Nothing
Terminal
In r4ds.tutorials: Tutorials for "R for Data Science"
library(learnr)
library(tutorial.helpers)
library(tidyverse)
library(knitr)
knitr::opts_chunk$set(echo = FALSE)
knitr::opts_chunk$set(out.width = '90%')
options(tutorial.exercise.timelimit = 60,
tutorial.storage = "local")
Introduction
This tutorial covers material which is not actually in R for Data Science (2e) by Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund. But the material is in keeping with the spirit of that book. Some of the material from Chapter 6 Workflow: scripts and projects appears here.
This tutorial introduces the structure and uses of the Terminal from within RStudio. The older, more general term for the terminal is the "command line." All modern operating systems provide a command line, from which sophisticated users can modify files and directories, using commands like pwd, ls, touch, mkdir, mv, rm, and cd. We also discuss regular expressions as well as some of the metacharacters (like, *, ^ and $) from which they are constructed.
Note that a default Windows installation is different from Mac or Linux. If you are using Windows, you must first install RTools. Download the latest version from here. Currently, the Rtools44 installer is what you want. The link is in the seventh paragraph of this page.
For the most part, Windows works like Mac/Unix. There are three main exceptions which are important for this tutorial:
-
Environment variables look like $R_HOME on Mac/Unix and %R_HOME% on Windows. That is, in both cases, we are using the R_HOME environment variable. We just access this variable differently depending on the operating system.
-
Directory separators are forward slashes -- / -- on Max/Unix and backward slashes -- \ -- on Windows.
-
Creating new files can work differently on Mac/Linux and Windows. To create a new empty file named new.txt, we would use touch new.txt on Mac/Linux. Assuming that you have installed RTools, touch should also work on Windows. If it doesn't work for you, try copy NUL new.txt to create an empty file named new.txt.
The tutorial defaults use Mac/Unix nomenclature. If you are using Windows, you need to translate, for example:
ls $R_HOME/etc
into
ls %R_HOME%\etc
Terminal
The Terminal tab is next to the Console tab within the Console pane in the lower left portion of RStudio. (Yes, it is a bit confusing that we call the entire structure the Console pane even though only one part of it is the Console tab.) We use the Console tab to talk to R. We use the Terminal tab to talk directly with the computer. Sadly, the Console and the Terminal speak different languages.
Exercise 1
Hit the "return" key (the "enter" key on Windows) two times in the Terminal to see what happens. The terminal has a string of characters ending in a \$ before your cursor, called the prompt. After a command has been executed, a prompt will be generated on a new line to let you know that Terminal is ready for a new command. Copy and paste the three (blank) lines from the Terminal as your answer below. We do a lot of copy/pasting of commands/responses, so we abbreviate those instructions as CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look something like:
Davids-MacBook-Pro-2:averages dkane$
Davids-MacBook-Pro-2:averages dkane$
Davids-MacBook-Pro-2:averages dkane$
Your answer will look different from mine. Default prompts vary from computer to computer. In my case, the first part of the prompt is the name of my computer: Davids-MacBook-Pro-2. The second part, separated with a colon, is the name of the directory, averages, in which I am running the tutorial. The third part, separated by a space, is dkane, my username.
The prompt acts as a quick way to tell you where in the computer you are. The Terminal is sensitive to which folder location you are in, just like the R Console is.
Exercise 2
Let's figure out the location of the folder in which we currently are. (Note that the terms "folder" and "directory" mean the same thing.) To see your current location within your computer, type the command pwd (present working directory) in the Terminal. Hit return/enter key to run the command.
Going forward, we will instruct you to "run" a given command. You do this by typing the command at the prompt and then hitting the return/enter key.
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look something like mine:
Davids-MacBook-Pro-2:averages dkane$ pwd
/Users/dkane/Desktop/projects/averages
Davids-MacBook-Pro-2:averages dkane$
Notice how the last directory (folder) in the path is included in the prompt.
Exercise 3
Let's see a list of what is where we are, i.e. in our working directory. Run ls. Note that this is the letter "L" and the letter "S", both in lowercase. It is not the number "1". CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
If you do not give it any more information, ls assumes that you want a list of what is in your current working directory.
Exercise 4
Let's make a directory called example. Run mkdir example. Run ls to confirm that the new directory exists inside of the current working directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
mkdir creates an empty directory. We --- and most other people --- use the terms "folder" and "directory" interchangeably.
Exercise 5
Move into the example directory by running cd example. Run pwd. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:averages dkane$ cd example
Davids-MacBook-Pro-2:example dkane$ pwd
/Users/dkane/Desktop/projects/averages/example
Davids-MacBook-Pro-2:example dkane$
The example directory is one level below the directory in which I started.
Exercise 6
Let's create a file called my.txt. Run touch my.txt. (Recall that if touch does not work on Windows for you, try copy NUL my.txt instead.)
Run ls to confirm that the new file exists inside the current directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Davids-MacBook-Pro-2:example dkane$ touch my.txt
Davids-MacBook-Pro-2:example dkane$ ls
my.txt
Davids-MacBook-Pro-2:example dkane$
touch creates an empty file.
Exercise 7
Make a copy of my.txt called my_2.txt by using the cp command. That is, run cp my.txt my_2.txt. Confirm that this worked by running ls. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ cp my.txt my_2.text
Davids-MacBook-Pro-2:example dkane$ ls
my.txt my_2.text
Davids-MacBook-Pro-2:example dkane$
Exercise 8
We rename files with the mv command, which is derived from move. The first argument is the file we want to rename, the second argument is the new name
Rename my.txt to fake.txt by running mv my.txt fake.txt. Run ls to confirm. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ mv my.txt fake.txt
Davids-MacBook-Pro-2:example dkane$ ls
fake.txt my_2.text
Davids-MacBook-Pro-2:example dkane$
From the computer's point of view, renaming a file is the same thing as moving a file. In fact, moving is more general since it allows us to change both the name and the location of a file.
Exercise 9
Let's remove the file fake.txt. Run rm fake.txt. Run ls to confirm. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ rm fake.txt
Davids-MacBook-Pro-2:example dkane$ ls
my_2.text
Davids-MacBook-Pro-2:example dkane$
Be careful with the rm command in the Terminal. Unlike moving files to Trash on your computer, it is (usually) irreversible.
Exercise 10
We want to remove the example directory. But we can't do that while we are "located" in that directory. That is, the computer is aware that our Terminal process --- the entity which is executing our commands like ls and cp --- is currently working from the example directory.
Run cd ... The "dot-dot" symbol --- .. --- references the directory which contains the current directory. Run pwd to confirm. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ cd ..
Davids-MacBook-Pro-2:averages dkane$ pwd
/Users/dkane/Desktop/projects/averages
Davids-MacBook-Pro-2:averages dkane$
Again, note how the prompt changed because we moved directories. The .. symbol --- two periods --- always indicates the directory one level up, i.e., the directory in which example is located.
Exercise 11
Run rm -r example to remove the directory example. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
-r is an option that allows us to delete a directory. The r stands for recursive because, in order to delete a directory, you must also (recursively) deleting every directory and file within that directory.
It is good to clean up. Don't leave junk files lying around.
Paths
You will practice using paths both inside and outside the current working directory. You will learn a few shortcuts to make this easier.
Exercise 1
By default, the Terminal in RStudio starts with a working directory which is the same as the folder in which the current R project resides, i.e., the folder with the .Rproj file in it. Run pwd to show your current working directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The Output pane (bottom right corner) in RStudio includes several tabs, the most important of which is the Files tab. Click on it. At the top of the Files tab, you will see a series of directories, separated by >, on your computer, beginning with the Home icon. This should match the path generated by pwd.
Exercise 2
Use mkdir to make a directory named paths inside your current working directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The new directory is created directly inside the working directory.
Exercise 3
Let's change the working directory to paths. Run cd paths. Run pwd to confirm that you have changed the working directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look something like:
Davids-MacBook-Pro-2:averages dkane$ cd paths
Davids-MacBook-Pro-2:paths dkane$ pwd
/Users/dkane/Desktop/projects/averages/paths
Davids-MacBook-Pro-2:paths dkane$
Note how the prompt changed after I ran the cd paths command. Before, the prompt included averages because that was the name of the current working directory. Using cd changed the current working directory to paths, causing the prompt to change as well.
Exercise 4
Use mkdir to make a directory called lessons inside paths by running mkdir lessons. Confirm that this worked by running ls. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:paths dkane$ mkdir lessons
Davids-MacBook-Pro-2:paths dkane$ ls
lessons
Davids-MacBook-Pro-2:paths dkane$
Because we have changed working directories, the lessons directory is created inside the paths directory. It is the only object in the paths directory.
Exercise 5
Make a directory within lessons called fruits by running mkdir lessons/fruits. In Windows, this would be mkdir lessons\fruits. The only difference between the Mac/Linux command and the Windows command is that the former uses a forward slash, /, to separate out directories while the latter uses a back slash, \.
Run ls lessons to check to see if fruits exists inside the lessons directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:paths dkane$ mkdir lessons/fruits
Davids-MacBook-Pro-2:paths dkane$ ls lessons/
fruits
Davids-MacBook-Pro-2:paths dkane$
We could not, as before, simply give fruits as an argument to mkdir because then the directory would be created directly inside paths, the current working directory, rather than within lessons. To refer to a location other than the working directory, we need to use a path, which describes the location directory by directory. The path above is called a relative path because it assumes the working directory as its starting point.
Exercise 6
Let's change our working directory to fruits. Run cd lessons/fruits. In Windows, cd lessons\fruits.
As you are typing this command, type only the f in fruits and then press the tab key (twice may be necessary on some computers). Pressing tab autocompletes the name of a file or directory.
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Get in the practice of using the tab key. Avoid typing whenever possible. Be lazy!
Exercise 7
Use touch to make a text file inside fruits, named pineapple.txt. Recall that your current location --- i.e., your working directory --- is now fruits. So, to make a new file within fruits, you just need touch pineapple.txt. Run ls to confirm. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:fruits dkane$ touch pineapple.txt
Davids-MacBook-Pro-2:fruits dkane$ ls
pineapple.txt
Davids-MacBook-Pro-2:fruits dkane$
pineapple.txt is still a relative path, but since the location is directly inside the assumed starting point, i.e. the working directory, the name of the file is all we need. If we had used lessons/fruits/apple.txt, as we would have had to do if our working directory were paths, we would have gotten an error because those directories would not be recognized within our actual starting point of fruits.
Exercise 8
Use touch to make two more text files inside fruits, named pear.txt and does-not-belong. That is, run touch pear.txt does-not-belong. Confirm by running ls. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:fruits dkane$ touch pear.txt does-not-belong
Davids-MacBook-Pro-2:fruits dkane$ ls
does-not-belong pear.txt pineapple.txt
Davids-MacBook-Pro-2:fruits dkane$
As always, note how the prompt reminds us that we are in the fruits directory.
Exercise 9
Let's change our working directory to lessons. Run cd .. to go to the folder immediately above the working directory. Use pwd to confirm that you are in the right directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:fruits dkane$ cd ..
Davids-MacBook-Pro-2:lessons dkane$ pwd
/Users/dkane/Desktop/projects/averages/paths/lessons
Davids-MacBook-Pro-2:lessons dkane$
.. is shorthand for the directory immediately above the current working directory. The phrase "current working directory" is a bit redundant. You don't need the word "current."
Exercise 10
Use mkdir to make a directory within lessons, named tbd. Run ls to confirm. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:lessons dkane$ mkdir tbd
Davids-MacBook-Pro-2:lessons dkane$ ls
fruits tbd
Davids-MacBook-Pro-2:lessons dkane$
Exercise 11
Use mv to move the file does-not-belong from the fruits directory to the tbd directory by running mv fruits/does-not-belong tbd. Run ls tbd to confirm. (Again, change forward slashes to backward slashes if you are using Windows.)
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:lessons dkane$ mv fruits/does-not-belong tbd
Davids-MacBook-Pro-2:lessons dkane$ ls tbd
does-not-belong
Davids-MacBook-Pro-2:lessons dkane$
We can act on files which are not in the working directory as long as we provide a path --- either relative, as here, or absolute --- to those files. In this case, neither mv nor ls are acting on the current directory. Instead, they are acting on lower directories: fruits and tbd.
Exercise 12
Use cd to change the working directory up to paths by running cd ... Confirm with pwd. Use mv and the . shorthand to move the directory tbd directly inside of paths by running mv lessons/tbd .. Confirm with ls. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:lessons dkane$ cd ..
Davids-MacBook-Pro-2:paths dkane$ pwd
/Users/dkane/Desktop/projects/averages/paths
Davids-MacBook-Pro-2:paths dkane$ mv lessons/tbd .
Davids-MacBook-Pro-2:paths dkane$ ls
lessons tbd
Davids-MacBook-Pro-2:paths dkane$
When using mv, there is no difference between moving a directory and moving a file.
Exercise 13
Move up one more directory, back to the original working directory, by running cd ... Confirm with pwd. Run rm -r paths to remove all the directories and files with which we have been working. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:paths dkane$ cd ..
Davids-MacBook-Pro-2:averages dkane$ pwd
/Users/dkane/Desktop/projects/averages
Davids-MacBook-Pro-2:averages dkane$ rm -r paths
Davids-MacBook-Pro-2:averages dkane$
In olden times, professional programmers would spend a lot of time learning the various options to commands like rm. Now, we just ask ChatGPT or a similar tool.
Important symbols
We have seen one important symbol --- .. --- already. This section will explore it along with . and ~. The most common English terms for these symbols are "dot" or ., "dot dot" for .., and "tilde" for ~. The . symbol indicates the current directory. The .. symbol is for the directory one above the current directory. The ~ symbol is for your "home" directory.
Exercise 1
Use mkdir symbols to create a new directory called symbols. cd into that directory by running cd symbols. Confirm the change with pwd. Confirm that the directory is empty by running ls.
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:averages dkane$ mkdir symbols
Davids-MacBook-Pro-2:averages dkane$ cd symbols
Davids-MacBook-Pro-2:symbols dkane$ pwd
/Users/dkane/Desktop/projects/averages/symbols
Davids-MacBook-Pro-2:symbols dkane$ ls
Davids-MacBook-Pro-2:symbols dkane$
The more practice we get with command line commands --- often called "shell" comamnds --- the easier it is to string together several of them in a row.
Exercise 2
But is the symbols directory really empty? Run ls -a to check. The - indicates an "option" to the ls command. The a option tells ls to return all the members of the directory.
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:symbols dkane$ ls -a
. ..
Davids-MacBook-Pro-2:symbols dkane$
Every directory, even an "empty" one includes . and ... The . is link to the current directory, i.e., to the symbols directory in which we are currently located. The .. is a link to the directory one level up, which is the averages directory in my case.
Exercise 3
Run ls .. to examine the contents of the directory one level above the current directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ ls ..
R averages.Rproj theory.html theory_files
README.md symbols theory.qmd
Davids-MacBook-Pro-2:symbols dkane$
Your answer will look different because you started this tutorial in a different directory, with different contents, then I did.
Exercise 4
Run ls ../.. to examine the contents of the directory two levels above the current directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ ls ../..
GBBO-Analysis mtc simmons
averages ncf soccer_player_birth_months
bootcamp numerai syllabi
boston-college organization tidycensus.tutorials
coordination primer tidymodels.tutorials
...
Davids-MacBook-Pro-2:symbols dkane$
I cut off the long list of directories in my projects directory. The symbols directory, in which we are current located, is in in that longer list.
Your answer will look different because you have a different collection of projects, presumably many fewer.
Exercise 5
Run pwd again. This returns the current working directory. Note that the return value is an absolute path. It tells you exactly where you --- meaning your Terminal session or instance --- are located on your computer.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ pwd
/Users/dkane/Desktop/projects/averages/symbols
Davids-MacBook-Pro-2:symbols dkane$
The absolute path for my current location, meaning my current working directory, contains these locations.
-
The starting / --- which would be a \ in Windows --- indicates the root, or origin of the file systems. There is no directory higher than the root directory.
-
Users followed by my user name, dkane. Most Mac/Linux machines follow this organization.
-
The next three directories are, first, projects, which is where I store all my R projects, second, averages, which just happens to be the name of the directory in which I started this tutorial, and, third, symbols, which is the directory we just created.
Exercise 6
Run cd without any argument. Doing so changes your current directory to your home directory because that is the default behavior for cd. Run pwd to confirm where you are. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ cd
Davids-MacBook-Pro-2:~ dkane$ pwd
/Users/dkane
Davids-MacBook-Pro-2:~ dkane$
In Mac/Linux, the most common location for a user's home directory is within the Users directory. Note how, after we run cd, the prompt changes to report ~ as the current working directory. ~ is the symbol for the current user's home directory.
Exercise 7
Use cd, along with the full path to the symbols directory which you determined above, to change the the working directory back to the symbols directory. Run pwd to confirm. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:~ dkane$ cd /Users/dkane/Desktop/projects/averages/symbols
Davids-MacBook-Pro-2:symbols dkane$ pwd
/Users/dkane/Desktop/projects/averages/symbols
Davids-MacBook-Pro-2:symbols dkane$
This is an example of using a "absolute" path to change locations.
Exercise 8
Run ls ~. The list should be identical to the list you generated above in the home directory. Because the home directory is used in the absolute path of so many files, its path --- generally something like /Users/your-user-name-here --- can be written with the shorthand ~, which is a tilde, pronounced TIL-D. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The shorthands we have learned so far, ., .., ~, stand for the text of the paths for the corresponding directory. They are not specific to any function and can be used in any situation where the text of the relevant path could be used.
Exercise 9
Confirm that you are currently located in the symbols directory by running pwd. Run cd .. to move one directory up, out of the symbols directory. Delete the symbols directory with rm -rf symbols. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:symbols dkane$ pwd
/Users/dkane/Desktop/projects/averages/symbols
Davids-MacBook-Pro-2:symbols dkane$ cd ..
Davids-MacBook-Pro-2:averages dkane$ rm -rf symbols
Davids-MacBook-Pro-2:averages dkane$
Note that rm -rf symbols and rm -rf symbols/, with the trailing forward slash, have the same effect. Except in rare circumstances --- although see an example before --- including the trailing forward slash in the name of a directory has no effect.
Options
Options modify the behavior of command line functions like ls.
Exercise 1
Use pwd to confirm that you are in your default working directory. Make a directory directly inside the working directory, named options, by running mkdir options. cd into options. Run ls to confirm that it is empty. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:averages dkane$ pwd
/Users/dkane/Desktop/projects/averages
Davids-MacBook-Pro-2:averages dkane$ mkdir options
Davids-MacBook-Pro-2:averages dkane$ cd options/
Davids-MacBook-Pro-2:options dkane$ ls
Davids-MacBook-Pro-2:options dkane$
Note how easy it is to string together several commands in order to accomplish our goals.
Exercise 2
Add a text file to the options directory, named .my-hidden.txt --- make sure to include the . at the front of the file name --- by running touch .my-hidden.txt. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Other than ., avoid using special characters or spaces anywhere in file names. These are difficult to work with in the Terminal.
Exercise 3
Run ls to look for the file you created. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should be something like:
Davids-MacBook-Pro-2:options dkane$ ls
Davids-MacBook-Pro-2:options dkane$
If you did the previous exercise correctly, you should not see the new file. This is because we prefixed the name with ., which hid the file from normal view. Files whose name begins with a . are called "hidden" files for this reason.
Exercise 4
Run ls -a. Using the option -a, you should be able to see all the files in the directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Options are rpreceded by a - and come before the argument. Your answer should look like:
Davids-MacBook-Pro-2:options dkane$ ls -a
. .. .my-hidden.txt
Davids-MacBook-Pro-2:options dkane$
The . file refers to the options directory itself. The .. refers to the directory in which the options directy is located. Every directory has both a . and a .. file inside of it, but we only see those files if we use the -a option.
Hidden files live all over your computer. You can turn on your ability to see hidden files in the R Studio Files pane (bottom right corner) by clicking the "More" button towards the top.
Exercise 5
The environmental variable R_HOME represents the path to a folder of set-up files that R has installed on your computer. Type and enter echo $R_HOME alone to make sure we are telling you the truth.
Recall that, on Windows, this would be echo %R_HOME% and cd %R_HOME%.
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:options dkane$ echo $R_HOME
/Library/Frameworks/R.framework/Resources
Davids-MacBook-Pro-2:options dkane$
Note how the prompt has changed because I am now in the options directory.
Exercise 6
Run ls $HOME. This should generate a list of the items in your home directory. $HOME is an environmental variable that represents the home directory.
If you are on Windows, you can try ls %HOME%, but, sometimes, %HOME% is not defined on Windows. In that case, ls %USERPROFILE% should work.
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
There are many different environmental variables for places throughout your computer. You can also make your own.
Exercise 7
Use pwd to confirm that you are still in options. Use ls to see what is inside R_HOME by running ls $R_HOME. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Don't worry about the details of these files. Our main point is that environmental variables are very handy because they make it easy to refer to a specific location on a computer, like where R is installed, even though the absolute path to this location is different on every person's computer.
Exercise 8
Run ls -l $R_HOME, so that we can see more information in a long list. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:options dkane$ ls -l $R_HOME
lrwxrwxr-x 1 root admin 26 Nov 27 11:20 /Library/Frameworks/R.framework/Resources -> Versions/Current/Resources
Davids-MacBook-Pro-2:options dkane$
This is an example of a situation in which $R_HOME and $R_HOME/ produce different results, as we will see in the next exercise. When the location pointed to be an environmental variable is a link, as in this case, using ls -l $R_HOME just gives us back the link.
Exercise 9
Run ls -l $R_HOME/. Just adding the trailing backward slash (or forward slash in Windows?) changes the output. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:options dkane$ ls -l $R_HOME/
total 200
-rw-rw-r-- 1 root admin 18011 Oct 31 21:02 COPYING
-rw-rw-r-- 1 root admin 488 Oct 31 21:02 Info.plist
lrwxrwxr-x 1 root admin 5 Nov 27 11:20 R -> bin/R
-rwxrwxr-x 1 root admin 70944 Oct 31 21:04 Rscript
-rw-rw-r-- 1 root admin 46 Oct 31 21:02 SVN-REVISION
drwxrwxr-x 28 root admin 896 Nov 27 11:20 bin
drwxrwxr-x 23 root admin 736 Nov 27 11:20 doc
...
In a long list, names are in the last column and file type is in the first: if the string in the first column begins with d it is a directory; if it begins with - it is a file; if it begins with l it is a link to another file or directory on the computer. The middle columns give, from left to right, the number of files, author, permission, file size (in bytes), and the date/time last modified.
Exercise 10
Check what is inside the doc directory by running ls -l $R_HOME/doc. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
As you could guess from the name, the directory contains mostly files, including AUTHORS.
Exercise 11
Let's make a copy of $R_HOME/doc/AUTHORS in options. Use the command cp, whose syntax is identical to mv, and the . shorthand. That is, run cp $R_HOME/doc/AUTHORS .. CP/CR.
On Windows, we would refer to this file as %R_HOME%\doc\AUTHORS. Recall that, in Windows, environment variables are surrounded by percentage signs -- % -- and directories are separated by backward slashes: \.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Like mv, cp can change a file name. Like mv, if the destination file name is omitted, cp will retain the same name by default.
Exercise 12
Try to use cp and . to copy the doc directory into options. You will get an error informing you that the thing you tried to copy was a directory. Run the same command using the option -r. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
As we have seen for rm, -r allows us to use cp with directories. This is different from mv, which does not need -r.
Exercise 13
Let's view just the initial lines of the AUTHORS. Run head AUTHORS. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Now you know how R got its name.
Exercise 14
Let's view more than just the initial 10 lines. The option -n allows you to specify the number of initial lines you want to see. Run head -n 18 AUTHORS. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The option -n takes an argument which allows head to display any number of initial lines.
Exercise 15
Use the command tail and the same -n option to view the last 15 lines of AUTHORS. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
If the argument of -nis greater than the number of lines in the file, head or tail will just print the whole file.
Exercise 16
Let's view the whole file at once. Run cat AUTHORS. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
cat stands for concatenate, which means "to chain together." While it is often used to a single text file, the command can take two arguments and print the files together.
Exercise 17
Run cat -n AUTHORS. Notice that -n has no argument. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
cat -n prints the text file with line numbers. Note that the names end at line 28.
Exercise 18
Let's make our own text file. Start by running echo which takes a quoted string, for example, "Your First and Last Name Here" as its argument. This "echoes" the argument by printing it in the next line of the terminal. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
echo can also take a string that is not in quotes as its argument.
Exercise 19
We can change the place that we echo to, from the Terminal to a text file, using > to redirect the output Run echo "Your First and Last Name Here" > test.txt. Then use ls to see if the file test.txt exists within your working directory. Then use cat to read this file. After you have confirmed that the file contains your name, use rm to remove test.txt. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Exercise 20
> can be used to redirect the output of any command, not just echo. Let's try to make a new text file in options with just the first 28 lines of AUTHORS called AUTHORS-fake. Run head -n 28 AUTHORS > AUTHORS-fake. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Exercise 21
Using >>, whose syntax is the same as >, we can append output to an existing document. Use echo and >> to append your name to the list of AUTHORS-fake. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Like >, >> is not limited to echo, but can be used to append the output of any command.
Exercise 22
Use tail and >> to append the last 11 lines of AUTHORS to AUTHORS-fake. Refer to the syntax in Exercise 18 if needed. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your fake is not great because your name is likely not placed in correct alphabetical order.
Exercise 23
Run cd .. to change your directory to the directory in which you started the tutorial. Run rm -r options to remove the options directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:options dkane$ cd ..
Davids-MacBook-Pro-2:averages dkane$ rm -r options
Davids-MacBook-Pro-2:averages dkane$
As usual, note how the prompt changes from Davids-MacBook-Pro-2:options dkane$ to Davids-MacBook-Pro-2:averages dkane$ as we move from the options directory to directory from which we started this tutorial, which is the averages directory in my case.
Wildcards
You will learn how to search for files by using wildcards to form regular expressions.
Exercise 1
Use pwd to confirm that you are in your default working directory. Use mkdir to create a directory named wildcards. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The mkdir command does not produce any output. To confirm that it had the desired effect, you could run ls.
Exercise 2
Change your working directory to wildcards using cd. Confirm the change with pwd. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
You answer should look something like:
Davids-MacBook-Pro-2:averages dkane$ cd wildcards/
Davids-MacBook-Pro-2:wildcards dkane$ pwd
/Users/dkane/Desktop/projects/averages/wildcards
Davids-MacBook-Pro-2:wildcards dkane$
Note how the prompt changed after we switche directories.
Keep track of your current location. There is a difference between being in the directory above wildcards and being inside of wildcards. Right now, you are inside wildcard.
Exercise 3
Using touch, Make three text files named hat.txt, cat.txt, and ate.txt. Confirm that you have done so by running ls. (No worries if you make a mistake. Just fix it by removing the misnamed file.) CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
touch can take multiple arguments, making a file for each one. touch hat.txt cat.txt ate.txt is equivalent to running touch three times.
Exercise 4
Terminal commands allow the use of wildcards. A wildcard * represents zero or more of any character, and it is used to work with similarly named files as a grouping.
Let's generate a list of all our files whose names contain the letter a. First simply try to run ls a. You will get an error message --- "No such file or directory" --- because there is no file named a in the working directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Though we have been using ls to return all the content of a directory, ls can also take a name as an argument, as above.
Exercise 5
Let's try again. Run ls a*. The only return will be ate.txt. Because you put * after a, ls returns only files that began with a. The "star" wildcard --- * --- matches anything. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Though * will match strings of any length, its positioning matters. a* is not the same thing as *a. The first matches any string (i.e., any file name) which starts with a. The second matches any string which ends with a.
Exercise 6
Now run ls *a*. This should return hat.txt cat.txt ate.txt. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Note that these regular expressions are case-sensitive. A regular expression is a "pattern" which you can use for many purposes, including as a search criteria.
Exercise 7
Make a list of all the files with names, before the suffix, which end in t by running ls *t.* CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
This should return hat.txt and cat.txt. Read this regular expression --- *t.* --- as matching any string which includes a t followed directly by a period, regardless of any characters which are also included, before or after. ate.txt is not matched because the t and the . are separated by e.
Exercise 8
Save the output of our list of all the file names that contained a to a new file names afiles.txt. Keep pressing the up arrow key to navigate through your previous commands until you get to the command you used above: ls *a*. Then add > afiles.txt afterwards and run the command. Run ls to confirm that it worked. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
You can use your up and down arrow keys to navigate command history. The > symbol outputs the result of the left-hand side command into the right-hand side location.
Exercise 9
Wildcards can be used with more than ls. Let's move hat.txt and cat.txt together into one directory.
First, make a new directory called seuss within the wildcards directory in which you are currently located.
Run ls to confirm. CP/CR
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
You answer should look like:
Davids-MBP:wildcards dkane$ mkdir seuss
Davids-MBP:wildcards dkane$ ls
afiles.txt ate.txt cat.txt hat.txt seuss
Davids-MBP:wildcards dkane$
The wildcards directory, in which you are currently located, now includes 5 items, one of which is the seuss directory.
Exercise 10
Run ls -l. CP/CR
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The -l option provides a long-format listing of the contents of the directory, including information about the type of content (file versus directory) and creation date/times. The leading d in the line for seuss indicates that it is a directory.
Exercise 11
Run ls *t.*. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Before moving or otherwise acting on a group of files, we often want to ensure that we have the correct grouping. Running ls with the appropriate regular expression is an easy way to test.
Exercise 12
Use the previous command (since we have confirmed that it generates the list of files we want to move) but replace ls with mv and then add seuss, which indicates the location to which we want to move the files. In other words, run mv *t.* seuss. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The mv command, like mkdir, does not produce any output. You need to check by hand to ensure it has done what you wanted.
Exercise 13
Run ls -R. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MBP:wildcards dkane$ ls -R
afiles.txt ate.txt seuss
./seuss:
cat.txt hat.txt
Davids-MBP:wildcards dkane$
The -R option to the ls command stands for recursive. We see, not simply the contents of the current directory (two files and the seuss directory) but also the contents of the seuss directory itself.
Exercise 14
Use cd .. to move out of the wildcards directory, one level up. Run pwd. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
In order to delete a directory, you can not be located within that directory. We want to delete (that is, "remove") the wildcards directory since we always want to clean up any temporary files/directories which we have created.
Exercise 15
Run rm wildcards. That command will fail because "wildcards: is a directory". You can't just rm directories in the same way that you rm files. Instead, you need to use rm -r, where the -r indicates recursive. Run rm -r wildcards. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Note that both wildcards and wildcards/ refer to the same entity, the wildcards directory. The Terminal often "adds" a forward slash (/) --- or, on Windows, a backward slash (\) --- to the end of directory names to indicate that the object is a directory, not simply a file.
Files
Downloading files and moving them to a sensible location is a core skill for data scientists.
Exercise 1
Confirm your location with pwd. Run mkdir files to create in a temporary directory in which to work. cd to that directory with cd files. Confirm that it is empty with ls. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:averages dkane$ pwd
/Users/dkane/Desktop/projects/averages
Davids-MacBook-Pro-2:averages dkane$ mkdir files
Davids-MacBook-Pro-2:averages dkane$ cd files/
Davids-MacBook-Pro-2:files dkane$ ls
Davids-MacBook-Pro-2:files dkane$
We often, as here, move to the directory in which we will be working. But we could have stayed in the starting directory, which is /Users/dkane/Desktop/projects/averages for me, and then worked from there, using files/ in the various commands to come.
Exercise 2
Every computer has a default directory in which files are downloaded. The most common name for this directory is Downloads and its most common location is your home directory.
Run ls ~/Downloads to examine the most likely location for that directory.
CP/CR.
If this command fails for you, then figure out where your default download location is and then adjust this command, and future commands, accordingly.
If, for some reason, you can't locate your Downloads directory, then just answer all the exercises in this section of the tutorial with "I could not find my Downloads directory."
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:files dkane$ ls ~/Downloads/
113-6439507-9501836.pdf
113-6441072-0767436.pdf
2024_11_06_10_29_42.pdf
223591000809.JPEG
Bassett.jpg
...
The ... indicates that there are many more files in this directory. I am not as organized as I ought to be. Try not to have your Downloads directory overrun with old files.
Exercise 3
In your browser, go to https://github.com/PPBDS/r4ds.tutorials.
This is the location for the R package which contains this tutorial. Click on the TODO.txt file, which should bring you to this URL:
https://github.com/PPBDS/r4ds.tutorials/blob/main/TODO.txt.
Click on the "Download raw file" symbol to download the DESCRIPTION file to your computer.
knitr:: include_graphics("images/download.png")
Run ls ~/Dowloads/T*. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:files dkane$ ls ~/Downloads/T*
/Users/dkane/Downloads/TODO.txt /Users/dkane/Downloads/Toronto.jpg
/Users/dkane/Downloads/TOM.pdf
Davids-MacBook-Pro-2:files dkane$
The * is a wildcard character, meaning that the ls command should return all the files which begin with a capital D. For me, there are three such files in my Downloads directory.
Note that, depending on your computer/setup, the file DESCRIPTION might or might not have a .txt suffix. The original file, located on Github, does not have one, but some computers, including mine, add the suffix automatically. If your downloaded file does not have the suffix, use DESCRIPTION in place of DESCRIPTION.txt in the upcoming exercises.
Exercise 4
Run ls ~/Downloads/TODO.txt. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:files dkane$ ls ~/Downloads/TODO.txt
/Users/dkane/Downloads/TODO.txt
Davids-MacBook-Pro-2:files dkane$
I often use ls to confirm that a file exists in the location in which I think it should. ls also returns the absolute path to the file.
Exercise 5
Run mv /Users/dkane/Downloads/TODO.txt .. Run ls to confirm that you have moved the TODO.txt file from the Downloads directory to the current working directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:files dkane$ mv /Users/dkane/Downloads/TODO.txt .
Davids-MacBook-Pro-2:files dkane$ ls
TODO.txt
Davids-MacBook-Pro-2:files dkane$
Recall that the . symbol indicates the current directory. Since we did not give a new name for the file, the old name is retained. We could have give the file a new name by using:
mv /Users/dkane/Downloads/TODO.txt TODO_2.txt
We also could gave used ~ to avoid providing the absolute path by running:
mv ~/Downloads/TODO.txt .
Exercise 6
Delete the file by running rm TODO.txt. Go one level up with cd ... Delete the files directory with rm -r files. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:files dkane$ rm TODO.txt
Davids-MacBook-Pro-2:files dkane$ cd ..
Davids-MacBook-Pro-2:averages dkane$ rm -r files/
Davids-MacBook-Pro-2:averages dkane$
grep
In a previous section, we used wildcards to create regular expressions in order to generate lists of file names which matched a specific pattern. In this section, we will use grep to look for words inside of files. Fortunately, wildcards and regular expressions work the same with grep.
Exercise 1
Make a directory called grepping using mkdir. Run ls. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
We call this folder grepping rather than grep because you should not use a command, like grep, as the name of a file or directory. It is possible to do this, just like it is possible to jump off a bridge. But, in both cases, you will probably regret it.
Exercise 2
cd into the grepping directory. Run this command:
printf "hat.txt\ncat.txt\nate.txt\n\n" > files.txt
The \n symbol will insert a new line between hat.txt, cat.txt, and ate.txt.
Run cat files.txt. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The extra \n at the end ensures that there is a blank line at the end of the file, which is always a good idea when dealing with text files.
Don't worry about the printf command. It is not used very often. We didn't use echo because it is annoying to use in the case of multiple lines of input when you are writing code which needs to work on both Mac/Unix and Windows.
Exercise 3
Let's search the text file for lines containing the letter "a". Run grep a files.txt. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
Remember to use the tab key to take advantage of auto-completion. Don't type! Tab complete!
This should return all three lines from the file, which are the names of the three files we initially created. The blank line is not returned because it does not include an "a".
grep is used to search for a string of characters within a text file. When it finds a match, it prints the line. You can put the regular expression, in this case a, in quotes but that is not required.
Exercise 4
Let's search through files.txt for lines that begin with the letter "a". Run grep ^a files.txt. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
This should return ate.txt.
^ is put at the beginning of a regular expression to indicate that the expression must occur at the beginning of a line. A dollar sign --- $ --- at the end of a regular expression indicates that the expression must occur at the end of the line.
We will not attempt the previous search we made of these files with wildcards because it is difficult, though possible, to search for strings with special characters like . with grep.
Exercise 5
Run ls $R_HOME --- ls %R_HOME% on Windows --- to make a list of the contents of the R home directory. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
R_HOME is an environment variable which should behave similarly regardless of your computer. There should be several directories and files in this listing, including COPYING and tests.
Exercise 6
Add > to ls $R_HOME to save this output to a new file named RHOME.txt located withing the grepping directory. That is, run
ls $R_HOME > RHOME.txt
or, on Windows,
ls %R_HOME% > RHOME.txt
Run ls. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The > symbol is known as the "output redirection operator." Because all the output has been sent (or redirected) into a new file, RHOME.txt, this command produces no output.
There are now two files in grepping: files.txt and R_HOME.txt.
Exercise 7
Run wc RHOME.txt. The wc command stands for word count. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
The first number returned by wc is the number of lines in the file. The second is the total number of words. The third is the number of characters. In this case, the number of lines is the same as the number of words.
Exercise 8
Use grep to search RHOME.txt for lines that contain R. That is, run:
grep R RHOME.txt
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
A mistyped grep command can cause the Terminal to get stuck and not generate a new prompt. If this happens, navigate to the top of the Terminal page and click the dropdown menu where Terminal says "busy." Select "Interrupt Terminal Command" from this menu in order to generate a new prompt and start again.
Exercise 9
Use grep and ^ to search RHOME.txt for lines that begin with R. That is, run:
grep ^R RHOME.txt
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
^ and $ are called metacharacters. It is often useful to put quotes around a regular expression which includes metacharacters.
Exercise 10
Use grep and $ to search RHOME.txt for lines that end with c. That is, run:
grep c$ RHOME.txt
CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
This should return two lines: doc and etc. (Your computer set up might be different, so don't worry if your answer is not the same.)
Exercise 11
Use grep to search RHOME.txt for lines than contain the string ib. That is, run:
grep ib RHOME.txt
CP/CR
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
egrep is an even more powerful version of grep. Learning more about egrep is beyond the scope of this tutorial.
Exercise 12
Use cd .. to change the working directory to the directory which is one level above your current location. This should be the default working directory from which we started. Run pwd. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
If you keep your R projects in the same place on your computer, only the last directory in the path for the default working directory will change between projects.
Exercise 13
Use rm -r to remove grepping. CP/CR.
question_text(NULL,
answer(NULL, correct = TRUE),
allow_retry = TRUE,
try_again_button = "Edit Answer",
incorrect = NULL,
rows = 3)
It is always a good idea to clean up after yourself. As the signs say when taking a hike in the forest: "Take only photos. Leave only footprints."
Summary
This tutorial covered material which is not actually in R for Data Science (2e) by Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund. But the material is in keeping with the spirit of that book. Some of the material from Chapter 6 Workflow: scripts and projects appeared here.
This tutorial introduced the structure and uses of the Terminal from within RStudio. The older, more general term for the terminal is the "command line." All modern operating systems provide a command line, from which sophisticated users can modify files and directories, using commands like pwd, ls, touch, mkdir, mv, rm, and cd. We also discussed regular expressions as well as some of the metacharacters (like, *, ^ and $) from which they are constructed.
Want to learn more about the command line and related topics? Read The Unix Workbench by Sean Kross.
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library(learnr) library(tutorial.helpers) library(tidyverse) library(knitr) knitr::opts_chunk$set(echo = FALSE) knitr::opts_chunk$set(out.width = '90%') options(tutorial.exercise.timelimit = 60, tutorial.storage = "local")
Introduction
This tutorial covers material which is not actually in R for Data Science (2e) by Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund. But the material is in keeping with the spirit of that book. Some of the material from Chapter 6 Workflow: scripts and projects appears here.
This tutorial introduces the structure and uses of the Terminal from within RStudio. The older, more general term for the terminal is the "command line." All modern operating systems provide a command line, from which sophisticated users can modify files and directories, using commands like pwd, ls, touch, mkdir, mv, rm, and cd. We also discuss regular expressions as well as some of the metacharacters (like, *, ^ and $) from which they are constructed.
Note that a default Windows installation is different from Mac or Linux. If you are using Windows, you must first install RTools. Download the latest version from here. Currently, the Rtools44 installer is what you want. The link is in the seventh paragraph of this page.
For the most part, Windows works like Mac/Unix. There are three main exceptions which are important for this tutorial:
-
Environment variables look like
$R_HOMEon Mac/Unix and%R_HOME%on Windows. That is, in both cases, we are using theR_HOMEenvironment variable. We just access this variable differently depending on the operating system. -
Directory separators are forward slashes --
/-- on Max/Unix and backward slashes --\-- on Windows. -
Creating new files can work differently on Mac/Linux and Windows. To create a new empty file named
new.txt, we would usetouch new.txton Mac/Linux. Assuming that you have installed RTools,touchshould also work on Windows. If it doesn't work for you, trycopy NUL new.txtto create an empty file namednew.txt.
The tutorial defaults use Mac/Unix nomenclature. If you are using Windows, you need to translate, for example:
ls $R_HOME/etc
into
ls %R_HOME%\etc
Terminal
The Terminal tab is next to the Console tab within the Console pane in the lower left portion of RStudio. (Yes, it is a bit confusing that we call the entire structure the Console pane even though only one part of it is the Console tab.) We use the Console tab to talk to R. We use the Terminal tab to talk directly with the computer. Sadly, the Console and the Terminal speak different languages.
Exercise 1
Hit the "return" key (the "enter" key on Windows) two times in the Terminal to see what happens. The terminal has a string of characters ending in a \$ before your cursor, called the prompt. After a command has been executed, a prompt will be generated on a new line to let you know that Terminal is ready for a new command. Copy and paste the three (blank) lines from the Terminal as your answer below. We do a lot of copy/pasting of commands/responses, so we abbreviate those instructions as CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look something like:
Davids-MacBook-Pro-2:averages dkane$ Davids-MacBook-Pro-2:averages dkane$ Davids-MacBook-Pro-2:averages dkane$
Your answer will look different from mine. Default prompts vary from computer to computer. In my case, the first part of the prompt is the name of my computer: Davids-MacBook-Pro-2. The second part, separated with a colon, is the name of the directory, averages, in which I am running the tutorial. The third part, separated by a space, is dkane, my username.
The prompt acts as a quick way to tell you where in the computer you are. The Terminal is sensitive to which folder location you are in, just like the R Console is.
Exercise 2
Let's figure out the location of the folder in which we currently are. (Note that the terms "folder" and "directory" mean the same thing.) To see your current location within your computer, type the command pwd (present working directory) in the Terminal. Hit return/enter key to run the command.
Going forward, we will instruct you to "run" a given command. You do this by typing the command at the prompt and then hitting the return/enter key.
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look something like mine:
Davids-MacBook-Pro-2:averages dkane$ pwd /Users/dkane/Desktop/projects/averages Davids-MacBook-Pro-2:averages dkane$
Notice how the last directory (folder) in the path is included in the prompt.
Exercise 3
Let's see a list of what is where we are, i.e. in our working directory. Run ls. Note that this is the letter "L" and the letter "S", both in lowercase. It is not the number "1". CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
If you do not give it any more information, ls assumes that you want a list of what is in your current working directory.
Exercise 4
Let's make a directory called example. Run mkdir example. Run ls to confirm that the new directory exists inside of the current working directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
mkdir creates an empty directory. We --- and most other people --- use the terms "folder" and "directory" interchangeably.
Exercise 5
Move into the example directory by running cd example. Run pwd. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:averages dkane$ cd example Davids-MacBook-Pro-2:example dkane$ pwd /Users/dkane/Desktop/projects/averages/example Davids-MacBook-Pro-2:example dkane$
The example directory is one level below the directory in which I started.
Exercise 6
Let's create a file called my.txt. Run touch my.txt. (Recall that if touch does not work on Windows for you, try copy NUL my.txt instead.)
Run ls to confirm that the new file exists inside the current directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Davids-MacBook-Pro-2:example dkane$ touch my.txt Davids-MacBook-Pro-2:example dkane$ ls my.txt Davids-MacBook-Pro-2:example dkane$
touch creates an empty file.
Exercise 7
Make a copy of my.txt called my_2.txt by using the cp command. That is, run cp my.txt my_2.txt. Confirm that this worked by running ls. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ cp my.txt my_2.text Davids-MacBook-Pro-2:example dkane$ ls my.txt my_2.text Davids-MacBook-Pro-2:example dkane$
Exercise 8
We rename files with the mv command, which is derived from move. The first argument is the file we want to rename, the second argument is the new name
Rename my.txt to fake.txt by running mv my.txt fake.txt. Run ls to confirm. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ mv my.txt fake.txt Davids-MacBook-Pro-2:example dkane$ ls fake.txt my_2.text Davids-MacBook-Pro-2:example dkane$
From the computer's point of view, renaming a file is the same thing as moving a file. In fact, moving is more general since it allows us to change both the name and the location of a file.
Exercise 9
Let's remove the file fake.txt. Run rm fake.txt. Run ls to confirm. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ rm fake.txt Davids-MacBook-Pro-2:example dkane$ ls my_2.text Davids-MacBook-Pro-2:example dkane$
Be careful with the rm command in the Terminal. Unlike moving files to Trash on your computer, it is (usually) irreversible.
Exercise 10
We want to remove the example directory. But we can't do that while we are "located" in that directory. That is, the computer is aware that our Terminal process --- the entity which is executing our commands like ls and cp --- is currently working from the example directory.
Run cd ... The "dot-dot" symbol --- .. --- references the directory which contains the current directory. Run pwd to confirm. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:example dkane$ cd .. Davids-MacBook-Pro-2:averages dkane$ pwd /Users/dkane/Desktop/projects/averages Davids-MacBook-Pro-2:averages dkane$
Again, note how the prompt changed because we moved directories. The .. symbol --- two periods --- always indicates the directory one level up, i.e., the directory in which example is located.
Exercise 11
Run rm -r example to remove the directory example. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
-r is an option that allows us to delete a directory. The r stands for recursive because, in order to delete a directory, you must also (recursively) deleting every directory and file within that directory.
It is good to clean up. Don't leave junk files lying around.
Paths
You will practice using paths both inside and outside the current working directory. You will learn a few shortcuts to make this easier.
Exercise 1
By default, the Terminal in RStudio starts with a working directory which is the same as the folder in which the current R project resides, i.e., the folder with the .Rproj file in it. Run pwd to show your current working directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The Output pane (bottom right corner) in RStudio includes several tabs, the most important of which is the Files tab. Click on it. At the top of the Files tab, you will see a series of directories, separated by >, on your computer, beginning with the Home icon. This should match the path generated by pwd.
Exercise 2
Use mkdir to make a directory named paths inside your current working directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The new directory is created directly inside the working directory.
Exercise 3
Let's change the working directory to paths. Run cd paths. Run pwd to confirm that you have changed the working directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look something like:
Davids-MacBook-Pro-2:averages dkane$ cd paths Davids-MacBook-Pro-2:paths dkane$ pwd /Users/dkane/Desktop/projects/averages/paths Davids-MacBook-Pro-2:paths dkane$
Note how the prompt changed after I ran the cd paths command. Before, the prompt included averages because that was the name of the current working directory. Using cd changed the current working directory to paths, causing the prompt to change as well.
Exercise 4
Use mkdir to make a directory called lessons inside paths by running mkdir lessons. Confirm that this worked by running ls. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:paths dkane$ mkdir lessons Davids-MacBook-Pro-2:paths dkane$ ls lessons Davids-MacBook-Pro-2:paths dkane$
Because we have changed working directories, the lessons directory is created inside the paths directory. It is the only object in the paths directory.
Exercise 5
Make a directory within lessons called fruits by running mkdir lessons/fruits. In Windows, this would be mkdir lessons\fruits. The only difference between the Mac/Linux command and the Windows command is that the former uses a forward slash, /, to separate out directories while the latter uses a back slash, \.
Run ls lessons to check to see if fruits exists inside the lessons directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:paths dkane$ mkdir lessons/fruits Davids-MacBook-Pro-2:paths dkane$ ls lessons/ fruits Davids-MacBook-Pro-2:paths dkane$
We could not, as before, simply give fruits as an argument to mkdir because then the directory would be created directly inside paths, the current working directory, rather than within lessons. To refer to a location other than the working directory, we need to use a path, which describes the location directory by directory. The path above is called a relative path because it assumes the working directory as its starting point.
Exercise 6
Let's change our working directory to fruits. Run cd lessons/fruits. In Windows, cd lessons\fruits.
As you are typing this command, type only the f in fruits and then press the tab key (twice may be necessary on some computers). Pressing tab autocompletes the name of a file or directory.
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Get in the practice of using the tab key. Avoid typing whenever possible. Be lazy!
Exercise 7
Use touch to make a text file inside fruits, named pineapple.txt. Recall that your current location --- i.e., your working directory --- is now fruits. So, to make a new file within fruits, you just need touch pineapple.txt. Run ls to confirm. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:fruits dkane$ touch pineapple.txt Davids-MacBook-Pro-2:fruits dkane$ ls pineapple.txt Davids-MacBook-Pro-2:fruits dkane$
pineapple.txt is still a relative path, but since the location is directly inside the assumed starting point, i.e. the working directory, the name of the file is all we need. If we had used lessons/fruits/apple.txt, as we would have had to do if our working directory were paths, we would have gotten an error because those directories would not be recognized within our actual starting point of fruits.
Exercise 8
Use touch to make two more text files inside fruits, named pear.txt and does-not-belong. That is, run touch pear.txt does-not-belong. Confirm by running ls. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:fruits dkane$ touch pear.txt does-not-belong Davids-MacBook-Pro-2:fruits dkane$ ls does-not-belong pear.txt pineapple.txt Davids-MacBook-Pro-2:fruits dkane$
As always, note how the prompt reminds us that we are in the fruits directory.
Exercise 9
Let's change our working directory to lessons. Run cd .. to go to the folder immediately above the working directory. Use pwd to confirm that you are in the right directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:fruits dkane$ cd .. Davids-MacBook-Pro-2:lessons dkane$ pwd /Users/dkane/Desktop/projects/averages/paths/lessons Davids-MacBook-Pro-2:lessons dkane$
.. is shorthand for the directory immediately above the current working directory. The phrase "current working directory" is a bit redundant. You don't need the word "current."
Exercise 10
Use mkdir to make a directory within lessons, named tbd. Run ls to confirm. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:lessons dkane$ mkdir tbd Davids-MacBook-Pro-2:lessons dkane$ ls fruits tbd Davids-MacBook-Pro-2:lessons dkane$
Exercise 11
Use mv to move the file does-not-belong from the fruits directory to the tbd directory by running mv fruits/does-not-belong tbd. Run ls tbd to confirm. (Again, change forward slashes to backward slashes if you are using Windows.)
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like this:
Davids-MacBook-Pro-2:lessons dkane$ mv fruits/does-not-belong tbd Davids-MacBook-Pro-2:lessons dkane$ ls tbd does-not-belong Davids-MacBook-Pro-2:lessons dkane$
We can act on files which are not in the working directory as long as we provide a path --- either relative, as here, or absolute --- to those files. In this case, neither mv nor ls are acting on the current directory. Instead, they are acting on lower directories: fruits and tbd.
Exercise 12
Use cd to change the working directory up to paths by running cd ... Confirm with pwd. Use mv and the . shorthand to move the directory tbd directly inside of paths by running mv lessons/tbd .. Confirm with ls. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:lessons dkane$ cd .. Davids-MacBook-Pro-2:paths dkane$ pwd /Users/dkane/Desktop/projects/averages/paths Davids-MacBook-Pro-2:paths dkane$ mv lessons/tbd . Davids-MacBook-Pro-2:paths dkane$ ls lessons tbd Davids-MacBook-Pro-2:paths dkane$
When using mv, there is no difference between moving a directory and moving a file.
Exercise 13
Move up one more directory, back to the original working directory, by running cd ... Confirm with pwd. Run rm -r paths to remove all the directories and files with which we have been working. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:paths dkane$ cd .. Davids-MacBook-Pro-2:averages dkane$ pwd /Users/dkane/Desktop/projects/averages Davids-MacBook-Pro-2:averages dkane$ rm -r paths Davids-MacBook-Pro-2:averages dkane$
In olden times, professional programmers would spend a lot of time learning the various options to commands like rm. Now, we just ask ChatGPT or a similar tool.
Important symbols
We have seen one important symbol --- .. --- already. This section will explore it along with . and ~. The most common English terms for these symbols are "dot" or ., "dot dot" for .., and "tilde" for ~. The . symbol indicates the current directory. The .. symbol is for the directory one above the current directory. The ~ symbol is for your "home" directory.
Exercise 1
Use mkdir symbols to create a new directory called symbols. cd into that directory by running cd symbols. Confirm the change with pwd. Confirm that the directory is empty by running ls.
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:averages dkane$ mkdir symbols Davids-MacBook-Pro-2:averages dkane$ cd symbols Davids-MacBook-Pro-2:symbols dkane$ pwd /Users/dkane/Desktop/projects/averages/symbols Davids-MacBook-Pro-2:symbols dkane$ ls Davids-MacBook-Pro-2:symbols dkane$
The more practice we get with command line commands --- often called "shell" comamnds --- the easier it is to string together several of them in a row.
Exercise 2
But is the symbols directory really empty? Run ls -a to check. The - indicates an "option" to the ls command. The a option tells ls to return all the members of the directory.
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:symbols dkane$ ls -a . .. Davids-MacBook-Pro-2:symbols dkane$
Every directory, even an "empty" one includes . and ... The . is link to the current directory, i.e., to the symbols directory in which we are currently located. The .. is a link to the directory one level up, which is the averages directory in my case.
Exercise 3
Run ls .. to examine the contents of the directory one level above the current directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ ls .. R averages.Rproj theory.html theory_files README.md symbols theory.qmd Davids-MacBook-Pro-2:symbols dkane$
Your answer will look different because you started this tutorial in a different directory, with different contents, then I did.
Exercise 4
Run ls ../.. to examine the contents of the directory two levels above the current directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ ls ../.. GBBO-Analysis mtc simmons averages ncf soccer_player_birth_months bootcamp numerai syllabi boston-college organization tidycensus.tutorials coordination primer tidymodels.tutorials ... Davids-MacBook-Pro-2:symbols dkane$
I cut off the long list of directories in my projects directory. The symbols directory, in which we are current located, is in in that longer list.
Your answer will look different because you have a different collection of projects, presumably many fewer.
Exercise 5
Run pwd again. This returns the current working directory. Note that the return value is an absolute path. It tells you exactly where you --- meaning your Terminal session or instance --- are located on your computer.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ pwd /Users/dkane/Desktop/projects/averages/symbols Davids-MacBook-Pro-2:symbols dkane$
The absolute path for my current location, meaning my current working directory, contains these locations.
-
The starting
/--- which would be a\in Windows --- indicates the root, or origin of the file systems. There is no directory higher than the root directory. -
Usersfollowed by my user name,dkane. Most Mac/Linux machines follow this organization. -
The next three directories are, first,
projects, which is where I store all my R projects, second,averages, which just happens to be the name of the directory in which I started this tutorial, and, third,symbols, which is the directory we just created.
Exercise 6
Run cd without any argument. Doing so changes your current directory to your home directory because that is the default behavior for cd. Run pwd to confirm where you are. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:symbols dkane$ cd Davids-MacBook-Pro-2:~ dkane$ pwd /Users/dkane Davids-MacBook-Pro-2:~ dkane$
In Mac/Linux, the most common location for a user's home directory is within the Users directory. Note how, after we run cd, the prompt changes to report ~ as the current working directory. ~ is the symbol for the current user's home directory.
Exercise 7
Use cd, along with the full path to the symbols directory which you determined above, to change the the working directory back to the symbols directory. Run pwd to confirm. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:~ dkane$ cd /Users/dkane/Desktop/projects/averages/symbols Davids-MacBook-Pro-2:symbols dkane$ pwd /Users/dkane/Desktop/projects/averages/symbols Davids-MacBook-Pro-2:symbols dkane$
This is an example of using a "absolute" path to change locations.
Exercise 8
Run ls ~. The list should be identical to the list you generated above in the home directory. Because the home directory is used in the absolute path of so many files, its path --- generally something like /Users/your-user-name-here --- can be written with the shorthand ~, which is a tilde, pronounced TIL-D. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The shorthands we have learned so far, ., .., ~, stand for the text of the paths for the corresponding directory. They are not specific to any function and can be used in any situation where the text of the relevant path could be used.
Exercise 9
Confirm that you are currently located in the symbols directory by running pwd. Run cd .. to move one directory up, out of the symbols directory. Delete the symbols directory with rm -rf symbols. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:symbols dkane$ pwd /Users/dkane/Desktop/projects/averages/symbols Davids-MacBook-Pro-2:symbols dkane$ cd .. Davids-MacBook-Pro-2:averages dkane$ rm -rf symbols Davids-MacBook-Pro-2:averages dkane$
Note that rm -rf symbols and rm -rf symbols/, with the trailing forward slash, have the same effect. Except in rare circumstances --- although see an example before --- including the trailing forward slash in the name of a directory has no effect.
Options
Options modify the behavior of command line functions like ls.
Exercise 1
Use pwd to confirm that you are in your default working directory. Make a directory directly inside the working directory, named options, by running mkdir options. cd into options. Run ls to confirm that it is empty. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:averages dkane$ pwd /Users/dkane/Desktop/projects/averages Davids-MacBook-Pro-2:averages dkane$ mkdir options Davids-MacBook-Pro-2:averages dkane$ cd options/ Davids-MacBook-Pro-2:options dkane$ ls Davids-MacBook-Pro-2:options dkane$
Note how easy it is to string together several commands in order to accomplish our goals.
Exercise 2
Add a text file to the options directory, named .my-hidden.txt --- make sure to include the . at the front of the file name --- by running touch .my-hidden.txt. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Other than ., avoid using special characters or spaces anywhere in file names. These are difficult to work with in the Terminal.
Exercise 3
Run ls to look for the file you created. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should be something like:
Davids-MacBook-Pro-2:options dkane$ ls Davids-MacBook-Pro-2:options dkane$
If you did the previous exercise correctly, you should not see the new file. This is because we prefixed the name with ., which hid the file from normal view. Files whose name begins with a . are called "hidden" files for this reason.
Exercise 4
Run ls -a. Using the option -a, you should be able to see all the files in the directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Options are rpreceded by a - and come before the argument. Your answer should look like:
Davids-MacBook-Pro-2:options dkane$ ls -a . .. .my-hidden.txt Davids-MacBook-Pro-2:options dkane$
The . file refers to the options directory itself. The .. refers to the directory in which the options directy is located. Every directory has both a . and a .. file inside of it, but we only see those files if we use the -a option.
Hidden files live all over your computer. You can turn on your ability to see hidden files in the R Studio Files pane (bottom right corner) by clicking the "More" button towards the top.
Exercise 5
The environmental variable R_HOME represents the path to a folder of set-up files that R has installed on your computer. Type and enter echo $R_HOME alone to make sure we are telling you the truth.
Recall that, on Windows, this would be echo %R_HOME% and cd %R_HOME%.
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:options dkane$ echo $R_HOME /Library/Frameworks/R.framework/Resources Davids-MacBook-Pro-2:options dkane$
Note how the prompt has changed because I am now in the options directory.
Exercise 6
Run ls $HOME. This should generate a list of the items in your home directory. $HOME is an environmental variable that represents the home directory.
If you are on Windows, you can try ls %HOME%, but, sometimes, %HOME% is not defined on Windows. In that case, ls %USERPROFILE% should work.
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
There are many different environmental variables for places throughout your computer. You can also make your own.
Exercise 7
Use pwd to confirm that you are still in options. Use ls to see what is inside R_HOME by running ls $R_HOME. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Don't worry about the details of these files. Our main point is that environmental variables are very handy because they make it easy to refer to a specific location on a computer, like where R is installed, even though the absolute path to this location is different on every person's computer.
Exercise 8
Run ls -l $R_HOME, so that we can see more information in a long list. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like this:
Davids-MacBook-Pro-2:options dkane$ ls -l $R_HOME lrwxrwxr-x 1 root admin 26 Nov 27 11:20 /Library/Frameworks/R.framework/Resources -> Versions/Current/Resources Davids-MacBook-Pro-2:options dkane$
This is an example of a situation in which $R_HOME and $R_HOME/ produce different results, as we will see in the next exercise. When the location pointed to be an environmental variable is a link, as in this case, using ls -l $R_HOME just gives us back the link.
Exercise 9
Run ls -l $R_HOME/. Just adding the trailing backward slash (or forward slash in Windows?) changes the output. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:options dkane$ ls -l $R_HOME/ total 200 -rw-rw-r-- 1 root admin 18011 Oct 31 21:02 COPYING -rw-rw-r-- 1 root admin 488 Oct 31 21:02 Info.plist lrwxrwxr-x 1 root admin 5 Nov 27 11:20 R -> bin/R -rwxrwxr-x 1 root admin 70944 Oct 31 21:04 Rscript -rw-rw-r-- 1 root admin 46 Oct 31 21:02 SVN-REVISION drwxrwxr-x 28 root admin 896 Nov 27 11:20 bin drwxrwxr-x 23 root admin 736 Nov 27 11:20 doc ...
In a long list, names are in the last column and file type is in the first: if the string in the first column begins with d it is a directory; if it begins with - it is a file; if it begins with l it is a link to another file or directory on the computer. The middle columns give, from left to right, the number of files, author, permission, file size (in bytes), and the date/time last modified.
Exercise 10
Check what is inside the doc directory by running ls -l $R_HOME/doc. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
As you could guess from the name, the directory contains mostly files, including AUTHORS.
Exercise 11
Let's make a copy of $R_HOME/doc/AUTHORS in options. Use the command cp, whose syntax is identical to mv, and the . shorthand. That is, run cp $R_HOME/doc/AUTHORS .. CP/CR.
On Windows, we would refer to this file as %R_HOME%\doc\AUTHORS. Recall that, in Windows, environment variables are surrounded by percentage signs -- % -- and directories are separated by backward slashes: \.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Like mv, cp can change a file name. Like mv, if the destination file name is omitted, cp will retain the same name by default.
Exercise 12
Try to use cp and . to copy the doc directory into options. You will get an error informing you that the thing you tried to copy was a directory. Run the same command using the option -r. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
As we have seen for rm, -r allows us to use cp with directories. This is different from mv, which does not need -r.
Exercise 13
Let's view just the initial lines of the AUTHORS. Run head AUTHORS. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Now you know how R got its name.
Exercise 14
Let's view more than just the initial 10 lines. The option -n allows you to specify the number of initial lines you want to see. Run head -n 18 AUTHORS. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The option -n takes an argument which allows head to display any number of initial lines.
Exercise 15
Use the command tail and the same -n option to view the last 15 lines of AUTHORS. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
If the argument of -nis greater than the number of lines in the file, head or tail will just print the whole file.
Exercise 16
Let's view the whole file at once. Run cat AUTHORS. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
cat stands for concatenate, which means "to chain together." While it is often used to a single text file, the command can take two arguments and print the files together.
Exercise 17
Run cat -n AUTHORS. Notice that -n has no argument. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
cat -n prints the text file with line numbers. Note that the names end at line 28.
Exercise 18
Let's make our own text file. Start by running echo which takes a quoted string, for example, "Your First and Last Name Here" as its argument. This "echoes" the argument by printing it in the next line of the terminal. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
echo can also take a string that is not in quotes as its argument.
Exercise 19
We can change the place that we echo to, from the Terminal to a text file, using > to redirect the output Run echo "Your First and Last Name Here" > test.txt. Then use ls to see if the file test.txt exists within your working directory. Then use cat to read this file. After you have confirmed that the file contains your name, use rm to remove test.txt. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Exercise 20
> can be used to redirect the output of any command, not just echo. Let's try to make a new text file in options with just the first 28 lines of AUTHORS called AUTHORS-fake. Run head -n 28 AUTHORS > AUTHORS-fake. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Exercise 21
Using >>, whose syntax is the same as >, we can append output to an existing document. Use echo and >> to append your name to the list of AUTHORS-fake. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Like >, >> is not limited to echo, but can be used to append the output of any command.
Exercise 22
Use tail and >> to append the last 11 lines of AUTHORS to AUTHORS-fake. Refer to the syntax in Exercise 18 if needed. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your fake is not great because your name is likely not placed in correct alphabetical order.
Exercise 23
Run cd .. to change your directory to the directory in which you started the tutorial. Run rm -r options to remove the options directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:options dkane$ cd .. Davids-MacBook-Pro-2:averages dkane$ rm -r options Davids-MacBook-Pro-2:averages dkane$
As usual, note how the prompt changes from Davids-MacBook-Pro-2:options dkane$ to Davids-MacBook-Pro-2:averages dkane$ as we move from the options directory to directory from which we started this tutorial, which is the averages directory in my case.
Wildcards
You will learn how to search for files by using wildcards to form regular expressions.
Exercise 1
Use pwd to confirm that you are in your default working directory. Use mkdir to create a directory named wildcards. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The mkdir command does not produce any output. To confirm that it had the desired effect, you could run ls.
Exercise 2
Change your working directory to wildcards using cd. Confirm the change with pwd. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
You answer should look something like:
Davids-MacBook-Pro-2:averages dkane$ cd wildcards/ Davids-MacBook-Pro-2:wildcards dkane$ pwd /Users/dkane/Desktop/projects/averages/wildcards Davids-MacBook-Pro-2:wildcards dkane$
Note how the prompt changed after we switche directories.
Keep track of your current location. There is a difference between being in the directory above wildcards and being inside of wildcards. Right now, you are inside wildcard.
Exercise 3
Using touch, Make three text files named hat.txt, cat.txt, and ate.txt. Confirm that you have done so by running ls. (No worries if you make a mistake. Just fix it by removing the misnamed file.) CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
touch can take multiple arguments, making a file for each one. touch hat.txt cat.txt ate.txt is equivalent to running touch three times.
Exercise 4
Terminal commands allow the use of wildcards. A wildcard * represents zero or more of any character, and it is used to work with similarly named files as a grouping.
Let's generate a list of all our files whose names contain the letter a. First simply try to run ls a. You will get an error message --- "No such file or directory" --- because there is no file named a in the working directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Though we have been using ls to return all the content of a directory, ls can also take a name as an argument, as above.
Exercise 5
Let's try again. Run ls a*. The only return will be ate.txt. Because you put * after a, ls returns only files that began with a. The "star" wildcard --- * --- matches anything. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Though * will match strings of any length, its positioning matters. a* is not the same thing as *a. The first matches any string (i.e., any file name) which starts with a. The second matches any string which ends with a.
Exercise 6
Now run ls *a*. This should return hat.txt cat.txt ate.txt. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Note that these regular expressions are case-sensitive. A regular expression is a "pattern" which you can use for many purposes, including as a search criteria.
Exercise 7
Make a list of all the files with names, before the suffix, which end in t by running ls *t.* CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
This should return hat.txt and cat.txt. Read this regular expression --- *t.* --- as matching any string which includes a t followed directly by a period, regardless of any characters which are also included, before or after. ate.txt is not matched because the t and the . are separated by e.
Exercise 8
Save the output of our list of all the file names that contained a to a new file names afiles.txt. Keep pressing the up arrow key to navigate through your previous commands until you get to the command you used above: ls *a*. Then add > afiles.txt afterwards and run the command. Run ls to confirm that it worked. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
You can use your up and down arrow keys to navigate command history. The > symbol outputs the result of the left-hand side command into the right-hand side location.
Exercise 9
Wildcards can be used with more than ls. Let's move hat.txt and cat.txt together into one directory.
First, make a new directory called seuss within the wildcards directory in which you are currently located.
Run ls to confirm. CP/CR
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
You answer should look like:
Davids-MBP:wildcards dkane$ mkdir seuss Davids-MBP:wildcards dkane$ ls afiles.txt ate.txt cat.txt hat.txt seuss Davids-MBP:wildcards dkane$
The wildcards directory, in which you are currently located, now includes 5 items, one of which is the seuss directory.
Exercise 10
Run ls -l. CP/CR
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The -l option provides a long-format listing of the contents of the directory, including information about the type of content (file versus directory) and creation date/times. The leading d in the line for seuss indicates that it is a directory.
Exercise 11
Run ls *t.*. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Before moving or otherwise acting on a group of files, we often want to ensure that we have the correct grouping. Running ls with the appropriate regular expression is an easy way to test.
Exercise 12
Use the previous command (since we have confirmed that it generates the list of files we want to move) but replace ls with mv and then add seuss, which indicates the location to which we want to move the files. In other words, run mv *t.* seuss. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The mv command, like mkdir, does not produce any output. You need to check by hand to ensure it has done what you wanted.
Exercise 13
Run ls -R. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MBP:wildcards dkane$ ls -R afiles.txt ate.txt seuss ./seuss: cat.txt hat.txt Davids-MBP:wildcards dkane$
The -R option to the ls command stands for recursive. We see, not simply the contents of the current directory (two files and the seuss directory) but also the contents of the seuss directory itself.
Exercise 14
Use cd .. to move out of the wildcards directory, one level up. Run pwd. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
In order to delete a directory, you can not be located within that directory. We want to delete (that is, "remove") the wildcards directory since we always want to clean up any temporary files/directories which we have created.
Exercise 15
Run rm wildcards. That command will fail because "wildcards: is a directory". You can't just rm directories in the same way that you rm files. Instead, you need to use rm -r, where the -r indicates recursive. Run rm -r wildcards. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Note that both wildcards and wildcards/ refer to the same entity, the wildcards directory. The Terminal often "adds" a forward slash (/) --- or, on Windows, a backward slash (\) --- to the end of directory names to indicate that the object is a directory, not simply a file.
Files
Downloading files and moving them to a sensible location is a core skill for data scientists.
Exercise 1
Confirm your location with pwd. Run mkdir files to create in a temporary directory in which to work. cd to that directory with cd files. Confirm that it is empty with ls. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:averages dkane$ pwd /Users/dkane/Desktop/projects/averages Davids-MacBook-Pro-2:averages dkane$ mkdir files Davids-MacBook-Pro-2:averages dkane$ cd files/ Davids-MacBook-Pro-2:files dkane$ ls Davids-MacBook-Pro-2:files dkane$
We often, as here, move to the directory in which we will be working. But we could have stayed in the starting directory, which is /Users/dkane/Desktop/projects/averages for me, and then worked from there, using files/ in the various commands to come.
Exercise 2
Every computer has a default directory in which files are downloaded. The most common name for this directory is Downloads and its most common location is your home directory.
Run ls ~/Downloads to examine the most likely location for that directory.
CP/CR.
If this command fails for you, then figure out where your default download location is and then adjust this command, and future commands, accordingly.
If, for some reason, you can't locate your Downloads directory, then just answer all the exercises in this section of the tutorial with "I could not find my Downloads directory."
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:files dkane$ ls ~/Downloads/ 113-6439507-9501836.pdf 113-6441072-0767436.pdf 2024_11_06_10_29_42.pdf 223591000809.JPEG Bassett.jpg ...
The ... indicates that there are many more files in this directory. I am not as organized as I ought to be. Try not to have your Downloads directory overrun with old files.
Exercise 3
In your browser, go to https://github.com/PPBDS/r4ds.tutorials.
This is the location for the R package which contains this tutorial. Click on the TODO.txt file, which should bring you to this URL:
https://github.com/PPBDS/r4ds.tutorials/blob/main/TODO.txt.
Click on the "Download raw file" symbol to download the DESCRIPTION file to your computer.
knitr:: include_graphics("images/download.png")
Run ls ~/Dowloads/T*. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
My answer looks like:
Davids-MacBook-Pro-2:files dkane$ ls ~/Downloads/T* /Users/dkane/Downloads/TODO.txt /Users/dkane/Downloads/Toronto.jpg /Users/dkane/Downloads/TOM.pdf Davids-MacBook-Pro-2:files dkane$
The * is a wildcard character, meaning that the ls command should return all the files which begin with a capital D. For me, there are three such files in my Downloads directory.
Note that, depending on your computer/setup, the file DESCRIPTION might or might not have a .txt suffix. The original file, located on Github, does not have one, but some computers, including mine, add the suffix automatically. If your downloaded file does not have the suffix, use DESCRIPTION in place of DESCRIPTION.txt in the upcoming exercises.
Exercise 4
Run ls ~/Downloads/TODO.txt. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:files dkane$ ls ~/Downloads/TODO.txt /Users/dkane/Downloads/TODO.txt Davids-MacBook-Pro-2:files dkane$
I often use ls to confirm that a file exists in the location in which I think it should. ls also returns the absolute path to the file.
Exercise 5
Run mv /Users/dkane/Downloads/TODO.txt .. Run ls to confirm that you have moved the TODO.txt file from the Downloads directory to the current working directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:files dkane$ mv /Users/dkane/Downloads/TODO.txt . Davids-MacBook-Pro-2:files dkane$ ls TODO.txt Davids-MacBook-Pro-2:files dkane$
Recall that the . symbol indicates the current directory. Since we did not give a new name for the file, the old name is retained. We could have give the file a new name by using:
mv /Users/dkane/Downloads/TODO.txt TODO_2.txt
We also could gave used ~ to avoid providing the absolute path by running:
mv ~/Downloads/TODO.txt .
Exercise 6
Delete the file by running rm TODO.txt. Go one level up with cd ... Delete the files directory with rm -r files. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Your answer should look like:
Davids-MacBook-Pro-2:files dkane$ rm TODO.txt Davids-MacBook-Pro-2:files dkane$ cd .. Davids-MacBook-Pro-2:averages dkane$ rm -r files/ Davids-MacBook-Pro-2:averages dkane$
grep
In a previous section, we used wildcards to create regular expressions in order to generate lists of file names which matched a specific pattern. In this section, we will use grep to look for words inside of files. Fortunately, wildcards and regular expressions work the same with grep.
Exercise 1
Make a directory called grepping using mkdir. Run ls. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
We call this folder grepping rather than grep because you should not use a command, like grep, as the name of a file or directory. It is possible to do this, just like it is possible to jump off a bridge. But, in both cases, you will probably regret it.
Exercise 2
cd into the grepping directory. Run this command:
printf "hat.txt\ncat.txt\nate.txt\n\n" > files.txt
The \n symbol will insert a new line between hat.txt, cat.txt, and ate.txt.
Run cat files.txt. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The extra \n at the end ensures that there is a blank line at the end of the file, which is always a good idea when dealing with text files.
Don't worry about the printf command. It is not used very often. We didn't use echo because it is annoying to use in the case of multiple lines of input when you are writing code which needs to work on both Mac/Unix and Windows.
Exercise 3
Let's search the text file for lines containing the letter "a". Run grep a files.txt. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
Remember to use the tab key to take advantage of auto-completion. Don't type! Tab complete!
This should return all three lines from the file, which are the names of the three files we initially created. The blank line is not returned because it does not include an "a".
grep is used to search for a string of characters within a text file. When it finds a match, it prints the line. You can put the regular expression, in this case a, in quotes but that is not required.
Exercise 4
Let's search through files.txt for lines that begin with the letter "a". Run grep ^a files.txt. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
This should return ate.txt.
^ is put at the beginning of a regular expression to indicate that the expression must occur at the beginning of a line. A dollar sign --- $ --- at the end of a regular expression indicates that the expression must occur at the end of the line.
We will not attempt the previous search we made of these files with wildcards because it is difficult, though possible, to search for strings with special characters like . with grep.
Exercise 5
Run ls $R_HOME --- ls %R_HOME% on Windows --- to make a list of the contents of the R home directory. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
R_HOME is an environment variable which should behave similarly regardless of your computer. There should be several directories and files in this listing, including COPYING and tests.
Exercise 6
Add > to ls $R_HOME to save this output to a new file named RHOME.txt located withing the grepping directory. That is, run
ls $R_HOME > RHOME.txt
or, on Windows,
ls %R_HOME% > RHOME.txt
Run ls. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The > symbol is known as the "output redirection operator." Because all the output has been sent (or redirected) into a new file, RHOME.txt, this command produces no output.
There are now two files in grepping: files.txt and R_HOME.txt.
Exercise 7
Run wc RHOME.txt. The wc command stands for word count. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
The first number returned by wc is the number of lines in the file. The second is the total number of words. The third is the number of characters. In this case, the number of lines is the same as the number of words.
Exercise 8
Use grep to search RHOME.txt for lines that contain R. That is, run:
grep R RHOME.txt
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
A mistyped grep command can cause the Terminal to get stuck and not generate a new prompt. If this happens, navigate to the top of the Terminal page and click the dropdown menu where Terminal says "busy." Select "Interrupt Terminal Command" from this menu in order to generate a new prompt and start again.
Exercise 9
Use grep and ^ to search RHOME.txt for lines that begin with R. That is, run:
grep ^R RHOME.txt
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
^ and $ are called metacharacters. It is often useful to put quotes around a regular expression which includes metacharacters.
Exercise 10
Use grep and $ to search RHOME.txt for lines that end with c. That is, run:
grep c$ RHOME.txt
CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
This should return two lines: doc and etc. (Your computer set up might be different, so don't worry if your answer is not the same.)
Exercise 11
Use grep to search RHOME.txt for lines than contain the string ib. That is, run:
grep ib RHOME.txt
CP/CR
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
egrep is an even more powerful version of grep. Learning more about egrep is beyond the scope of this tutorial.
Exercise 12
Use cd .. to change the working directory to the directory which is one level above your current location. This should be the default working directory from which we started. Run pwd. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
If you keep your R projects in the same place on your computer, only the last directory in the path for the default working directory will change between projects.
Exercise 13
Use rm -r to remove grepping. CP/CR.
question_text(NULL, answer(NULL, correct = TRUE), allow_retry = TRUE, try_again_button = "Edit Answer", incorrect = NULL, rows = 3)
It is always a good idea to clean up after yourself. As the signs say when taking a hike in the forest: "Take only photos. Leave only footprints."
Summary
This tutorial covered material which is not actually in R for Data Science (2e) by Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund. But the material is in keeping with the spirit of that book. Some of the material from Chapter 6 Workflow: scripts and projects appeared here.
This tutorial introduced the structure and uses of the Terminal from within RStudio. The older, more general term for the terminal is the "command line." All modern operating systems provide a command line, from which sophisticated users can modify files and directories, using commands like pwd, ls, touch, mkdir, mv, rm, and cd. We also discussed regular expressions as well as some of the metacharacters (like, *, ^ and $) from which they are constructed.
Want to learn more about the command line and related topics? Read The Unix Workbench by Sean Kross.
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