Conversion of written material to RMarkdown

[katherinehebert]

Please read through the presenter and developer protocol carefully and refer back to it regularly as you work, for help with the GitHub workflow. For RMarkdown help, refer to this cheatsheet.

• [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.

[pedrohbraga]

General issues

• [ ] Add a few quick questions or challenges to improve the flow of this workshop;
• [x] Add presenter notes.

Specific issues related to the presentation

• [x] Increment Slide 44 (Generalized Linear Models)
• [x] The summary on slide 59 is overflowing the screen. Would it be possible to use .small[] to make it smaller, or alternatively, to control the number of output lines so that there is no overflow?
• [x] Increment Slide 60, from the introduction of Challenge 1.
• [x] Slide 82 and 83, typos and use 2\. to correctly list the paragraphs.
• [x] Slide 88. Modelling count data is overflowing.
• [x] Slide 90. This question can be a little problematic because we should always look into the error distribution to make these decisions about GLM, and not the raw data distribution.
• [x] Slide 93. Poisson behind the scenes. Increment slides between Steps 2 and 3.
• [x] Slide 95. Prevent overflowing of the summary output.
• [x] Slide 99. Overdispersion. Consider incrementing the slide in half.
• [x] Add your name to the contributor list