To participate in either of these workshops, you will need a laptop with a user account that has software installation privileges to install the software described below. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select “Run as administrator” instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
In addition, you will need an up-to-date web browser.
To make best use of the workshop time please have the necessary programs and R packages installed prior to the start of the workshop. If you have any questions you can email the workshop instructor at the email listed on the main page of this website.
Click the arrows to expand the section to show installation and setup instructions for each program.
R (Both workshops)
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. The project website is https://www.r-project.org.
Windows (Video Tutorial). Install R by downloading and running this .exe file from CRAN(https://cran.r-project.org/index.html).
macOS (Video Tutorial). Install R by downloading and running this .pkg file from CRAN.
Linux You can download the binary files for your distribution from CRAN(https://cran.r-project.org/index.html). Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R).
Installation notes:
R Studio (Both workshops)
To interact with R, we use the Integrated Development Environment (IDE) called RStudio (https://www.rstudio.com). The R Studio IDE is installed after you have installed R.
Setting preferences in R Studio to retain sanity while debugging
This will ensure that when you restart R you do not “carry forward” objects such as data sets that you were working on in a prior assignment.
You should make a habit to completely shut down R studio when you are done working. Your open tabs will be saved, but your environment will be cleared. This is a good thing.
R Packages (Both workshops)
R is considered an Open Source software program. That means many (thousands) of people contribute to the software. They do this by writing commands (called functions) to make a particular analysis easier, or to make a graphic prettier.
When you download R, you get access to a lot of functions that we will use. However these other user-written packages add so much good stuff that it really is the backbone of the customizability and functionality that makes R so powerful of a language.
You only have to install packages once per R installation.
To get started type in the console the following command to install the rmarkdown package.
install.packages("rmarkdown")When the console returns to showing a > (and the stop sign in the top right corner of the Console window goes away), R is done doing what you asked it to do and ready for you to give it another command. You should get a message that looks similar to the message below.
The downloaded binary packages are in
C:\Users\Robin\AppData\Local\Temp\Rtmpi8NAym\downloaded_packagesSome packages use functions that live in other packages. These are called dependencies and will be automatically installed when you tell R to install a new package. 99% of the time you will not have to install them manually on your own.
Now that you’re a package installing pro, go ahead and install the following packages that pertain to your selected workshop.
📖 Workshop 12: Reproducible Reports using R Markdown
🌎 Workshop 13: Website building
R is case sensitive. If you see a message such as the one below, check for a typo.
Warning in install.packages :
package ‘ggplot’ is not available (for R version 3.5.1)The correct package name is ggplot2, not ggplot.
LaTeX (Reproducible Research workshop only)
To create a PDF directly from your source code you will have to install a lightweight version of \(LaTeX\) (a document processing program). This allows you to make professional looking reports.
Run the following code lines one at a time, waiting for the first one to finish before starting the next. This process can take up to 10 minutes.
install.packages("tinytex")
tinytex::install_tinytex()If at any time it asks you to update or install any other packages, say yes to all of them.
Git & GitHub (Website building workshop only)
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on https://github.com.
Instructions to install Git can be found at https://www.atlassian.com/git/tutorials/install-git
To share your code and publish your website you will also need a GitHub account at https://github.com. Basic GitHub accounts are free. We encourage you to create a GitHub account prior to the workshop if you don’t have one already. Please consider what personal information you’d like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
Note: This workshop is not an lesson on git. We will use git to do a few things and we will interact with GitHub, but we will not go into details about version control.
Hugo (Website building workshop only)
Hugo (https://gohugo.io) is a static site generator, that is used by the R package blogdown to create dynamic websites. blogdown has a helper function to do this installation for us.
blogdown::install_hugo()[OPTIONAL] Create a Netlify account (Website building workshop only)
The blog-aware website that we will be building needs to be hosted somewhere other than GitHub. For beginners, it is recommended to use Netlify for the following reasons
You can sign up and make an account at https://www.netlify.com/
More info/options about deploying/hosting blogdown websites: https://bookdown.org/yihui/blogdown/deployment.html