Conversion of written material to RMarkdown

[linley-sherin]

• [x] Remove symbols inherited from conversion from wiki to RMarkdown. We converted the content from our wiki to RMarkdown files, which has left a few symbols (such as '\' before punctuation symbols) scattered throughout the text. Please remove these symbols within the text.
  • [x] Update the code chunks to match the presentation. Verify that all code shown in the presentation is present in the RMarkdown version. The wiki and presentations were developed along different timelines, so certain code chunks may need to be inserted for the first time, or completely changed. This is particularly important for the exercises (or challenges) in the presentations.
  • [x] Add supporting images from the presentation and the wiki to the RMarkdown. These images include any image that is not coded in the presentations, including diagrams to explain contents or methods in greater detail.
  • [x] Verify the code. Verify that the code chunks work, and that relevant outputs (tables, figures, etc.) are being shown correctly in the book.
  • [x] Verify the writing. Reading through the text to improve the grammar and syntax is greatly appreciated, if time permits.