Workshop outline

Introduction (~10 min)
- Phase: final-paper.Rmd
- Show “final paper” Rmd (has all the things: table one, multi-panel plot, etc)
- Your turn
  - Get in groups, introduce, KNIT (to HTML)! Read through Rmd + output, what does it do? Annotate, narrate.
Session: R Markdown Basics (40 min)
- Phase: first-eda.Rmd (an exploratory data analysis)
- Basic anatomy of this Rmd doc (4 key components) (~5 min)
- YAML (~5 min)
- Markdown (~5 min)
  - Headers
  - Lists
  - Links and images
  - Equations
  - Tables
- Code (~5 min)
  - Code chunks
  - Inline code
- Output (~5 min)
  - Chunk options
- How it all fits together (~5 min)
- Your turn (~10 min)
  - Change output format in YAML to distill::distill_article (note! default global knitr echo = FALSE for this output format!)
  - Change some code chunks to include=FALSE
  - I have echo = TRUE set as a global option; turn this to FALSE then set the most critical code chunks to echo = TRUE
  - (Perhaps?) add more meaningful headers and chunk names (then look at in up/down nav and how to show document outline in RStudio)
Session: Tables (45 min)
- Phase: first-progress.Rmd (a first progress report)
- Change the output format to word! (~5 min)
- Make table one with arsenal::tableby() (~20 min):
  - remember to point out knitr code chunk options to results="asis"
  - grouped by arm with details on sex and age in each group
  - ungrouped, with stats on BMI, sex, Age in each group
  - control digits
  - export table
- Consider flextable here?
- Your turn (~10 min)
Session: Data and workflows (50 min)
- Phase: first-draft.Rmd (a first draft manuscript)
Session: Graphics (45 min)
- Phase: final-paper.Rmd (a mock paper, based on mock data)