[R] help speeding up simple Theil regression function
Brad Schneid
bps0002 at auburn.edu
Sun Oct 21 20:06:57 CEST 2012
Hello,
I am working on a simple non-parametric (Theil) regression function and and
am following Hollander and Wolfe 1999 text. I would like some help making
my function faster. I have compared with pre-packaged version from "MBLM",
which isnt very fast either, but it appears mine is faster with N = 1000
(see results below). I plan on running this function repeatedly, and I
generally have data lengths of ~ N = 6000 or more.
# My function following Hollander and Wolfe text, Chapter 9
np.lm <-function(dat, X, Y, ...){
# Ch 9.2: Slope est. (X) for Thiel statistic
combos <- combn(nrow(dat), 2)
i.s <- combos[1,]
j.s <- combos[2,]
num <- vector("list", length=length(i.s))
dom <- vector("list", length=length(i.s))
for(i in 1:length(i.s)){
num[[i]] <- dat[j.s[i],Y] - dat[i.s[i],Y]
dom[[i]] <- dat[j.s[i],X] - dat[i.s[i],X]
}
X <- median( sort( do.call(c, num) / do.call(c, dom) ) )
# Ch 9.4: Intercept est. for Thiel statistic
Intercept <- median(dat[,"Y"] - X*dat[,"X"])
out <- data.frame(Intercept, X)
return(out)
} # usage: np.lm(dat, X=1, Y=2)
################################################################
library("mblm") # I will compare to mblm() function
X <- rnorm(1000)
Y <- rnorm(1000)
dat <- data.frame(X, Y)
system.time(np.lm(dat, X=1, Y=2) )
user system elapsed
118.610 0.130 119.144
109.000 0.040 109.416 # ran it twice
86.190 0.100 86.589 # 3rd time
system.time( mblm(Y~X, dat, repeated=F) )
user system elapsed
1509.200 87.670 1602.987
# not waiting on that to run again
OK, mine appears to be way faster... oddly, mblm() seemed faster with
smaller (n=100) datasets
Can someone please tell me how they would improve the np.lm() function to
make it quicker, or faster with some other tricks (parallel?.. Ive never
done that.).
Thank you ahead of time for any help.
Brad
Ubuntu 10.04
Intel i5 CPU 4*(650 @ 3.20GHz)
11.6 GiB memory
R version 2.15.0 (2012-03-30)
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