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...how to improve the speed of the code below, or any general suggestions on how I may accomplish this task. Thanks for your time, Juliet To run this code, first enter the model matrices (matrices given at bottom): # X_red <- as.matrix(read.table("clipboard",header=F),nrow=18,byrow=T) # X_full <- as.matrix(read.table("clipboard",header=F),nrow=18,byrow=T) library(combinat) # make some example data; the actual data is 700x800 myData <- matrix(sample(c(1:3),500,replace=TRUE),nrow=100,ncol=5) # the response is binary response <- c(rep(1,50),rep(0,50)) # initalize permut...