rmd4medicine
Preface
Prework
Workshop outline
Uplevels
Warmup
Introduction
0.1
First look
0.2
First report
0.3
First draft
I R Markdown Basics
Introduction
1
Basic Anatomy
2
Using R Markdown in RStudio
3
Whole document metadata
3.1
All about YAML
3.2
Changing output formats
3.3
Adding output options
4
Add text with Markdown
4.1
Headers
4.2
Text & Images
5
Add code
6
Use chunk options
6.1
How it all works
7
Uplevel
7.1
Adding output formats
7.2
Adding multiple YAML keys
7.3
Live preview without reknitting
7.4
Beef up your YAML
7.5
Knit with parameters
7.6
Knit from the command line
7.7
Extend your R Markdown
7.8
R Markdown templates
7.9
GitHub
II Tables
Introduction
8
Janitor tabyls
9
Make a “Table 1”
9.1
The arsenal package
9.2
The tableone package
10
Markdown tables
11
kable tables
12
flextable
13
Uplevel
13.1
HTML widgets (DT)
13.2
Tables for EDA
III Data + Workflows
Introduction
14
Projects and files
15
Importing data
16
Using data
17
Dealing with other people’s data
18
R Markdown collections
19
Uplevel
19.1
GitHub
19.2
Collaborating
19.3
Datapasta
19.4
Reprex
IV Graphics
Introduction
20
Controlling size
21
Controlling resolution
22
Adding captions & references
23
Exporting all graphics
24
Multi-panel
25
Uplevel
Appendix
A
Colophon
B
License
Published with bookdown
R Markdown for Medicine
Chapter 14
Projects and files
What goes where