10 R Functions for Linux Commands and Vice-versa

This post will go through 10 different Linux commands and their R alternatives. If you’re interested in learning more R functions for working with files like some of those below, also check out this post.

How to list all the files in a directory

Linux	R	What does it do?
ls	list.files()	Lists all the files in a directory
ls -R	list.files(recursive = TRUE)	Recursively lists all the files in a directory and all sub-directories
ls | grep “something”	list.files(pattern = “something”)	Lists all the files in a directory containing the regex “something”

R

list.files("/path/to/directory")
 
 
list.files("/path/to/do/directory", recursive = TRUE)
 
 
# search for files containing "something" in their name
list.files("/path/to/do/directory", pattern = "something")
 
 
# search for all CSV files
list.files("/path/to/do/directory", pattern = ".csv")

Linux

ls /path/to/directory
 
 
ls -R /path/to/directory
 
 
# search for files containing "something" in their name
ls /path/to/directory | grep "something"
 
 
# search for all CSV files
ls /path/to/directory | grep ".csv"

Getting the top records in a file / object

Linux	R	What does it do?
head	head()	Prints the top n records of a file (Linux) / data frame or other object (R)

R

# let df be a data frame
head(df)
 
head(df, 10)

Linux

head -6 some_file.txt
 
head -10 some_file.txt

Getting the current directory

Linux	R	What does it do?
pwd	getwd()	Gets the current directory

R

getwd()

Linux

pwd

Changing the directory

Linux	R	What does it do?
cd	setwd()	Change the current working directory

R

setwd("/path/to/new/directory")

Linux

cd /path/to/new/directory

How to count the number of files in a directory

Linux	R	What does it do?
ls -1 | wc -l	length(list.files(…))	Counts the number of files in a directory

R

length(list.files("/path/to/some/directory"))

Linux

ls -1 | wc -l

How to check file permissions

Linux	R	What does it do?
ls -l	file.info()	Returns the file permissions (Linux) / additional info (R)

R

file.info("/path/to/directory/file.txt")

file.info returns additional information about a file besides file permissions, including size, created time, last modified time, and last access time. If you just want to get permissions of the file, just run this:

file.info("/path/to/directory/file.txt")$mode

The permissions are returned in octal; to translate what this octal result means into read / write etc. abilities, see this link.

Linux

ls -l /path/to/directory/file.txt

How to create a new directory

Linux	R	What does it do?
mkdir	dir.create()	Creates a new directory

R

# create folder in current directory
dir.create("new_folder")
 
# create folder in different directory
dir.create("/path/to/new_directory")

Linux

# create folder in current directory
mkdir new_folder
 
# create folder in different directory
mkdir /path/to/new_directory

How to create a new file

Linux	R	What does it do?
touch	file.create()	Creates a new file

R

# create a file in current directory
file.create("new_file.txt")
 
# create file in different directory
file.create("/path/to/directory/new_file.txt")

Linux

# create a file in current directory
touch new_file.txt
 
# create file in different directory
touch /path/to/directory/new_file.txt

How to count the number of lines, words, and characters in a file

Though it’s possible to get the number of lines, words, and characters in a file using base R, it’s simpler to do so with the hyperSpec package.

Just use install.packages to install if needed:

install.packages("hyperSpec")

Running the below line of code will print out a data frame with the number of characters, words, and lines in the input file. Similarly, the Linux wc command will print out the same information for a file.

Linux	R	What does it do?
wc	wc()	Lists the number of characters, words, and lines in a file

R

library(hyperSpec)
 
wc("/path/to/directory/file.txt")

Linux

wc /path/to/directory/file.txt

How to copy a file

Linux	R	What does it do?
cp	file.copy()	Copy a file

R

# copy file.txt to new_directory
file.copy("/path/to/directory/file.txt", "/path/to/new_directory")

Linux

# option 1
cp /path/to/directory/file.txt /path/to/new_directory
 
# option 2
cp /path/to/directory/file.txt /path/to/new_directory/file.txt

Originally posted on TheAutomatic.net.