spe.scores <- scores(spe.h.pca, display="species", choices=c(1,2)) # species scores on the first two PCA axes
site.scores <- scores(spe.h.pca, display="sites", choices=c(1,2)) # sites scores on the first two PCA axes
#Note: if you don’t specify the number of principal components to extract (e.g. choices=c(1,2) or choices=c(1:2) then all of the scores will be extracted for all of the principal components.