R CMD BATCH

Before we can submit jobs to the cluster, we first need to go over how to run jobs from the command line on our own local machine. Let’s say we have the following commands in a file called sim.R:

File:
sim.R 
N <- 10000
p <- numeric(N)
n <- 10
for (i in 1:N) {
  x <- rnorm(n)
  y <- rnorm(n, sd=3)
  p[i] <- t.test(x, y, var.equal=TRUE)$p.value
}
save(p, file="sim.RData")

I.e., we generate data from two normal distributions, one of which has a variance 9 times larger than the other, but then carry out a t-test in which we assume equal variance. This process is repeated 10,000 times. Now, we can submit this from the command line using

> 
R CMD BATCH --no-save --no-restore sim.R .sim.Rout

NOTE: All you really need is R CMD BATCH sim.R; the above options avoid generating or loading .Rhistory files and save the console text as a hidden file.