2015-12-15
Preface
What?
R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R. It combines the core syntax of markdown (an easy-to-write plain text format) with embedded R code chunks that are run so their output can be included in the final document. R Markdown documents are fully reproducible (they can be automatically regenerated whenever underlying R code or data changes).
It happened everyday
- Data preparation
- Modeling
- Generating report
- Something wrong in your data
- Repeat 1 ~ 4
Why?
- Automate
- Periodic documents
- Adapted documents
- Faster to implement
- Reproducible
- Less errors
- Diferent formats
- Html
- Presentations
Research Pipeline
Roger D. Peng, Reproducible Research: Concepts and Ideas p.10 on Coursera
how to start?
Installing R Markdown
RStudio — Install the latest version of RStudio
Other environments — Install the rmarkdown package.
Overview
- YAML Metadata: YAML document options
- Markdown: Article text
- R Code Chunk: Executible R code
Rendering Output
- RStudio: "Knit" command (Ctrl+Shift+K)
- Command line:
rmarkdown::renderfunction
rmarkdown::render("input.Rmd")
Create a HTML Document
Markdown Basics
Markdown Quick Reference
Emphasis
*italic* **bold** _italic_ __bold__
I am italic
I am bold
Headers
Setext:
Header 1 ============= Header 2 -------------
atx:
# Header 1 ## Header 2 ### Header 3
Lists
Unordered List:
* Item 1
* Item 2
+ Item 2a
- Item 2b
Ordered List:
1. Item 1
2. Item 2
3. Item 3
+ Item 3a
+ Item 3b
Unordered List:
- Item 1
- Iteivm 2
- Item 2a
- Item 2b
Ordered List:
- Item 1
- Item 2
- Item 3
- Item 3a
- Item 3b
Links & Images
A plain http address or add a link to a phrase.
Link:
[rugbcn-r-users-group](http://www.meetup.com/es/rugbcn-barcelona-r-users-group/)
Image:
Plain Code Blocks
Plain code blocks are displayed in a fixed-width font but not evaulated.
``` This text is displayed verbatim / preformatted ```Specify the language of the block is avaliable
```r x = rnorm(10) ```x = rnorm(10)
Embedding Equations
- LaTeX
Inline equation:
$equation$\(\frac{1}{n} \sum_{i=i}^{n} x_i\)Display equation:
$$equation$$\[\frac{1}{n} \sum_{i=i}^{n} x_i\]- Useful Resources
- Daum Equation Editor: Chrome Plugin
- Online LaTeX Equation Editor
Tables
First Header | Second Header ------------- | ------------- Content Cell | Content Cell Content Cell | Content Cell
| First Header | Second Header |
|---|---|
| Content Cell | Content Cell |
| Content Cell | Content Cell |
Text Color
You can color content using base color classes red, blue, green, yellow, and gray (or variations of them e.g. red2, red3, blue2, blue3, etc.).
<div class="red2"> This text is red </div>
- red red2 red3
- blue blue2 blue3
- green green2 green3
- yellow yellow2 yellow3
- gray gray2 gray3
R Code Chunks
Overview
R code will be evaluated and printed
```{r}
summary(cars$dist)
```
summary(cars$dist)
## Min. 1st Qu. Median Mean 3rd Qu. Max. ## 2.00 26.00 36.00 42.98 56.00 120.00
Named R code chunk.
```{r plot}
summary(cars)
plot(cars)
```
- Easy Navigation in RStudio
Basic Chunk Options
echo(TRUE): whether to include R source code in the output fileeval(TRUE): whether to evaluate the code chunkmessage(TRUE): whether to preserve messages emitted by message()include(TRUE): if include=FALSE, nothing will be written into the output document, but the code is still evaluated and plot files are generatedwarning(TRUE): whether to preserve warnings in the output
Set global chunk options:
knitr::opts_chunk$set()
Plots
dev('png'): figure format(png, jpeg, tiff, svg, …)fig.path('figure/'): figure pathfig.width(7): figure widthfig.height(7): figure heightdpi(72): DPI (dots per inch)
```{r dev='svg', fig.path='myplot',fig.width=5, fig.height=5}
plot(iris)
```
Inline R Code
I counted 'r 1+1' red trucks on the highway.
I counted 2 red trucks on the highway.
Other Cool Stuff
ggvis code
library(knitr)
library(ggvis)
mtcars %>%
ggvis(x = ~wt, y = ~mpg) %>%
layer_smooths(se=TRUE, opacity := 0.5, opacity.hover := 0.75) %>%
layer_points(fill = ~factor(cyl), size := 50, size.hover := 200) %>%
set_options(hover_duration = 250)
DataTable code
library(DT) datatable(mtcars,options=list(pageLength=3))