Let’s start by learning about RStudio, the Integrated Development Environment (IDE).
Rstudio should already be installing on the machines you are using and can be found through the Start Menu. To install on your own machine you need to install R and then install RStudio.
The RStudio IDE open source product is free under the Affero General Public License (AGPL) v3. RStudio IDE is also available with a commercial license and priority email support from RStudio, Inc.
We will use RStudio IDE to write code, navigate the files found on our computer, inspect the variables we are going to create, and visualize the plots we will generate. RStudio can also be used for other things (e.g. version control, developing packages, writing Shiny apps) that we will not cover during the workshop.
RStudio is divided into 4 “Panes”: the editor for your scripts and documents (top-left, in the default layout), the R console (bottom-left), your environment/history (top-right), and your files/plots/packages/help/viewer (bottom-right). The placement of these panes and their content can be customized (see menu, RStudio -> Preferences -> Pane Layout). One of the advantages of using RStudio is that all the information you need to write code is available in a single window. Additionally, with many shortcuts, autocompletion, and highlighting for the major file types you use while developing in R, RStudio will make typing easier and less error-prone.
The basis of programming is that we write down instructions for the computer to follow, and then we tell the computer to follow those instructions. We write, or code, instructions in R because it is a common language that both the computer and we can understand. We call the instructions commands and we tell the computer to follow the instructions by executing (also called running) those commands.
There are two main ways of interacting with R: using the console or by using script files (plain text files that contain your code). We want our code and workflow to be reproducible. In other words, we want to write code in a way that anyone can easily replicate, such they can obtain the same results from our code on their computer.
The console pane (in RStudio, the bottom left panel) is the place where R is
waiting for you to tell it what to do, and where it will show the results of a
command that has been executed. You can type commands directly into the console
and press Enter to execute those commands, but they will be forgotten when you
close the session. It is better to enter the commands in the script editor, and
save the script. This way, you have a complete record of what you did, you can
easily show others how you did it and you can do it again later on if needed.
RStudio allows you to execute commands directly from the script editor by using
the `Ctrl` + `Enter` shortcut. The command on the current
line in the script or all of the commands in the currently selected text will be
sent to the console and executed when you press `Ctrl` +
`Enter`.
At some point in your analysis you may want to check the content of variable or the structure of an object, without necessarily keep a record of it in your script. You can type these commands and execute them directly in the console. RStudio provides the `Ctrl` + `1` and `Ctrl` + `2` shortcuts allow you to jump between the script and the console windows.
If R is ready to accept commands, the R console shows a > prompt. If it
receives a command (by typing, copy-pasting or sent from the script editor using
`Ctrl` + `Enter`), R will try to execute it, and when
ready, show the results and come back with a new >-prompt to wait for new
commands.
If R is still waiting for you to enter more data because it isn’t complete yet,
the console will show a + prompt. It means that you haven’t finished entering
a complete command. This is because you have not ‘closed’ a parenthesis or
quotation, i.e. you don’t have the same number of left-parentheses as
right-parentheses, or the same number of opening and closing quotation marks. If
you’re in RStudio and this happens, click inside the console window and press
Esc; this will cancel the incomplete command and return you to the > prompt.