The command line

When using a computer we are mostly used to using a graphical user interface. This is made up of icons and windows and is mainly interacted with using a mouse. This is often referred to as a point and click approach.

One of the downsides of a point and click approach in the scope of reproducible research is that giving instructions is often difficult and they can be ambiguous.

Another approach is to use the command line. This is a small window in to which we type commands and lets us give precise (reproducible) commands to the computer.

Identify and open your command line interface.

First, it is important to note that this will now differ (but not substantially) depending on whether or not you're on a Windows machine:

  • Windows: we will choose to use Anaconda Prompt (which was installed on your machine when you installed Anaconda).
  • nix (another way to describe Mac OS and/or Linux machines): we will use the system terminal.

Finding your current location

Let us first find out which directory (folder) we are currently in:



This stands for "current directory".



This stands for "present working directory"

  1. Type this command in
  2. Press Enter

It should list where you are currently located in your command line interface.

Seeing what is in your current location

To view the contents of the current directory:



This stands for "directory".



This stands for "list"

  1. Type this command in.
  2. Press Enter

You should see a list of the various files and directory in your current directory.

Open your current directory in a graphical user interface and compare.

Creating a directory

To create a directory:

mkdir <directory_name>

Experiment with creating a directory for this workshop:

mkdir rsd-workshop

If your directory structure looked like this:

|--- home/
     |--- research
     |--- photos

It will now look something like:

|--- home/
     |--- research
     |--- photos
     |--- rsd-workshop

Moving to another location

On both Windows and nix if you want to enter a directory that is in your current diractory type:

cd <directory>

To move in to the rsd-workshop directory we created previously:

cd rsd-workshop

As an exercise, move in to that directory and create two further directories:

|--- rsd-workshop
     |--- tex
     |--- src

These two directories stand for LaTeX (tex) and source code (src): we will use these later on in the course.

If you now wanted to go back to the "parent" directory:

cd ..

Where .. is short hand for a previous directory.

Experiment with these, in combination with the command to find your current location as well as the command to list the contents of your directory.

Copying files

To copy a file:


copy <file> <new_file_directory_and_name>


cp <file> <new_file_directory_and_name>

Experiment with copying any file.

Moving/renaming files

To move a file:


move <file> <new_file_directory_and_name>


mv <file> <new_file_directory_and_name>

Experiment with moving any file.

Note that if you want to rename a file you can do this by passing the new name in the same directory.

WARNING When using the command line interface you will not be prompted for confirmation if move/mv were to overwrite another file. Be careful.

Deleting files

To delete a file:


del <file>


rm <file>

Copying and removing directories

To copy a directory:


xcopy <dir> <target>


cp -r <dir> <target>

To remove a directory:


rmdir /s <dir>


rm -r <dir>

Tip: Tab completion

Most command line tools allow for command tab completion. This means you can start typing the first few letters of a file or a directory and press tab which will complete the rest. This is a very useful tool to ensure you don't make mistakes when typing.

You can also use the up/down arrow keys to cycle through your previous commands. This also helps avoid repetitive typing.