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| ## ----env, include=FALSE, echo=FALSE, cache=FALSE------------------------- | ||
| library("knitr") | ||
| opts_chunk$set(fig.align = 'center', | ||
| fig.show = 'hold', | ||
| tidy = FALSE, | ||
| par = TRUE, | ||
| prompt = TRUE, | ||
| eval = TRUE, | ||
| stop_on_error = 1L, | ||
| comment = NA) | ||
| options(replace.assign = TRUE, | ||
| width = 55) | ||
| set.seed(1) | ||
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| ## ----fun, tidy = FALSE--------------------------------------------------- | ||
| myFun <- function(i, j = 1) { | ||
| mn <- min(i, j) | ||
| mx <- max(i, j) | ||
| k <- rnorm(ceiling(i * j)) | ||
| return(k[k > mn/mx]) | ||
| } | ||
| myFun(1.75, 4.45) | ||
| myFun(1.75) ## j = 1 by default | ||
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| ## ----scoping------------------------------------------------------------- | ||
| x <- 1 | ||
| f1 <- function(x) { | ||
| x <- x + 10 | ||
| x | ||
| } | ||
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| f1(x) | ||
| x ## unchanged | ||
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| ## ----scoping2------------------------------------------------------------ | ||
| f2 <- function() { | ||
| x <- x + 10 | ||
| x | ||
| } | ||
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| f2() | ||
| x ## still unchanged | ||
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| ## ----fun2fun------------------------------------------------------------- | ||
| make.power <- function(n) | ||
| function(x) x^n | ||
| square <- make.power(2) | ||
| cube <- make.power(3) | ||
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| ## ----fun2funexplore------------------------------------------------------ | ||
| square | ||
| get("n", environment(square)) | ||
| square(2) | ||
| cube(2) | ||
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| ## ----fun2fun2------------------------------------------------------------ | ||
| (rbramp <- colorRampPalette(c("red", "blue"))) | ||
| rbramp(3) | ||
| rbramp(7) | ||
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| ## ----plt----------------------------------------------------------------- | ||
| plt <- function(n, ...) | ||
| plot(1:n, ...) | ||
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| ## ----pltex, dev='pdf', fig.width = 8, fig.height = 4--------------------- | ||
| par(mfrow = c(1, 2)) | ||
| plt(5, pch = 19, type = "b") | ||
| plt(10, col = rbramp(10), pch = 15) | ||
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| ## ----args---------------------------------------------------------------- | ||
| args(cat) | ||
| args(rm) | ||
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| ## ----lapply-------------------------------------------------------------- | ||
| lapply(1:2, rnorm) | ||
| lapply(1:2, rnorm, 10, 2) | ||
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| ## ----sapply-------------------------------------------------------------- | ||
| library(fortunes) | ||
| lapply(sample(315, 1), fortune) | ||
| sapply(sample(315, 1), fortune) | ||
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| ## ----apply--------------------------------------------------------------- | ||
| set.seed(10) | ||
| m <- matrix(rnorm(10), ncol = 2) | ||
| apply(m, 1, myFun) | ||
| apply(m, 1, myFun) | ||
| apply(m, 1, max) ## Biobase::rowMax | ||
| apply(m, 2, min) ## Biobse::rowMin | ||
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| ## ----mapply-------------------------------------------------------------- | ||
| mapply(rep, 1:4, 4:1) | ||
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| ## ----tapply-------------------------------------------------------------- | ||
| dfr <- data.frame(f1 = sample(LETTERS[1:2], 10, replace = TRUE), | ||
| f2 = sample(LETTERS[3:4], 10, replace = TRUE), | ||
| x = rnorm(10)) | ||
| tapply(dfr$x, dfr$f1, mean) | ||
| tapply(dfr$x, dfr$f2, mean) | ||
| tapply(dfr$x, list(dfr$f1, dfr$f2), mean) | ||
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| ## ----anon---------------------------------------------------------------- | ||
| m | ||
| apply(m, 1, function(x) ifelse(mean(x) > 0, mean(x), max(x))) | ||
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| ## ----N, echo = FALSE----------------------------------------------------- | ||
| N <- 1e4 | ||
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| ## ----ll, cache = TRUE---------------------------------------------------- | ||
| ll <- lapply(sample(N), rnorm) | ||
| f <- function(x) mean(x) * length(x) | ||
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| ## ----time1, cache = TRUE------------------------------------------------- | ||
| res1 <- c() | ||
| system.time({ | ||
| for (i in 1:length(ll)) | ||
| res1[i] <- f(ll[[i]]) | ||
| }) | ||
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| ## ----time2, cache = TRUE------------------------------------------------- | ||
| res2 <- numeric(length(ll)) | ||
| system.time({ | ||
| for (i in 1:length(ll)) | ||
| res2[i] <- f(ll[[i]]) | ||
| }) | ||
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| ## ----time3, cache = TRUE------------------------------------------------- | ||
| system.time(res3 <- sapply(ll, f)) | ||
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| ## ----replicatetime, cache = TRUE----------------------------------------- | ||
| summary(replicate(50, system.time(res3 <- sapply(ll, f))["elapsed"])) | ||
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| ## ----benchmarkfun-------------------------------------------------------- | ||
| sol2 <- function(x) { | ||
| n <- length(x) | ||
| ans <- numeric(n) | ||
| for (i in 1:n) { | ||
| ans[i] <- f(x[[i]]) | ||
| } | ||
| ans | ||
| } | ||
| sol3 <- function(x) | ||
| sapply(x, f) | ||
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| ## ----benmark, cache = TRUE----------------------------------------------- | ||
| library("microbenchmark") | ||
| microbenchmark(sol2(ll), sol3(ll), times = 200) | ||
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| ## ----profiling, eval=FALSE----------------------------------------------- | ||
| ## Rprof("sol3.Rprof") | ||
| ## tmp <- replicate(10, sol3(ll)) | ||
| ## Rprof(NULL) | ||
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| ## ----opts0, echo=FALSE--------------------------------------------------- | ||
| oldwidth <- options()$width | ||
| options(width = 100) | ||
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| ## ----smryprof, size = 'small'-------------------------------------------- | ||
| summaryRprof("sol3.Rprof") | ||
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| ## ----opts1, echo=FALSE--------------------------------------------------- | ||
| options(width = oldwidth) | ||
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| ## ----id1----------------------------------------------------------------- | ||
| identical(res1, res2) | ||
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| ## ----id3----------------------------------------------------------------- | ||
| identical3 <- | ||
| function(x,y,z) identical(x,y) && identical (y,z) | ||
| identical3(res1, res2, res3) | ||
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| ## ----sqrtx--------------------------------------------------------------- | ||
| x <- sqrt(2) | ||
| x * x == 2 | ||
| identical(x*x, 2) | ||
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| ## ----alleqsqrt----------------------------------------------------------- | ||
| all.equal(x * x, 2) | ||
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| ## ----stopifnot----------------------------------------------------------- | ||
| stopifnot(x * x == 2) | ||
| stopifnot(all.equal(x * x, 2)) | ||
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| ## ----pvec---------------------------------------------------------------- | ||
| library("parallel") | ||
| detectCores() | ||
| mclapply(1:3, function(x) Sys.getpid(), mc.cores = 3) | ||
| mclapply(1:3, function(x) Sys.getpid(), mc.cores = 2) | ||
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| ## ----solpar, cache = TRUE------------------------------------------------ | ||
| solmc <- function(x) | ||
| mclapply(x, f) | ||
| solpar <- function(x, cl) | ||
| parLapply(cl, x, f) | ||
| sol3 <- function(x) | ||
| lapply(x, f) | ||
| cl <- makeCluster(4) | ||
| stopifnot(identical3(sol3(ll), solmc(ll), solpar(ll, cl))) | ||
| stopCluster(cl) | ||
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| ## ----pbench, echo = FALSE------------------------------------------------ | ||
| cat(scan('pbench.R', what = "", strip.white = FALSE, sep = "\n"), sep = "\n") | ||
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| ## ----printpbench, echo=FALSE--------------------------------------------- | ||
| load("pbench.rda") | ||
| microbenchmark:::print.microbenchmark(pbench) | ||
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| ## ----oops, echo=FALSE---------------------------------------------------- | ||
| e <- function(i) { | ||
| x <- 1:4 | ||
| if (i < 5) x[1:2] | ||
| else x[-1:2] | ||
| } | ||
| f <- function() sapply(1:10, e) | ||
| g <- function() f() | ||
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| ## ----error, eval=FALSE, prompt = FALSE----------------------------------- | ||
| ## > g() | ||
| ## Error in x[-1:2] (from #3) : only 0's may be mixed with negative subscripts | ||
| ## > g | ||
| ## function() f() | ||
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| ## ----traceback, eval=FALSE, prompt = FALSE------------------------------- | ||
| ## > traceback() | ||
| ## 5: FUN(1:10[[5L]], ...) | ||
| ## 4: lapply(X = X, FUN = FUN, ...) | ||
| ## 3: sapply(1:10, e) at #1 | ||
| ## 2: f() at #1 | ||
| ## 1: g() | ||
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| ## ----erroronly, eval=FALSE, prompt=FALSE--------------------------------- | ||
| ## Error in x[-1:2] (from #3) : only 0's may be mixed with negative subscripts | ||
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| ## ----showe, eval=FALSE, prompt=FALSE------------------------------------- | ||
| ## e | ||
| ## function(i) { | ||
| ## x <- 1:4 | ||
| ## if (i < 5) x[1:2] | ||
| ## else x[-1:2] | ||
| ## } | ||
| ## e(5) | ||
| ## Error in x[-1:2] (from #3) : only 0's may be mixed with negative subscripts | ||
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| ## ----debugmode, eval=FALSE, prompt=FALSE--------------------------------- | ||
| ## > debug(e) | ||
| ## > e(5) | ||
| ## debugging in: e(5) | ||
| ## debug at #1: { | ||
| ## x <- 1:4 | ||
| ## if (i < 5) | ||
| ## x[1:2] | ||
| ## else x[-1:2] | ||
| ## } | ||
| ## Browse[2]> | ||
| ## debug at #2: x <- 1:4 | ||
| ## Browse[2]> | ||
| ## debug at #3: if (i < 5) x[1:2] else x[-1:2] | ||
| ## Browse[2]> ls() | ||
| ## [1] "i" "x" | ||
| ## Browse[2]> i | ||
| ## [1] 5 | ||
| ## Browse[2]> x | ||
| ## [1] 1 2 3 4 | ||
| ## Browse[2]> | ||
| ## debug at #3: x[-1:2] | ||
| ## Browse[2]> x[-1:2] | ||
| ## Error in x[-1:2] (from #3) : only 0's may be mixed with negative subscripts | ||
| ## Browse[2]> x[-(1:2)] | ||
| ## [1] 3 4 | ||
| ## Browse[2]> Q | ||
| ## > undebug(e) | ||
| ## > fix(e) | ||
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| ## ----sessioninfo, results='asis', echo=FALSE----------------------------- | ||
| toLatex(sessionInfo()) |
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