The midterm will cover the material from the Course Notes from Section 3.2 - Section 4.9; this is the material since the previous midterm. That said, the material on this midterm does build on the previous material, so you should have the relevant competencies from the first part of the semester.
My general advice for studying is to (i) study the notes that you have take in class, (ii) study the Course Notes, and (iii) for topics where you still have any doubts, follow the cross-references from the Course Notes to the textbook for an additional reference.
R questions are fair game for the exam though the exam will focus relatively more on the more recent topics in statistics and on linear regression. This means that you should expect relatively more questions from the statistics/regression portion of the class as well as relatively more difficult questions from those topics.
Finally, I have provided some extra questions here. My recommendation is to study some before you try to answer these questions. We will cover (some of) these questions in class on Monday.