Intermediate programming with R

Setting up a project

Learning Objectives

Create directories and files
Understand the difference between absolute and relative paths

Before we start using R, we will first review the basics of the Unix shell by setting up our project. Open the terminal in OS X or Linux, or Git Bash in Windows.

Our project will explore the citations and alternative metrics (altmetrics) for articles published in the PLOS family of journals between 2003 and 2010. The data set was compiled by Priem et al. 2012 (publication, code).

First create a new directory to store the project files called altmetrics and then change to that directory.

mkdir altmetrics
cd altmetrics

Repeat this process to create a subdirectory to store the data files.

mkdir data
cd data

Download the two data files using the links below. Save them to the data subdirectory.

Downloading files from the command line

When possible, it is best to download files from the command line because that makes the analysis more reproducible. Different systems have different tools installed, which is why we manually downloaded the files for this lesson. Some options include wget, curl, and rsync. As an example, here is how to perform the download using wget.

wget https://raw.githubusercontent.com/jdblischak/r-intermediate-altmetrics/gh-pages/data/counts-raw.txt.gz
wget https://raw.githubusercontent.com/jdblischak/r-intermediate-altmetrics/gh-pages/data/counts-norm.txt.gz

If wget isn’t installed on your machine, try curl:

curl -O "https://raw.githubusercontent.com/jdblischak/r-intermediate-altmetrics/gh-pages/data/counts-raw.txt.gz"
curl -O  "https://raw.githubusercontent.com/jdblischak/r-intermediate-altmetrics/gh-pages/data/counts-norm.txt.gz"

The first file, counts-raw.txt.gz, contains the raw counts for each of the articles across all the metrics. The second file, counts-norm.txt.gz, contains the counts for each of the articles across all the metrics after they have been normalized across disciplines and years.

Confirm that the files downloaded by listing the files in data.

ls

counts-norm.txt.gz counts-raw.txt.gz

Now move back up a directory to altmetrics. One option would be to specify the absolute path to this directory, e.g. ~/altmetrics/ if you created the directory in your home folder. However, an easier option is to use a relative path, which is dependent on the directory you are currently in. The shortcut to move to the directory above is two periods: ...

cd ..

Now you should be in the altmetrics directory. If you ran the above command again, you would be moved to the directory where you created altmetrics.

To create files, we’ll use the simple text editor nano. As an argument, you provide the name of an existing file to edit or the name of a new file to create. If you call nano without specifying a filename, it will prompt you for a filename when saving. Create a file to practice.

nano example-file

The commands are listed at the bottom of the screen. The ^ stands for Ctrl, thus to save type Ctrl-W and to exit type Ctrl-X.

Remove the file with rm.

rm example-file

Create a README file

It is a convention to have a file named README in a project directory to explain what it contains (both for others and your future self). Use nano to create a README file. Include the date and explain that this directory was created for a Software Carpentry workshop.