If you are participating in this workshop series, we are so excited to help you acquire new or hone existing technical and interpersonal skills in the realm of synthesis science! To ensure that you get the most out of this workshop series, we recommend that you take the following steps before the first week.
If your organization has a dedicated IT team that has sole power to install software on your computer, you will need to contact them before the workshop to do the installation bits of the preparation steps we outline below.
1 Install R
“R” is the coding language we’ll use throughout the workshop series. Follow the relevant instructions for your operating system here: r-project.org
2 Install Positron
Positron is the integrated development environment (IDE) we’ll use to write code to support the synthesis work you all will be accomplishing during (and after!) the workshop series. Follow the relevant instructions for your operating system here: positron.posit.co
You may already be familiar and comfortable with RStudio (we are too!). Positron is the next generation IDE developed by the same folks who made RStudio, and it has better integration for Quarto, as well as Python and other coding languages. Because this is the direction R for data science is heading, we figured it is worth making the leap for this workshop.
That said, nearly everything in this workshop will work equally well in RStudio!
3 Install Necessary R Packages
So-called “base R” contains some useful, fundamental operations from the moment you install it. However, there are a variety of external packages that contain more specific tools that can also be extremely useful to you. Most of these we will provide installation instructions for in the lessons that use them, but there are a few that it will benefit you to install now. In the “Console” pane of Positron, choose an option:
This is the built-in function to install packages in R. This is what you will most likely see “in the wild” and works well.
install.packages("usethis")
install.packages("gitcreds")Do not use install.packages() in a script, though, since it will re-install the package every time you run it - not good practice for reproducibility or performance.
The librarian package is an improved way to install and manage R packages. It will test to see if the package is already installed, and if not, it will install it for you, and then load the package. This takes the place of install.packages("<packagename>"); library(packagename).
install.packages("librarian")
librarian::shelf(usethis, gitcreds)- 1
-
The
shelffunction will automatically install the packages that you don’t already have and then load all the identified libraries
Because librarian::shelf() checks to see if a package has already been installed, it is safe to include in a script!
4 Install Quarto
Quarto is the software we’ll use to create computational notebook files. You may have previously worked with other types of notebook files (e.g., R Markdown files, Jupyter notebooks), but Quarto offers a number of advantages that make using it worthwhile. Follow the relevant instructions for your operating system here: quarto.org/docs/get-started
5 Install Git
Git is the name of the software that we can use to do “version control” for the code files we’ll develop. We’ll get into this more later but for now, it is enough to know this is analogous to Microsoft Word’s “track changes” feature but with some extra features that are great for code files.
Installing Git differs slightly depending on your computer’s operating system so check out the tabs below for the right option for you. These instructions are modified from Jennifer Bryan’s excellent “Happy Git and GitHub for the useR” ebook.
Run the following command line code.
xcode-select --installFor more detailed instructions, see here.
Install Git for Windows (a.k.a. “Git Bash”). When asked about “Adjusting your PATH environment”, select “Git from the command line and also from 3rd-party software”.
For more detailed instructions, see here.
Install Git via your distro’s package manager (in the Terminal).
If you use Ubuntu or Debian Linux that code is as follows:
sudo apt-get install gitIf instead you use Fedora or RedHat Linux the code is instead:
sudo yum install gitFor more detailed instructions, see here.
Check that the installation was successful by running the following command line code in the terminal (you may need to restart your computer first):
git --versionIf successful, you should see something like git version 2.40.1.windows.1.
6 Make a GitHub Account
GitHub is a nice web interface for collaborating with other people who use Git. Later in the lifecycle of a project, GitHub is also useful for sharing and publicizing your code beyond of your team.
Please make a profile at github.com.
- If you have a .edu address, we recommend using that, as an educational account gives free access to certain privileges (you can always link an edu account later)
- Consider adding a profile photo. Doing so will make you stand out relative to the default ‘space invader’ image your account will start with.