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May 4, 2022 09:23
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Benchmark comparison of for-loops versus apply()/sapply() in 3 different versions of R (2.5.0, 3.0.0, 4.2.0)
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| > ############################################################################ | |
| > | |
| > # A comparison of for-loops versus apply() and sapply() for 1) computing the | |
| > # row means in a matrix and 2) for computing the means of all elements in a | |
| > # list. For task 1), we can also examine the performance of rowMeans() as a | |
| > # specialized / vectorized function and for task 2), we can also compare | |
| > # sapply() with vapply() (note: vapply() was added in version R-2.12.0). Also, | |
| > # for the for-loop, we can examine what the impact is of pre-allocating the | |
| > # vector in which to store the results versus 'growing' the vector in each | |
| > # iteration. | |
| > # | |
| > # Notes: Not using a package like 'microbenchmark' for the timings since this | |
| > # might not be available in older versions of R. The Sys.sleep() calls after | |
| > # each timing allow the CPU to cool a bit to avoid that the performance is | |
| > # impacted by thermal throttling. | |
| > | |
| > ############################################################################ | |
| R version 2.5.0 (2007-04-23) | |
| Copyright (C) 2007 The R Foundation for Statistical Computing | |
| ISBN 3-900051-07-0 | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| Natural language support but running in an English locale | |
| R is a collaborative project with many contributors. | |
| Type 'contributors()' for more information and | |
| 'citation()' on how to cite R or R packages in publications. | |
| Type 'demo()' for some demos, 'help()' for on-line help, or | |
| 'help.start()' for an HTML browser interface to help. | |
| Type 'q()' to quit R. | |
| > ############################################################################ | |
| > | |
| > # for-loops versus apply() (versus rowMeans()) for computing row means | |
| > | |
| > n <- 2000 | |
| > x <- matrix(runif(n*n), nrow=n, ncol=n) | |
| > | |
| > f1 <- function(x) { | |
| + nr <- nrow(x) | |
| + m <- rep(NA_real_, nr) | |
| + for (i in 1:nr) { | |
| + m[i] <- mean(x[i,]) | |
| + } | |
| + return(m) | |
| + } | |
| > f2 <- function(x) { | |
| + m <- c() | |
| + for (i in 1:nrow(x)) { | |
| + m <- c(m,mean(x[i,])) | |
| + } | |
| + return(m) | |
| + } | |
| > | |
| > f3 <- function(x) apply(x, 1, mean) | |
| > f4 <- function(x) rowMeans(x) | |
| > | |
| > system.time(replicate(100, f1(x))); Sys.sleep(10) | |
| user system elapsed | |
| 5.556 0.008 5.564 | |
| > system.time(replicate(100, f2(x))); Sys.sleep(10) | |
| user system elapsed | |
| 5.835 0.008 5.843 | |
| > system.time(replicate(100, f3(x))); Sys.sleep(10) | |
| user system elapsed | |
| 9.105 0.008 9.114 | |
| > system.time(replicate(100, f4(x))); Sys.sleep(10) | |
| user system elapsed | |
| 0.894 0.000 0.894 | |
| > | |
| > ############################################################################ | |
| > | |
| > # for-loops versus sapply() (and vapply()) for computing list element means | |
| > | |
| > x <- replicate(10000, runif(1000), simplify=FALSE) | |
| > | |
| > f1 <- function(x) { | |
| + n <- length(x) | |
| + m <- rep(NA_real_, n) | |
| + for (i in 1:n) { | |
| + m[i] <- mean(x[[i]]) | |
| + } | |
| + return(m) | |
| + } | |
| > f2 <- function(x) { | |
| + m <- c() | |
| + for (i in 1:length(x)) { | |
| + m <- c(m,mean(x[[i]])) | |
| + } | |
| + return(m) | |
| + } | |
| > f3 <- function(x) sapply(x, mean) | |
| > f4 <- function(x) vapply(x, mean, numeric(1)) | |
| > | |
| > system.time(replicate(100, f1(x))); Sys.sleep(10) | |
| user system elapsed | |
| 7.955 0.004 7.959 | |
| > system.time(replicate(100, f2(x))); Sys.sleep(10) | |
| user system elapsed | |
| 10.905 0.003 10.909 | |
| > system.time(replicate(100, f3(x))); Sys.sleep(10) | |
| user system elapsed | |
| 8.345 0.013 8.358 | |
| > system.time(replicate(100, f4(x))); Sys.sleep(10) | |
| Error in f4(x) : could not find function "vapply" | |
| Timing stopped at: 0 0 0 0 0 | |
| > | |
| > ############################################################################ | |
| R version 3.0.0 (2013-04-03) -- "Masked Marvel" | |
| Copyright (C) 2013 The R Foundation for Statistical Computing | |
| Platform: x86_64-unknown-linux-gnu (64-bit) | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| Natural language support but running in an English locale | |
| R is a collaborative project with many contributors. | |
| Type 'contributors()' for more information and | |
| 'citation()' on how to cite R or R packages in publications. | |
| Type 'demo()' for some demos, 'help()' for on-line help, or | |
| 'help.start()' for an HTML browser interface to help. | |
| Type 'q()' to quit R. | |
| > ############################################################################ | |
| > | |
| > # for-loops versus apply() (versus rowMeans()) for computing row means | |
| > | |
| > n <- 2000 | |
| > x <- matrix(runif(n*n), nrow=n, ncol=n) | |
| > | |
| > f1 <- function(x) { | |
| + nr <- nrow(x) | |
| + m <- rep(NA_real_, nr) | |
| + for (i in 1:nr) { | |
| + m[i] <- mean(x[i,]) | |
| + } | |
| + return(m) | |
| + } | |
| > f2 <- function(x) { | |
| + m <- c() | |
| + for (i in 1:nrow(x)) { | |
| + m <- c(m,mean(x[i,])) | |
| + } | |
| + return(m) | |
| + } | |
| > | |
| > f3 <- function(x) apply(x, 1, mean) | |
| > f4 <- function(x) rowMeans(x) | |
| > | |
| > system.time(replicate(100, f1(x))); Sys.sleep(10) | |
| user system elapsed | |
| 5.110 0.011 5.122 | |
| > system.time(replicate(100, f2(x))); Sys.sleep(10) | |
| user system elapsed | |
| 5.433 0.000 5.433 | |
| > system.time(replicate(100, f3(x))); Sys.sleep(10) | |
| user system elapsed | |
| 7.546 0.012 7.558 | |
| > system.time(replicate(100, f4(x))); Sys.sleep(10) | |
| user system elapsed | |
| 0.808 0.000 0.809 | |
| > | |
| > ############################################################################ | |
| > | |
| > # for-loops versus sapply() (and vapply()) for computing list element means | |
| > | |
| > x <- replicate(10000, runif(1000), simplify=FALSE) | |
| > | |
| > f1 <- function(x) { | |
| + n <- length(x) | |
| + m <- rep(NA_real_, n) | |
| + for (i in 1:n) { | |
| + m[i] <- mean(x[[i]]) | |
| + } | |
| + return(m) | |
| + } | |
| > f2 <- function(x) { | |
| + m <- c() | |
| + for (i in 1:length(x)) { | |
| + m <- c(m,mean(x[[i]])) | |
| + } | |
| + return(m) | |
| + } | |
| > f3 <- function(x) sapply(x, mean) | |
| > f4 <- function(x) vapply(x, mean, numeric(1)) | |
| > | |
| > system.time(replicate(100, f1(x))); Sys.sleep(10) | |
| user system elapsed | |
| 6.902 0.008 6.910 | |
| > system.time(replicate(100, f2(x))); Sys.sleep(10) | |
| user system elapsed | |
| 13.252 0.012 13.265 | |
| > system.time(replicate(100, f3(x))); Sys.sleep(10) | |
| user system elapsed | |
| 6.884 0.000 6.884 | |
| > system.time(replicate(100, f4(x))); Sys.sleep(10) | |
| user system elapsed | |
| 5.815 0.000 5.814 | |
| > | |
| > ############################################################################ | |
| R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | |
| Copyright (C) 2022 The R Foundation for Statistical Computing | |
| Platform: x86_64-pc-linux-gnu (64-bit) | |
| R is free software and comes with ABSOLUTELY NO WARRANTY. | |
| You are welcome to redistribute it under certain conditions. | |
| Type 'license()' or 'licence()' for distribution details. | |
| Natural language support but running in an English locale | |
| R is a collaborative project with many contributors. | |
| Type 'contributors()' for more information and | |
| 'citation()' on how to cite R or R packages in publications. | |
| Type 'demo()' for some demos, 'help()' for on-line help, or | |
| 'help.start()' for an HTML browser interface to help. | |
| Type 'q()' to quit R. | |
| > ############################################################################ | |
| > | |
| > # for-loops versus apply() (versus rowMeans()) for computing row means | |
| > | |
| > n <- 2000 | |
| > x <- matrix(runif(n*n), nrow=n, ncol=n) | |
| > | |
| > f1 <- function(x) { | |
| + nr <- nrow(x) | |
| + m <- rep(NA_real_, nr) | |
| + for (i in 1:nr) { | |
| + m[i] <- mean(x[i,]) | |
| + } | |
| + return(m) | |
| + } | |
| > f2 <- function(x) { | |
| + m <- c() | |
| + for (i in 1:nrow(x)) { | |
| + m <- c(m,mean(x[i,])) | |
| + } | |
| + return(m) | |
| + } | |
| > | |
| > f3 <- function(x) apply(x, 1, mean) | |
| > f4 <- function(x) rowMeans(x) | |
| > | |
| > system.time(replicate(100, f1(x))); Sys.sleep(10) | |
| user system elapsed | |
| 4.980 0.016 4.996 | |
| > system.time(replicate(100, f2(x))); Sys.sleep(10) | |
| user system elapsed | |
| 5.383 0.000 5.384 | |
| > system.time(replicate(100, f3(x))); Sys.sleep(10) | |
| user system elapsed | |
| 5.814 0.203 6.019 | |
| > system.time(replicate(100, f4(x))); Sys.sleep(10) | |
| user system elapsed | |
| 0.76 0.00 0.76 | |
| > | |
| > ############################################################################ | |
| > | |
| > # for-loops versus sapply() (and vapply()) for computing list element means | |
| > | |
| > x <- replicate(10000, runif(1000), simplify=FALSE) | |
| > | |
| > f1 <- function(x) { | |
| + n <- length(x) | |
| + m <- rep(NA_real_, n) | |
| + for (i in 1:n) { | |
| + m[i] <- mean(x[[i]]) | |
| + } | |
| + return(m) | |
| + } | |
| > f2 <- function(x) { | |
| + m <- c() | |
| + for (i in 1:length(x)) { | |
| + m <- c(m,mean(x[[i]])) | |
| + } | |
| + return(m) | |
| + } | |
| > f3 <- function(x) sapply(x, mean) | |
| > f4 <- function(x) vapply(x, mean, numeric(1)) | |
| > | |
| > system.time(replicate(100, f1(x))); Sys.sleep(10) | |
| user system elapsed | |
| 4.960 0.008 4.969 | |
| > system.time(replicate(100, f2(x))); Sys.sleep(10) | |
| user system elapsed | |
| 12.000 0.012 12.013 | |
| > system.time(replicate(100, f3(x))); Sys.sleep(10) | |
| user system elapsed | |
| 6.098 0.000 6.098 | |
| > system.time(replicate(100, f4(x))); Sys.sleep(10) | |
| user system elapsed | |
| 4.931 0.000 4.932 | |
| > | |
| > ############################################################################ |
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