Example of efficiently using "`apply`" with a sparse matrix in R.

apply-sp.R

library(Matrix)

X <- rsparsematrix(1e4, 1e4, density = 0.01)

system.time(
  test <- apply(X, 1, mean)
)

system.time(
  test2 <- rowMeans(X)
)

apply1_sp <- function(X, FUN) {
  res <- numeric(nrow(X))
  X2 <- as(X, "dgTMatrix")
  tmp <- tapply(X2@x, X2@i, FUN)
  res[as.integer(names(tmp)) + 1] <- tmp
  res
}

system.time(
  test3 <- apply1_sp(X, sum) / ncol(X)
)
stopifnot(isTRUE(all.equal(test3, test)))