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## Information

###

## 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 two 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.

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.

###

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.

###

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`. CP/CR.

###

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.

###

`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.

###

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`. Run `ls` to confirm that the new file exists inside the current directory. CP/CR.

###

    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.

###

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.

###

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.

###

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.

###

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.

`-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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

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.

###

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.

###

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.

###

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.

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.

###

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.

###

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.

###

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.

###

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.

###

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.

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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: `\`.

###

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.

###

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.

###

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.

###

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.

###

If the argument of `-n`is 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.

###

`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.

###

`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.

###

`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.

###

### 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.

###

### 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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

`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.

###

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.

###

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.

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.

###

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.

###

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

###

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

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.”

###

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.

Run `ls ~/Dowloads/T*`. CP/CR.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

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.

###

`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.

###

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.

###

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.

###

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.

###

`^` 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.

###

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

###

`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.

###

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.

###

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.

## Download answers

###

When you have completed this tutorial, follow these steps:

1. Click the button to download a file containing your answers.
2. Save the file onto your computer in a convenient location.

Download HTML
(If no file seems to download, try clicking with the alternative button on the download button and choose "Save link as...")

# Terminal

#### David Kane