YAML Header !
Optional section of render (e.g. pandoc)
options written as key:value pairs (YAML).
At start of file
Between lines of - - -
Text!
Narration formatted with markdown, mixed with:
Code Chunks!
Chunks of embedded code. Each chunk:
Begins with ```{r}
ends with ```
R Markdown will run the code and append the results to the doc.
It will use the location of the .Rmd file as the working directory
Interactive!
Documents
Turn your report into an interactive Shiny !
document in 4 steps
1. Add runtime: shiny to the YAML header.
2. Call Shiny input functions to embed input objects.
3. Call Shiny render functions to embed reactive output.
4. Render with rmarkdown::run or click Run Document in
RStudio IDE
---
output: html_document
runtime: shiny
---
```{r, echo = FALSE}
numericInput("n",
"How many cars?", 5)
renderTable({
head(cars, input$n)
})
```
Embed a complete app into your document with
shiny::shinyAppDir()
NOTE: Your report will rendered as a Shiny app, which means
you must choose an html output format, like html_document,
and serve it with an active R Session.
RStudio® is a trademark of RStudio, Inc. • CC BY SA RStudio • info@rstudio.com • 844-448-1212 • rstudio.com • Learn more at rmarkdown.rstudio.com • rmarkdown 1.6 • Updated: 2016-02
R Markdown : : CHEAT SHEET
Open a new .Rmd file at File ▶ New File ▶ !
R Markdown. Use the wizard that opens to pre-
populate the file with a template
Write document by editing template
Knit document to create report; use knit button or
render() to knit
Preview Output in IDE window
Publish (optional) to web server
Examine build log in R Markdown console
Use output file that is saved along side .Rmd
1
2
3
4
5
6
7
modify
chunk
options
run all
previous
chunks
run
current
chunk
insert
code
chunk
go to
code
chunk
run code
chunk(s)
1
2
3
4
5
6
7
publish
show
outline
synch publish
button to
accounts at
rpubs.com,
shinyapps.io
RStudio !
Connect
Reload document
Find in document
File path to output document
set
preview
location
What is R Markdown?
Insert with `r <code>`. Results appear as text without code.
One or more lines surrounded with ```{r} and ```. Place chunk
options within curly braces, aer r. Insert with
Options not listed above: R.options, aniopts, autodep, background, cache.comments, cache.lazy, cache.rebuild, cache.vars, dev, dev.args, dpi,
engine.opts, engine.path, fig.asp, fig.env, fig.ext, fig.keep, fig.lp, fig.path, fig.pos, fig.process, fig.retina, fig.scap, fig.show, fig.showtext, fig.subcap, interval,
out.extra, out.height, out.width, prompt, purl, ref.label, render, size, split, tidy.opts
Embed code with knitr syntax
Built with `r getRversion()` Built with 3.2.3
INLINE CODE CODE CHUNKS
```{r echo=TRUE}
getRversion()
```
Set with knitr::opts_chunk$set(), e.g.
```{r include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Use rmarkdown::render() to render/knit at cmd line. Important args:
Workflow
input - file to render
output_format
render
Parameters
Parameterize your documents to reuse with
different inputs (e.g., data, values, etc.)
---
params:
n: 100
d: !r Sys.Date()
---
Today’s date
is `r params$d`
1. Add parameters · Create and set
parameters in the header as sub-
values of params
2. Call parameters · Call parameter
values in code as params$<name>
3. Set parameters · Set values wth
Knit with parameters or the params
argument of render():
render("doc.Rmd", params = list(n = 1,
d = as.Date("2015-01-01"))
output_options - !
List of render !
options (as in YAML)
output_file
output_dir
params - list of
params to use
envir - environment !
to evaluate code
chunks in
encoding - of input
file
.rmd Structure
.Rmd files · An R Markdown
(.Rmd) file is a record of your
research. It contains the code that a
scientist needs to reproduce your work
along with the narration that a reader
needs to understand your work.
Reproducible Research · At the click of a
button, or the type of a command, you
can rerun the code in an R Markdown file
to reproduce your work and export the
results as a finished report.
Dynamic Documents · You can choose
to export the finished report in a variety
of formats, including html, pdf, MS
Word, or RTF documents; html or pdf
based slides, Notebooks, and more.
cache - cache results for future knits (default =
FALSE)
cache.path - directory to save cached results in
(default = "cache/")
child - file(s) to knit and then include (default =
NULL)
collapse - collapse all output into single block
(default = FALSE)
comment - prefix for each line of results (default = '##')
dependson - chunk dependencies for caching
(default = NULL)
echo - Display code in output document (default =
TRUE)
engine - code language used in chunk (default =
'R')
error - Display error messages in doc (TRUE) or
stop render when errors occur (FALSE) (default =
FALSE)
eval - Run code in chunk (default = TRUE)
message - display code messages in !
document (default = TRUE)
results (default = 'markup')!
'asis' - passthrough results!
'hide' - do not display results!
'hold' - put all results below all code
tidy - tidy code for display (default = FALSE)
warning - display code warnings in document
(default = TRUE)
fig.align - 'le', 'right', or 'center' (default =
'default')
fig.cap - figure caption as character string (default
= NULL)
fig.height, fig.width - Dimensions of plots in
inches
highlight - highlight source code (default = TRUE)
include - Include chunk in doc aer running
(default = TRUE)