Before you arrive

Image: Data Visualization and R Bookshelf by Richard Layton.

To get the most out of the workshop, you should have the essential software installed and running on your computer several days before the workshop to give you time to contact us with questions if anything goes amiss.

If you are trying R for the first time, it is vital that you attempt to set up your computer with the necessary software in advance or it will be difficult to keep up.

As you work your way through this pre-workshop assignment, you will encounter R code chunks to type. Clicking the Copy to Clipboard icon in the top right corner of the code chunk copies the code to your clipboard, saving some typing time. For example:

# sample code chunk
x <- 10

Already use R?

If you are already an R and RStudio integrated development environment (IDE) user, this is a great time to check for updates.

Updating RStudio

  • RStudio menu Help > Check for Updates will tell you if you are current or not.
  • To update, close RStudio on your machine, download the new version from Posit).

Update your packages

How to upgrade all out-of-date packages in What They Forgot to Teach You About R by Jennifer Bryan and Jim Hester.

Updating R

The easiest way to update R is to simply download the newest version. RStudio will automatically use the latest you’ve installed.

Alternatively, Windows users can use the installr package:

  • Install the installr package
  • If open, close R and RStudio
  • Navigate to your most recent Rgui.exe file located in your Programs directory, e.g., C:\Program Files\R\R-4.3.3\bin\x64\Rgui.exe
  • Right-click on Rgui.exe and run as administrator
  • In the R GUI window that appears, run the commands
    # Windows users only
    library("installr")
    updateR()

Updating your R library

How to transfer your library when updating R also by Bryan and Hester. Requires the fs package.

New to R?

This section is for anyone who has not yet installed R or RStudio.

The first steps are to install R and RStudio. Both R and RStudio are free. Windows users may have to login as an Administrator before installing the software.

Once the installation is complete, you can take a 2-minute tour of the RStudio interface.

The same video includes a longer (7 minute) tour of the four quadrants (panes) in RStudio if you are interested.

Start the setup

Once you have R and RStudio up and running on your system, we have a short set of setup instructions to help prepare you for the workshop R tutorials.

We start by creating an RStudio Project file and directory. You can recognize an R project file by its .Rproj suffix.

(Optional) If you prefer your instructions with commentary,

  • Start with a Project (02:34–04:50) by R Ladies Sydney (Richmond, 2018)
  • If you follow the instructions on the video, then when finished, use File > Close to close any open projects you created. Then create a new project for the Institute as follows.

Create an RStudio Project for the MIDFIELD Institute:

  • RStudio, File > New Project… > New Directory > New Project
  • Or, click the New Project button in the Console ribbon,

rstudio new project button

In the dialog box that appears,

  • Type the workshop name as the directory name, for example, midfield-institute-2024
  • Use the browse button to select a location on your computer to create the project folder
  • Click the Create Project button

You now have the RStudio Project for the MIDFIELD Institute up and running. If you happen to close the project, simply click on the midfield-institute-2024.Rproj file to re-open your work.

Tip

Using RStudio projects. For more information about RStudio projects in general, see the RStudio Project support page.

Add some folders

If your Institute Project is still open, the “Files” pane should show one item in your project directory. If not, click on the midfield-institute-2024.Rproj file to re-open your work.

Add three folders to the main project folder. To create folders:

  • use your usual method of creating new folders on your machine
  • or you can use the New Folder button in the Files pane

We use the folders as follows:

  • data data files (for data not included in an R package)
  • scripts R scripts that operate on data to produce results
  • results publication-ready graphs and tabulated results

For a video guide,

Tip

Organizing a computational project. If you are interested in a comprehensive set of “good enough practices” for scientific computing, we highly recommend (Wilson et al., 2017). The sections on data management, software, collaboration, and project organization are particularly useful to consider at the beginning of a project.

Install CRAN packages

The fundamental unit of shareable code in R is the package. For the R novice, an R package is like an “app” for R—a collection of functions, data, and documentation for doing work in R that is easily shared with others (Wickham, 2014).

Most packages are obtained from the CRAN website (The Comprehensive R Archive Network, 2018-04-22). To install a CRAN package using RStudio:

  • Launch RStudio

The RStudio interface has several panes. We want the Files/Plots/Packages pane.

  • Select the Packages tab

rstudio packages pane

Next,

  • Click Install on the ribbon
  • In the dialog box, type the name of the package. For our first package, type data.table to install the data.table package (Dowle & Srinivasan, 2021)
  • Check the Install dependencies box
  • Click the Install button

During the installation, Windows users might get a warning message about Rtools, something like:

WARNING: Rtools is required to build R packages but is not currently installed. Please download etc.

Rtools is needed for packages with C/C++/FORTRAN code from source—which does not apply to us. You may ignore the warning and carry on.

In the RStudio Console, you should see a message like this one,

package 'data.table' successfully unpacked and MD5 sums checked

If successful, the package will appear in the Packages pane, e.g.,

rstudio packages pane

Repeat the process for the following packages:

checkmate
ggplot2
wrapr
curl

Alternatively, you can install them all at once by typing in the Console:

packages_we_use <- c("data.table", "ggplot2", "checkmate", "wrapr", "curl")
install.packages(packages_we_use)

Install midfieldr

Install with:

# type in the RStudio Console 
install.packages("midfieldr")
Tip

If you get an error message like the one below, it means that the packages in the dependencies list have not been installed.

The remedy is to install any packages listed in the error message and then install midfieldr again.

Once midfieldr is successfully installed, you can confirm the installation by running the following lines to bring up the package help page in the Help window.

# type in the RStudio Console 
library("midfieldr")
?midfieldr

If the installation is successful, the code chunk above should produce a view of the help page as shown here.

midfiedr help page pane

Install midfielddata

Because of its size, the data package is stored in a drat repository instead of CRAN. Installation takes time; please be patient and wait for the Console prompt “>” to reappear.

Type (or copy and paste) the following lines in the RStudio Console.

# type in the RStudio Console  
install.packages("midfielddata", 
                 repos = "https://MIDFIELDR.github.io/drat/", 
                 type = "source")
# be patient

Once the Console prompt “>” reappears, you can confirm a successful installation by viewing the package help page. In the Console, run:

# type in the RStudio Console  
library("midfielddata")
?midfielddata

If the installation is successful, the code chunk above should produce a view of the help page as shown here.

midfiedldata help page pane

Finish the setup

As a final task, save your open files and close RStudio.

If you get a prompt about saving your workspace image, the answer is No. 

You can turn this prompt off by reopening RStudio and use the pulldown menu:

  • Tools > Global Options…
  • In the dialog box, Save workspace to .RData on exit: Select “Never”

Homework

If you are new to R (or new to the ggplot2 or data.table packages), we recommend you complete the three pre-workshop tutorials for an introduction to R including manipulating data and creating charts.

Completing these tutorials before attending the Institute will make your time with us that much more productive.

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References

Dowle, M., & Srinivasan, A. (2021). Data.table: Extension of ‘data.frame‘. https://CRAN.R-project.org/package=data.table
Richmond, J. (2018). Basic Basics Lesson 1: An opinionated tour of RStudio. https://youtu.be/kfcX5DEMAp4
The Comprehensive R Archive Network. (2018-04-22). https://cran.r-project.org/
Wickham, H. (2014). Advanced R. Taylor & Francis.
Wilson, G., Bryan, J., Cranston, K., Kitzes, J., Nederbragt, L., & Teal, T. K. (2017). Good enough practices in scientific computing. PLoS Comput Biol, 13(6). https://doi.org/10.1371/journal.pcbi.1005510