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rvegan

Type of correlation used by protest in vegan

The protest function in vegan returns a "Correlation in a symmetric Procrustes rotation". My assumption is that it evaluates the linear relationship between two sets of continuous variables (i.e. coordinates), and is therefore a Pearson correlation (rather than Spearman). Is this correct, or is it something more nuanced?

Solution

  • Although the documentation does not explicitly state whether vegan::protest uses Pearson or Spearman correlation, by doing some testing we can see that vegan::protest uses Pearson correlation

    cor(iris[c("Sepal.Length", "Sepal.Width")], method="pearson" ) # gives -0.1176
cor(iris[c("Sepal.Length", "Sepal.Width")], method="spearman" ) # gives -0.1668

library(vegan)
protest(iris[,c("Sepal.Length")], iris[,c("Sepal.Width")]) # gives 0.1176