README.md

In hoxo-m/pforeach: An easy way to parallel processing in R

pforeach - Easy to parallel processing in R

Koji MAKIYAMA

Overview

There is a parallel processing code using the foreach package:

library(doParallel)
cl <- makeCluster(detectCores())
registerDoParallel(cl)
foreach(i = 1:3, .combine=c) %dopar% {
  i**2
}
stopCluster(cl)

## [1] 1 4 9

It can be simplified using pforeach() instead of foreach():

library(pforeach)
pforeach(i = 1:3)({
  i**2
})

## [1] 1 4 9

How to install

install.packages("devtools") # if you have not installed "devtools" package
devtools::install_github("hoxo-m/pforeach")

To simplify!

With other packages

Using foreach():

library(doParallel)
library(dplyr) # With other package
cl <- makeCluster(detectCores())
registerDoParallel(cl)
# You must indicate .packages parameter.
foreach(i = 1:3, .combine=c, .packages="dplyr") %dopar% {
  iris[i, ] %>% select(-Species) %>% sum
}
stopCluster(cl)

## [1] 10.2  9.5  9.4

Using pforeach():

library(pforeach)
library(dplyr) # With other package
# You need not to mind that.
pforeach(i = 1:3)({
  iris[i, ] %>% select(-Species) %>% sum
})

## [1] 10.2  9.5  9.4

With enclosed variables

Using foreach():

# You must indicate .export parameter. 
library(doParallel)
square <- function(x) x**2
execute <- function() {
  cl <- makeCluster(detectCores())
  registerDoParallel(cl)
  result <- foreach(i = 1:3, .combine=c, .export="square") %dopar% {
    square(i)
  }
  stopCluster(cl)
  result
}
execute()

## [1] 1 4 9

Using pforeach():

# Need not to mind!
library(pforeach)
square <- function(x) x**2
execute <- function() {
  pforeach(i = 1:3)({
    square(i)
  })
}
execute()

## [1] 1 4 9

Rows and Columns

Iterations for data frame can simplify using rows() and cols() instead of iterators::iter().

Using iter():

library(doParallel)
cl <- makeCluster(detectCores())
registerDoParallel(cl)
data <- iris[1:5, ]
foreach(row = iter(data, by="row"), .combine=c) %dopar% {
  sum(row[-5])
}
stopCluster(cl)

## [1] 10.2  9.5  9.4  9.4 10.2

Using rows():

library(pforeach)
data <- iris[1:5, ]
pforeach(row = rows(data))({
  sum(row[-5])
})

## [1] 10.2  9.5  9.4  9.4 10.2

Using cols():

library(pforeach)
data <- iris[, 1:4]
pforeach(col = cols(data))({
  mean(col)
})

## [1] 5.843 3.057 3.758 1.199

Options

Cores

You can indicate number of cores for parallel processing with .cores parameter.

pforeach(i = 1:3, .cores = 2)({
  i**2
})

If you set minus value to .cores for example .cores = -1, it means .cores = detectCores() - 1.

pforeach(i = 1:3, .cores = -1)({
  i**2
})

Fix random seed

If you want to fix random seed, set .seed parameter:

library(pforeach)
pforeach(i = 1:3, .seed = 12345)({
  rnorm(1)
})

## [1]  0.74543 -0.06048 -0.40347

Do not parallel

If you want to change a parallel code to the non-parallel code with pforeach, you just only add one character "n".

library(pforeach)
npforeach(i = 1:3)({
  i**2
})

## [1] 1 4 9

Application

Parallelized random forest code with foreach is below:

library(doParallel)
library(randomForest)
library(kernlab)

data(spam)
cores <- detectCores()

cl <- makePSOCKcluster(cores)
registerDoParallel(cl)

fit.rf <- foreach(ntree=rep(250, cores), .combine=combine, 
                  .export="spam", .packages="randomForest") %dopar% {
  randomForest(type ~ ., data = spam, ntree = ntree)
}

stopCluster(cl)

Using pforeach:

library(pforeach)
library(randomForest)
library(kernlab)

data(spam)

fit.rf <- pforeach(ntree=rep(250, .cores), .c=combine)({
  randomForest(type ~ ., data = spam, ntree = ntree)
})

hoxo-m/pforeach documentation built on May 17, 2019, 4:53 p.m.