Where do files live? In trees.

• The base of the tree is called the root and denoted /.
• Each branch is called a directory or folder.
• Other branches can split off a branch. We say that the “directory can contain other directories.”
  • These are sometimes called “sub-directories” but there’s no real distinction; they’re all directories.
• In addition to branches splitting off, there can be leaves. A directory can contain files (as well as directories).

Every file is contained within a directory. Every directory (except root) is contained with another directory.

The path to a file is the sequence of directories between the root and the file.

The path to a file is the sequence of directories between the root and the file.

In this directory tree …

• there is a file file1 that is contained within the Jane directory.
• In turn, Jane is contained within Home which is contained within root (/).

The file path is /Home/Jane/file1

• There is another, completely distinct file names file1. It’s path is /Home/Pablo/file1.
• There are two directories named /Tmp. One is /Home/Tmp. The other is /Home/Jane/Tmp.

Every file on the computer has a unique identifier consisting of the path and the file name.

A similar idea applies to the files available through the Internet.

• Instead of / as root, there is a protocol as root, typically http:// or https://.
• There is a domain name that describes which computer(s) contain the file, e.g. http://github.com.
• Following the domain name is the path to the file, e.g. http://github.com/dtkaplan/comp110/.
• The file itself is at the end of the path, e.g. http://github.com/dtkaplan/comp110/index.html.

The “Working Directory”

Every Rmd file is contained within a directory. This is called the working directory.

• When you refer to another file, you are allowed to give just the part of the path that stems from the working directory.

Example:

• Your Rmd file is in /Home. Within your Rmd file, you can refer to /Home/Jane/file1 as simply Jane/file1. This is called a relative path.
• Paths beginning with root (/) are called absolute paths.

Relative paths are useful because often you will move an entire directory (and it’s contents) to another computer. The absolute path name will probably change. But the relative path remains the same.

Filetype extensions

All computer files are sequences of bits. The software that reads a file interprets the bits according to a specified format. There are different standard formats for different purposes.

Some common filename extensions for the sort of web resources you will be using:

• .png for pictures
• .jpg or .jpeg for photographs
• .csv or .Rdata for data files
• .Rmd for the human editable text of a document (called R Markdown)
• .html for web pages themselves

Finding a file path

Most people are used to locating a file by using a file browser.

You click on a directory and then can examine the files and sub-directories contained within that directory.

file.choose(): A handy R function for finding the file path of a file using a file browser:

A typical dialog works like this:

1. You give the command file.choose() in the R console. (Don’t use file.choose() in an Rmd file.)
2. You navigate in the familiar way up and down the directories.
3. You select the file you were looking for.
4. The file name and (absolute) path of the file are displayed, e.g. /Home/Jane/mydata.csv.

5. You copy that name into your Rmd file, e.g.

   Cases <- read.csv("/Home/Jane/mydata.csv")

Author: Daniel T. Kaplan