Rmarkdown cheatsheet-2.0

render()
RStudio Pro FeaturesWorkflow
Debug ModeEmbed code with knitr syntax
learn more at rmarkdown.rstudio.com
Rmd
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.
Use rmarkdown::render()
to render/knit at cmd line.
Important args:
input - file to render
output_format
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
R Markdown Cheat Sheet
RStudio® is a trademark of RStudio, Inc. • CC BY RStudio • info@rstudio.com • 844-448-1212 • rstudio.com Learn more at rmarkdown.rstudio.com • RStudio IDE 0.99.879 • Updated: 02/16More cheat sheets at http://www.rstudio.com/resources/cheatsheets/
Debug ModeParameters
.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.
Dynamic Documents
You can choose to export the
finished report as a html, pdf,
MS Word, ODT, RTF, or
markdown document; or as a
html or pdf based slide show.
Rmd
.Rmd structure
Modify
chunk
options
Run all
previous
chunks
Run
current
chunk
Insert
code
chunk
Go to
code
chunk
Run
code
chunk(s)
Set
preview
location
Open in
window
Save Find and
replace
Open a new .Rmd file at File ▶ New File ▶ R Markdown.
Use the wizard that opens to pre-populate the file with a
template
1 Write document
by editing template2
Spell
Check
Publish Show
outline
Knit document to create report
Use knit button or render() to knit3
Examine build log
in R Markdown console6
Preview Output
in IDE window4
Use output file that is
saved alongside .Rmd7
Publish (optional)
to web or server5
Reload document
Find in document
File path to
output document
Synch publish button
to accounts at
• rpubs.com,
• shinyapps.io
• RStudio Connect
Debug ModeInteractive Documents
Optional section of
render (e.g. pandoc)
options written as
key:value pairs (YAML).
• At start of file
• Between lines of - - -
YAML Header
Narration formatted with
markdown, mixed with:
Text
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
Code chunks
Turn your report into an interactive
Shiny document in 4 steps
* 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.
1 Add runtime: shiny to the
YAML header.
2 Call Shiny input functions to embed
input objects.
4 Render with rmarkdown::run or click
Run Document in RStudio IDE
3 Call Shiny render functions to embed
reactive output.
---
output: html_document
runtime: shiny
---
```{r, echo = FALSE}
numericInput("n",
"How many cars?", 5)
renderTable({
head(cars, input$n)
})
```
Embed a complete app into your document with
shiny::shinyAppDir()
Inline code
Insert with `r <code>`. Results appear as text without code.
Built with
`r getRversion()`
Global options
Set with knitr::opts_chunk$set(), e.g.
```{r include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r echo=TRUE}
getRversion()
```
Code chunks
One or more lines surrounded
with ```{r} and ```. Place
chunk options within curly
braces, after r. Insert with
cache - cache results for future knits
(default = FALSE)
cache.path - directory to save cached
results in (default = "cache/")
child - file(s) to knit and then include
(default = NULL)
collapse - collapse all output into single
block (default = FALSE)
comment - prefix for each line of results
(default = '##')
dependson - chunk dependencies for
caching (default = NULL)
echo - Display code in output document
(default = TRUE)
engine - code language used in chunk
(default = 'R')
error - Display error messages in doc
(TRUE) or stop render when errors occur
(FALSE) (default = FALSE)
eval - Run code in chunk (default =
TRUE)
message - display code messages in
document (default = TRUE)
results (default = 'markup')
'asis' - passthrough results
'hide' - do not display results
'hold' - put all results below all code
tidy - tidy code for display (default =
FALSE)
warning - display code warnings in
document (default = TRUE)
fig.align - 'left', 'right', or 'center' (default
= 'default')
fig.cap - figure caption as character
string (default = NULL)
fig.height, fig.width - Dimensions of
plots in inches
highlight - highlight source code
(default = TRUE)
include - Include chunk in doc after
running (default = TRUE)
Important chunk options
Parameterize your documents to reuse with
diﬀerent inputs (e.g., data sets, values, etc.)
Add parameters
1 Create and set
parameters in the
header as sub-values
of params
---
params:
n: 100
d: !r Sys.Date()
---
Call parameters
2 Call parameter
values in code as
params$<name>
Today’s date
is `r params$d`
Set parameters
3 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"))
Indent 2
spaces
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

RStudio® is a trademark of RStudio, Inc. • CC BY RStudio • info@rstudio.com • 844-448-1212 • rstudio.com More cheat sheets at http://www.rstudio.com/resources/cheatsheets/
Debug ModePandoc’s Markdown Debug ModeSet render options with YAML
Plain text
End a line with two spaces
to start a new paragraph.
*italics* and **bold**
`verbatim code`
sub/superscript^2^~2~
~~strikethrough~~
escaped: * _
endash: --, emdash: ---
equation: $A = pi*r^{2}$
equation block:
$$E = mc^{2}$$
> block quote
# Header1 {#anchor}
## Header 2 {#css_id}
### Header 3 {.css_class}
#### Header 4
##### Header 5
###### Header 6

textbf{Tex ignored in HTML}
<em>HTML ignored in pdfs</em>
<http://www.rstudio.com>
[link](www.rstudio.com)
Jump to [Header 1](#anchor)
image:
![Caption](smallorb.png)
* unordered list
+ sub-item 1
+ sub-item 2
- sub-sub-item 1
* item 2
Continued (indent 4 spaces)
1. ordered list
2. item 2
i) sub-item 1
A. sub-sub-item 1
(@) A list whose numbering
continues after
(@) an interruption
Term 1
: Definition 1
| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
| 12 | 12 | 12 | 12 |
| 123 | 123 | 123 | 123 |
| 1 | 1 | 1 | 1 |
- slide bullet 1
- slide bullet 2
(>- to have bullets appear on click)
horizontal rule/slide break:
***
A footnote [^1]
[^1]: Here is the footnote.
Debug ModeCitations and Bibliographies
Set bibliography file and CSL 1.0 Style
file (optional) in the YAML header1
Use citation keys in text
2
Render. Bibliography will be added to end
of document3
Create citations with .bib, .bibtex, .copac, .enl, .json,
.medline, .mods, .ris, .wos, and .xml files
Smith cited [@smith04].
Smith cited without author [-@smith04].
@smith04 cited in line.
---
bibliography: refs.bib
csl: style.csl
---
Debug ModeCreate a Reusable template
1 Create a new package with a
inst/rmarkdown/templates directory
2 In the directory, Place a folder that contains:
• template.yaml (see below)
• skeleton.Rmd (contents of the template)
• any supporting files
4 Access
template in
wizard at File ▶
New File ▶
R Markdown
3 Install the package
---
name: My Template
---
template.yaml
Write with syntax on the left to create eﬀect on right (after render)
Debug ModeTable suggestions
Several functions format R data into tables
data <- faithful[1:4, ]
```{r results = "asis"}
print(xtable::xtable(data, caption = "Table with xtable"),
type = "html", html.table.attributes = "border=0"))
```
```{r results = "asis"}
stargazer::stargazer(data, type = "html",
title = "Table with stargazer")
```
```{r results = 'asis'}
knitr::kable(data, caption = "Table with kable")
```
sub-option description
citation_package The LaTeX package to process citations, natbib, biblatex or none X X X
code_folding Let readers to toggle the display of R code, "none", "hide", or "show" X
colortheme Beamer color theme to use X
css CSS file to use to style document X X X
dev Graphics device to use for figure output (e.g. "png") X X X X X X X
duration Add a countdown timer (in minutes) to footer of slides X
fig_caption Should figures be rendered with captions? X X X X X X X
fig_height, fig_width Default figure height and width (in inches) for document X X X X X X X X X X
highlight Syntax highlighting: "tango","pygments","kate","zenburn","textmate" X X X X X
includes File of content to place in document (in_header, before_body, after_body) X X X X X X X X
incremental Should bullets appear one at a time (on presenter mouse clicks)? X X X
keep_md Save a copy of .md file that contains knitr output X X X X X X
keep_tex Save a copy of .tex file that contains knitr output X X
latex_engine Engine to render latex, "pdflatex", "xelatex", or "lualatex" X X
lib_dir Directory of dependency files to use (Bootstrap, MathJax, etc.) X X X
mathjax Set to local or a URL to use a local/URL version of MathJax to render X X X
md_extensions Markdown extensions to add to default definition or R Markdown X X X X X X X X X X
number_sections Add section numbering to headers X X
pandoc_args Additional arguments to pass to Pandoc X X X X X X X X X X
preserve_yaml Preserve YAML front matter in final document? X
reference_docx docx file whose styles should be copied when producing docx output X
self_contained Embed dependencies into the doc X X X
slide_level The lowest heading level that defines individual slides X
smaller Use the smaller font size in the presentation? X
smart Convert straight quotes to curly, dashes to em-dashes, … to ellipses, etc. X X X
template Pandoc template to use when rendering file X X X X X
theme Bootswatch or Beamer theme to use for page X X
toc Add a table of contents at start of document X X X X X X X
toc_depth The lowest level of headings to add to table of contents X X X X X X
toc_float Float the table of contents to the left of the main content X
html
pdf
word
odt
rtf
md
ioslides
slidy
beamer
Options not listed: extra_dependencies, fig_crop, fig_retina, font_adjustment, font_theme, footer, logo, html_preview,
reference_odt, transition, variant, widescreen
When you render, R Markdown
1. runs the R code, embeds results and text into .md file with knitr
2. then converts the .md file into the finished format with pandoc
Set a document’s
default output format
in the YAML header:
---
output: html_document
---
# Body
output value creates
html_document html
pdf_document pdf (requires Tex )
word_document Microsoft Word (.docx)
odt_document OpenDocument Text
rtf_document Rich Text Format
md_document Markdown
github_document Github compatible markdown
ioslides_presentation ioslides HTML slides
slidy_presentation slidy HTML slides
beamer_presentation Beamer pdf slides (requires Tex)
Customize output
with sub-options
(listed at right):
---
output:
html_document:
code_folding: hide
toc_float: TRUE
---
# Body
Indent 2
spaces
Indent 4
spaces
# Tabset {.tabset .tabset-fade .tabset-pills}
## Tab 1
text 1
## Tab 2
text 2
### End tabset
Use .tabset css class
to place sub-headers
into tabs
html tabsets
gituhb
Learn more in
the stargazer,
xtable, and
knitr packages.
Learn more at rmarkdown.rstudio.com • RStudio IDE 0.99.879 • Updated: 02/16

Rmarkdown cheatsheet-2.0

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