R/icc.R

In dustinfife/fifer: A Biostatisticians Toolbox for Various Activities, Including Plotting, Data Cleanup, and Data Analysis

##' Compute the ICC from a lmer (package lme4) model
##'
##' This function will extract the variances from a mixed model and output the value of the ICC
##'	
##' Recall that the equation for the ICC is var(school)/[var(school)+ var(person)]. This forumla extracts the necessary variances from the mixed model and computes it. 
##' @param model a lmer model
##' @return the ICC
##' @author Dustin Fife
##' @export
##' @import lme4
##' @examples
##' data(alcuse)
##' require(lme4)
##' model = lmer(ALCUSE~1|ID, data=alcuse)
##' icc(model)
icc = function(model){
	#### compute ICC
	var.components = as.data.frame(VarCorr(model))$vcov
	ICC = var.components[1]/sum(var.components)
	
	#### find out average cluster size
	id.name = names(coef(model))
	clusters = nrow(matrix(unlist((coef(model)[id.name]))))
	n = length(residuals(model))
	average.cluster.size = n/clusters
	
	#### compute design effects
	design.effect = 1+ICC*(average.cluster.size-1)
	
	#### return stuff
	list(icc=ICC, design.effect=design.effect)
	
}