Gen_Perms.R

library(combinat)
library(plyr)
# Generate data
borough <- c(rep("Bronx",6), rep("Manhattan",6))
year <- rep(2001:2006,2)
gradrate <- runif(12,.5,1)
data <- data.frame(borough,year,gradrate)


grads <- read.csv("GradCleanup.csv")
grads <-rename(grads, c("Cohort"="year", "Borough"= "borough", "GradRate"="gradrate"))
data <- subset(grads, year>2001)
data <- subset(data, borough %in% c("Manhattan", "Bronx"))

system.time(perms <- permn(data$gradrate))

f <- function(x){data <- data.frame(borough,year,x); names(data) <- c("borough", "year", "gradrate"); data}
system.time(perm_data <- llply(perms, f))
save.image("GenPerms.RData")

RunPermTest.R

load("GenPerms.RData")
library(plyr)

run_test <- function(results){
	data <- data.frame(borough = borough[c(-1,-7)],year = year[c(-1,-7)],grad_rate = results)

	test <- wilcox.test(subset(data, borough=="Bronx")[["grad_rate"]],
		                subset(data, borough=="Manhattan")[["grad_rate"]],
		                paired=1, exact=0)
	pvalue <- test$p.value
	pvalue
}

tmp <- list(perms[[1]], perms[[2]], perms[[3]])

st_runTest <- proc.time()
results <- ldply(tmp,run_test)
et_runTest <- proc.time()
et_runTest - st_runTest

rm(list=("perms"))
save.image("TestResults.RData")