When R is installed on Windows, it automatically writes the version being installed into the registry as the current version of R. And this will also be the version that RStudio uses. You can choose the version of R that you want to use by holding the Ctrl key during the launch of RStudio.

On Linux, you can use a command with R to see which version of R, RStudio uses. If you want RStudio to use another version of R (maybe you want to use an older version or because you had to install R in your Documents folder because of missing admin rights) you can overwrite the settings with the following export: RSTUDIO_WHICH_R=/usr/local/bin/R. This line has to be added to your ~/.profile file.

One of the most important menus in the source editor is what you find when you click on the magic stick. If you forgot what exact arguments the selected function needs, just hit the Tab button and you will see a list of available arguments with a description, if available:

You can then scroll through the list and select the argument you want to use. This is especially useful when you have functions that can be called with a lot of different arguments; it would be very time-consuming to open the package documentation for every function call.

You can also find direct links to the help or function definition, which shows you where the current function is defined.

After that, you can find the functions, Extract Function and Extract Variable. These functions help you in creating functions. When you click on Extract Function or use the shortcut, Ctrl + Alt + X, RStudio creates a function from your selection and inserts it in the source code.

After executing the command, your code will look like this:

The next button is the Compile Notebook button. This helps you compile your currently opened source file into a notebook with the format, HTML, PDF, or MS Word:

The compiled report will then open in a new window.

This is the code we used for the preceding example; if you want to reproduce it, type the following code:

x <- 10 + (1:20)/10
y <- x^2 + rnorm(length(x))
plot(x, y)

On the extreme right of the source code menu, you will find the buttons needed to run the code. These buttons are:

If you want to execute a single line, or rather, if you want to run the current line where your cursor is, you can use the Run button or the shortcut, Ctrl + Enter. After the execution, the cursor will jump to the next line in the source file.

If you want to execute several lines of code, you can select the lines and press the Run button.

RStudio supports both automatic and user-defined folding for regions of code. This is a very handy feature, especially when you work with functions and larger scripts. It lets you hide and show blocks to make the code easier to navigate.

RStudio automatically folds the following regions in the source editor:

The output looks like this:

To define a code section on your own and to make it easier to navigate in larger source files, you can use three methods:

So, the line can start with any number of pound signs (#), but is has to end with at least four or more -, =, or # characters. RStudio then automatically defines the following code as the section. To navigate between code sections, you can use the Jump To menu at the bottom of the editor.

The menu at the bottom, on the right-hand side lets you choose the file format of the currently opened source file. Normally, RStudio chooses the right format automatically. If you change it manually, the code completion and the syntax highlighting will adapt to the new settings.

RStudio offers visual debuggers to help you understand code and find bugs and problems. Therefore, it uses the debugging functions of R but integrates them seamlessly into the RStudio user interface. You can find these tools in the Debug tab of the menu, or by pressing Alt + D:

You can set breakpoints right in the source editor by clicking on the number of the line, or by pressing Shift + F9:

The debugger output can help you find bugs in your code in a better way. In this example, the debugger output is debug.R:10. This means that we should look into the tenth line of the source file:

The History pane shows all the commands you entered in the console, and it also lets you send the selected command back from the history directly to the console with the To Console button or back to the opened source code file with the To Source button. You can also delete commands from the history by selecting them and pressing the paper icon with the red close sign above the history. Or you can clear the whole history by clicking the broom icon:

This pane is one of RStudio's biggest enhancements in comparison to the normal R console. The Files pane shows you all the files in the current working directory. It includes information about the file size and when the data was last modified. Clicking on an item will open it with the appropriate application.

The Plot pane in RStudio handles all of your graphics output. This makes working with graphical output much easier than in the regular R console, as it opens a new window for every graphic.

Furthermore, the Plot pane gives some more tools. These tools include the option to zoom into a graphic. This will open a new window with a bigger version of the current plot. This plot will then arrange itself to the current window size.

You can also export the current plotted graphic with the Export button. The Export menu has three options:

When you choose the Save as Image... option, RStudio will open a popup that lets you define the export image format, the directory, and the file name, as well as the width and height.

The Save as PDF... option will create a single page PDF document with your plot. Based on the width and height settings, it will be either in the landscape or portrait format.

RStudio also offers the option to publish your plots on RPubs. This is a free and very simple web service from the makers of RStudio to upload R graphics and R Markdown documents, which will then be publicly available on the web and you can share the link. We will talk about the possibilities of R markdown in a later chapter.

When you click on the Publish button, a window will open and guide you through the process.

After clicking on Publish, a new browser window will open and show your uploaded report:

The Package pane helps you install, update, or load packages. It gives you an overview about all installed packages, a short description, and the installed version.

If you tick a checkbox in front of a package, it will automatically be loaded, and if you remove the tick again, RStudio will automatically detach it from the environment. So, it basically unloads it again.

The Packages pane also provides a handy tool to install new packages with the help of a graphical interface. We just have to click on the Install button and we will be guided through the installation process. The Install packages dialog also allows us to install packages that we have saved locally on our computer:

You can see next what RStudio does in the R console:

A big advantage of the R language is that every package on CRAN will come with package documentation. You can find these files on the CRAN website but RStudio bundles them in a handy Help pane. You can search the help through the search bar, or you can just press F1:

The Viewer pane in RStudio can be used to view local web content, such as web graphics created with packages such as rCharts, googleVis, and others. It can also show local web applications created with Shiny or OpenCPU.

Now, we will click on Save as Web Page... in the Export menu.

The export menu of the viewer pane offers, basically, the same option to export your work but replaces the Save as image option with Save as Web Page. This creates a standalone web page.