What is the fastest way to extract the min from each column in a matrix?
Moved all the benchmarks to the answer below.
## TEST DATA
set.seed(1)
matrix.inputs <- list(
"Square Matrix" = matrix(sample(seq(1e6), 4^2*1e4, T), ncol=400), # 400 x 400
"Tall Matrix" = matrix(sample(seq(1e6), 4^2*1e4, T), nrow=4000), # 4000 x 40
"Wide-short Matrix" = matrix(sample(seq(1e6), 4^2*1e4, T), ncol=4000), # 40 x 4000
"Wide-tall Matrix" = matrix(sample(seq(1e6), 4^2*1e5, T), ncol=4000), # 400 x 4000
"Tiny Sq Matrix" = matrix(sample(seq(1e6), 4^2*1e2, T), ncol=40) # 40 x 40
)
The sos
package is great for answering these sorts of questions.
library("sos")
findFn("colMins")
library("matrixStats")
?colMins
http://finzi.psych.upenn.edu/R/library/matrixStats/html/rowRanges.html
Oddly enough, for the one example I tried colMins
was slower. Perhaps someone can point out what's funny about my example?
set.seed(101); z <- matrix(runif(1e6),nrow=1000)
library(rbenchmark)
benchmark(colMins(z),apply(z,2,min))
## test replications elapsed relative user.self sys.self
## 2 apply(z, 2, min) 100 14.290 1.00 7.216 7.057
## 1 colMins(z) 100 25.585 1.79 15.509 9.852