 

spp3 <- c(0, 0, 0, 0, 1) 

bank.plot.nmds <- data.frame(spp1, spp2, spp3) 

Each column represents a species and each row represents a single plot. The NMDS won't converge but with this limited dataset but it should still work for the question.

library(vegan)

nmds1 <- metaMDS(bank.plot.nmds, trymax = 200, k = 3)

fortify(nmds1)

I thought fortify would provide a table with each species' coordinates? Perhaps there is a better way to extract these values?

Answer 1

Install my {ggvegan} package from GitHub, which provides a fortify() method for these objects.

https://gavinsimpson.github.io/ggvegan/