Chapter 4 Testing the software

4.1 Testing R and RStudio

  1. Go to http://140.232.222.154:8787

  2. Log in using your Clark username without the @clarku.edu (e.g. my user would be jtabima) and the BIOL123 password all in capitals

  3. You should see a window like this:

RStudio panels

You should have three panes open (or probably four). The one in the left that says R version XXX is your console. Most of the code goes there, both input and output.

On the upper right you have the environment/history pane. The environment stores and shows you all the files being used by the current R session that are saved in your RAM. We will rarely use the environment in this course, but its still an important feature to know how much memory is being used, how many files are loaded and if our objects are actually being used by R. The history panel will show you all the previously used code.

Finally, the lower right has the Files, Plots, Packages, Help, and Viewer panes. These panes show exactly that: The files in the folder you are in, the plots generated by R, the R packages that will be loaded, and the help for the different R packages. The Viewer panel is a special feature that is used by some packages, we will use it later.

  1. Now, you will see the menu in the top. Click on the new file element and lets do our first R notebook.

  2. Click on new file, and then R notebook

RStudio panels

We will talk on class about R notebooks and why they are important for our course!

4.2 Testing Atom

  1. To test Atom, download the atom_test file from the moodle page

  2. Open Atom in Applications

  3. Use File -> Open and open atom_test

  4. You should see this:

RStudio panels

We will use Atom to open more of these kinds of files that have no programs associated with them! Atom can open any text file that is unformatted, as well as many scripts and programs. We won’t go so deep into these other elements (Remember, this is an Introduction course!) but we can discuss them in the lab.