What are Folders (and Directories)?

One thing computers do is store a lot of files. For example, my laptop has about 1.1 million files on it, from programmes to run the operating system, to important photos like this

Arwen with beer

We need some way of organsising these files. This is done using directories. And unless you want to get technical, directories are the same as folders.

Essentially, a directory is a virtual container for files. So for ST2304 I have a directory to keep all of the files in. It has a file called LearningObjectives.docx, and a lot other directories, e.g. Exams and Week01 Introduction. These contain more files, e.g. Week01 Introduction contains files like Lecture1.pdf.

Because directories can contain directories, we can have a whole structure directories, which looks like a tree. So for this course I used Dropbox, and have a Teaching directory (alongside other directories for different projects. One is called Dog Faces). In the Teaching directory I have directories for the different courses, including one called ST2304. In there I have the directories for each week’s material.

Structuring directories like this makes it easier to find files, and also easier to write code that will do something with all of the files in a directory. All computers use directories, even if they are largely hidden from you.

How do directories work?

Although there are differences between different operating systems in the details, the basic way directories work is the same. Their structure is like a tree: each directory can have several subdirectories (and each subdirectories is only in one parent directory).

If we want to find a file on a computer, we need to know what directory it is in. We write this by writing the directories as a filepath. For example, the file path for this course on my laptop is /work/bohara/Dropbox/Teaching/ST2304/. At the base of the tree are directories like bin/ and dev/, which hold files that the operating system needs. It also has a directory called work/, which has one subdirectory: bohara/.

The /work/bohara/ directory is my “home” when I log onto my laptop. Everything under this in the tree is specific to me: if I added an account for Zaphod Beeblebrox, then he would have a /home/zaphodb/ folder, and could put his files in there. We can follow the same logic further: Dropbox/Teaching/ST2304/ is the rest of the filepath, and gets us to the directory for this course. This file is in the Week 2 sub-directory, so this file is (before I move it to the web!): /work/bohara/Dropbox/Teaching/ST2304/Week02 One Parameter/Directories.html

Note that we use forward slashes between the directory names. Other operating systems might be different.

So, if I want to (say) copy this file to the directory for next week, I could fire up the command line and do this:

copy /work/bohara/Dropbox/Teaching/ST2304/Week02/Directories.html /work/bohara/Dropbox/Teaching/ST2304/Week03/Directories.html

(modern operating systems have a GUI (“Graphical User Interface”) which hides this from you: you click on a file, use Ctrl-C to copy, navigate to the new folder and use Ctrl-V to paste)

But that is horrible to write. So there are a couple of shortcuts:

One is the use of the home directory. If the computer thinks I am in my home directory (/work/bohara/), then if I save a file from somewhere else, it will save it in my home directory. Some programmes don’t do this, for example my web browser will, by default, save a file in /work/bohara/Downloads. So if I want to copy a file into my home directory, I could do this:

copy /work/bohara/Dropbox/Teaching/ST2304_2020/Week02/Directories.html Directories.html

The other shortcut is the use of relative paths. If I am in my home directory, I can use directories relative to that. So, for example, if I am in my home directory, I can refer to the Dropbox sub-directory as /work/bohara/Dropbox/, or more simply as Dropbox/. The advantage of this is that if I cange to another directory that has Dropbox installed, I can still use the same relative path.

Relative paths can be used like this to got down the directory tree, but what about up? To do this you can use ../. So, if I wanted to go from my home directory to say, Zaphod Beeblebrox’s, I could use ../zaphodb/. The .. takes me up one level, and then zaphodb/ is his home directory.

Windows

(note: this is being written by someone who hasn’t used Windows seriously for over a decade)

Windows uses the basic system described above, but it tries to hide the details. But there are a couple of notable differences:

  • Windows uses back slashes, \, between directory names. So on Windows Dropbox/Teaching/ST2304_2020/Week02/Directories.html is Dropbox\\Teaching\\ST2304_2020\\Week02\\Directories.html
  • Windows is not case sensitive, so Dropbox\\Teaching is the same as Dropbox\\TEACHING
  • Windows uses drives in the file structure. Your hard drive is C:. When you add other drives, e.g. an external drive, or a USB stick, or a network drive, it gets a new letter. For example, NTNU uses M: as your home drive on the NTNU system.
  • For some files, Windows give you a name in Norwegian (or whatever language you are using), even though internally the English name is used. This will get confusing, because if you access the files through R, you will have to use the English name.

This means that your file names will look different, e.g. my home directory would be C:\\Users\\bobhara.

Linux

Linux is based on Unix, so it uses the same file system layout, which is what I described above. One helpful trick is that you can specify your home directory with ~. So if you are in another directory, you can get to a file with ~/Dropbox/Teaching/ST2304_2020/Week02/Directories.html

Mac

Macs use a Unix operating system, so they basically act like Linux (only without the penguins).

If you want to find the full filepath for a particular file on a Mac you should locate the file in Finder:

Finder

Then right-click the file and select ‘Get info’/ ‘Vis info’. In the example below, you can see that my file is saved at ~/Users/emilygs/Dropbox/ST2304_2020/Week02 One Parameter/Directories.Rmd.

Result of Get Info

Directories in R

When you are using R, you will be able to access the directory structure in the same way. Above I have been discussing home directories, and R has the same thing, but it’s called a working directory, i.e. the directory you are working in. You can find out what it is with getwd():

getwd()
## [1] "/Users/robertoh/git_repos/ST2304/Week02 One Parameter"

You can see that this is not my home directory. This is because I ran this code from a different directory. If I want to change my working directory, I can use setwd():

setwd("~/Dropbox/Teaching/ST2304/Week03 Confidence Intervals/")

Which is the directory for the material for week 3. So once I start working on that material, I can use that as my working directory.

I can also do things with the files, like see them, copy them etc. ?files lists the functions to do that. You may not need these during the course, but for if you do…

dir()
file.copy("Arwen.JPG", "ABird.JPG") # copy a file
file.remove("ABird.JPG") # remove a file

# Look in Week 3's directory
dir("../../ST2304/Week03 Confidence Intervals/")

file.exists("Directories.html") # Does this file exist?
file.exists("https://www.math.ntnu.no/emner/ST2304/2020v/Week01/test_data.csv") # Yes, web addresses also work!

Some advice

https://imgs.xkcd.com/comics/documents.png