Test for interaction effect in 2-way ANOVA using permutation

permuteinteraction.R

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## Permutation test for interaction between 2 main effects ##
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#Based on http://r.789695.n4.nabble.com/Randomization-of-a-two-way-ANOVA-td874581.html

#Read in data
data <- read.csv('final.project.data.csv',h=T)

#Full model with interaction
full.mod <- aov(Preymort~Predator*Pesticide,data=data)
actualval <- summary(full.mod)[[1]][["F value"]][3]

#Model with main effects only
simple.mod <- aov(Preymort~Predator+Pesticide,data=data)
base.fit <- simple.mod$fitted.values
base.res <- simple.mod$residuals

#Number of permutations
nperm = 500
nulldist <- vector(length=nperm)

for (i in 1:nperm){
  
  #Rearrange residuals and add back to fitted values
  newres <- sample(base.res)
  newdat <- base.fit + newres
  
  #Analyze new data with full model and extract interaction F
  newfit <- aov(newdat ~ data$Predator*data$Pesticide)  
  nulldist[i] <- summary(newfit)[[1]][["F value"]][3]
}

#Plot distribution and calculate quasi-p
hist(nulldist)
abline(v=actualval,col='red')
quasi.p <- mean(nulldist>actualval)