An updated version of this post (with all the code the isn't rendered here) can be found here>> So you've run an ANOVA and found that your residuals are neither normally distributed, nor homogeneous, or that you are in violation of any other assumptions . Naturally you want to run some a-parametric analysis... but how? In this post I will demonstrate how to run a permutation test ANOVA (easy!) and how to run bootstrap follow-up analysis (a bit more challenging) in a mixed design (both within- and between-subject factors) ANOVA. I've chosen to use a mixed design model in this demonstration for two reasons: I've never seen this done before. You can easily modify this code (change / skip some of these steps) to accommodate purely within- or purely between-subject designs. Permutation ANOVA Running a permutation test for your ANOVA in R is as easy as... running an ANOVA in R, but substituting aov with aovperm from the permuco package . library(pe...
Cognition | Neurophysiology | Stats