In RichieHonor/PermutateR: Performs a Permutation Test

Downloading the package

library("devtools")
install_github("RichieHonor/PermutateR")

Generate data for examples

#Y (Dependent) variables: 
y1 = rnorm(1000)


#X (independent) variables:
#A numeric variable : 
x1 = y1 + rnorm(1000)

# A Categorical variable
x2=rep(c("a","b"),each=500)


#Generate data frame
Data<-data.frame(y1,x1,x2)
Data

Performing permutation tests

library(PermutateR)
library(ggplot2)
library(dplyr)
library(glmmTMB)
library(lme4)

#Testing interaction by extracting the test statistics of a likelyhood ratio test
Fit<-lm(y1~x1*x2)
permTest_LR_int(Fit,"x1:x2","x1","Pr(>F)",10)

Fit<-glm(y1~x1*x2)
permTest_LR_int(Fit,"x1:x2","x1","Deviance",10)

Fit<-glmmTMB(y1~x1*x2)
permTest_LR_int(Fit,"x1:x2","x1","Pr(>Chisq)",10)


#Testing Main effect using likelihood ratio test (can be performed using the other function, but this one is ~50% faster)
Fit<-lm(y1~x1)
permTest_LR(Fit,"x1","Pr(>F)",10)

Fit<-glm(y1~x1)
permTest_LR(Fit,"x1","Deviance",10)

Fit<-glmmTMB(y1~x1)
permTest_LR(Fit,"x1","Pr(>Chisq)",10)



#Testing only the coefficient from the summary output (i.e. the contrast). 
Fit<-lm(y1~x1)
permTest_Contrast(Fit,"x1","x1","Pr(>|t|)",10)

Fit<-glm(y1~x1)
permTest_Contrast(Fit,"x1","x1","Pr(>|t|)",10)