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Software Carpentry: Introduction to Scientific Reproducibility with R

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Project Management With RStudio

Overview

Teaching: 20 min
Exercises: 10 min
Questions

  • How can I manage my projects in R?

Objectives

  • Create self-contained projects in RStudio

Introduction

The scientific process is naturally incremental, and many projects start life as random notes, some code, then a manuscript, and eventually everything is a bit mixed together.

Most people tend to organize their projects like this:

There are many reasons why we should ALWAYS avoid this:

  1. It is really hard to tell which version of your data is the original and which is the modified;
  2. It gets really messy because it mixes files with various extensions together;
  3. It probably takes you a lot of time to actually find things, and relate the correct figures to the exact code that has been used to generate it;

A good project layout will ultimately make your life easier:

A possible solution

Fortunately, there are tools and packages which can help you manage your work effectively.

One of the most powerful and useful aspects of RStudio is its project management functionality. We’ll be using this today to create a self-contained, reproducible project.

Challenge 1: Creating a self-contained project

We’re going to create a new project in RStudio:

  1. Click the “File” menu button, then “New Project”.
  2. Click “New Directory”.
  3. Click “New Project”.
  4. Type in the name of the directory to store your project, e.g. “my_project”.
  5. If available, select the checkbox for “Create a git repository.”
  6. Click the “Create Project” button.

The simplest way to open an RStudio project once it has been created is to click through your file system to get to the directory where it was saved and double click on the .Rproj file. This will open RStudio and start your R session in the same directory as the .Rproj file. All your data, plots and scripts will now be relative to the project directory. RStudio projects have the added benefit of allowing you to open multiple projects at the same time each open to its own project directory. This allows you to keep multiple projects open without them interfering with each other.

Challenge 2: Opening an RStudio project through the file system

  1. Exit RStudio.
  2. Navigate to the directory where you created a project in Challenge 1.
  3. Double click on the .Rproj file in that directory.

Best practices for project organization

Although there is no “best” way to lay out a project, there are some general principles to adhere to that will make project management easier:

Treat data as read only

This is probably the most important goal of setting up a project. Data is typically time consuming and/or expensive to collect. Working with them interactively (e.g., in Excel) where they can be modified means you are never sure of where the data came from, or how it has been modified since collection. It is therefore a good idea to treat your data as “read-only”.

Data Cleaning

In many cases your data will be “dirty”: it will need significant preprocessing to get into a format R (or any other programming language) will find useful. This task is sometimes called “data munging”. Storing these scripts in a separate folder, and creating a second “read-only” data folder to hold the “cleaned” data sets can prevent confusion between the two sets.

Treat generated output as disposable

Anything generated by your scripts should be treated as disposable: it should all be able to be regenerated from your scripts.

There are lots of different ways to manage this output. Having an output folder with different sub-directories for each separate analysis makes it easier later. Since many analyses are exploratory and don’t end up being used in the final project, and some of the analyses get shared between projects.

Tip: Good Enough Practices for Scientific Computing

Good Enough Practices for Scientific Computing gives the following recommendations for project organization:

  1. Put each project in its own directory, which is named after the project.
  2. Put text documents associated with the project in the doc directory.
  3. Put raw data and metadata in the data directory, and files generated during cleanup and analysis in a results directory.
  4. Put source for the project’s scripts and programs in the src directory, and programs brought in from elsewhere or compiled locally in the bin directory.
  5. Name all files to reflect their content or function.

Separate function definition and application

One of the more effective ways to work with R is to start by writing the code you want to run directly in a .R script, and then running the selected lines (either using the keyboard shortcuts in RStudio or clicking the “Run” button) in the interactive R console.

When your project is in its early stages, the initial .R script file usually contains many lines of directly executed code. As it matures, reusable chunks get pulled into their own functions. It’s a good idea to separate these functions into two separate folders; one to store useful functions that you’ll reuse across analyses and projects, and one to store the analysis scripts.

Tip: avoiding duplication

You may find yourself using data or analysis scripts across several projects. Typically you want to avoid duplication to save space and avoid having to make updates to code in multiple places.

In this case, making “symbolic links”, which are essentially shortcuts to files somewhere else on a filesystem, can let you use existing code without having to move or copy it. Plus, any changes made to that code will only have to be made once.

On Linux and OS X you can use the ln -s command, and on Windows you can either create a shortcut or use the mklink command from the windows terminal.

Saving data in the data directory

Now we have a good directory structure we will now place/save the data file in the data/ directory. This is where your files for the workshop will be saved.

Challenge 3 - Workshop Data Files

Download the gapminder data from here.

  1. Download the file (CTRL + S, right mouse click -> “Save as”, or File -> “Save page as”)
  2. Make sure it’s saved under the name gapminder_data.csv
  3. Save the file in the data/ folder within your project.

We will load and inspect these data later.

Challenge 4

It is useful to get some general idea about the dataset, directly from the command line, before loading it into R. Understanding the dataset better will come in handy when making decisions on how to load it in R. Use the command-line shell to answer the following questions:

  1. What is the size of the file?
  2. How many rows of data does it contain?
  3. What kinds of values are stored in this file?

Solution to Challenge 4

By running these commands in the shell:

ls -lh data/gapminder_data.csv

-rw-rw-r-- 1 travis travis 80K Jul 27 17:20 data/gapminder_data.csv

The file size is 80K.

wc -l data/gapminder_data.csv

1705 data/gapminder_data.csv

There are 1705 lines. The data looks like:

head data/gapminder_data.csv

country,year,pop,continent,lifeExp,gdpPercap
Afghanistan,1952,8425333,Asia,28.801,779.4453145
Afghanistan,1957,9240934,Asia,30.332,820.8530296
Afghanistan,1962,10267083,Asia,31.997,853.10071
Afghanistan,1967,11537966,Asia,34.02,836.1971382
Afghanistan,1972,13079460,Asia,36.088,739.9811058
Afghanistan,1977,14880372,Asia,38.438,786.11336
Afghanistan,1982,12881816,Asia,39.854,978.0114388
Afghanistan,1987,13867957,Asia,40.822,852.3959448
Afghanistan,1992,16317921,Asia,41.674,649.3413952

Tip: command line in RStudio

The Terminal tab in the console pane provides a convenient place directly within RStudio to interact directly with the command line.

Version Control

It is important to use version control with projects. Go here for a good lesson which describes using Git with RStudio.

Key Points

  • Use RStudio to create and manage projects with consistent layout.

  • Treat raw data as read-only.

  • Treat generated output as disposable.

  • Separate function definition and application.

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