rmd4medicine
Preface
Warmup
Introduction
0.1
First look
0.2
First report
0.3
First draft
I R Markdown Basics
Introduction
0.4
Formative assessments
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
7.10
The arsenal package
7.11
The tableone package
7.12
HTML widgets (DT)
7.13
Tables for EDA
III Data + Workflows
Introduction
7.14
GitHub
7.15
Collaborating
7.16
Datapasta
7.17
Reprex
IV Graphics
Introduction
8
Controlling size
9
Controlling resolution
10
Adding captions & references
11
Exporting all graphics
12
Multi-panel
13
Uplevel
Appendix
Published with bookdown
R Markdown for Medicine
Chapter 6
Use chunk options
play with include, echo (change the package loading chunk to include = TRUE)
use setup chunks to change all chunk options (fig.path!)
6.1
How it all works