render()
RStudio Pro Features
Workflow
Debug ModeEmbed code with knitr syntax
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 CheatSheet
CC BY RStudio
Debug Mode
Parameters
.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 template
2
Spell
Check
Publish
Show
outline
Knit document to create report
Use knit button or render() to knit
3
Examine build log
in R Markdown console
6
Preview Output
in IDE window
4
Use output file that is
saved alongside .Rmd
7
Publish (optional)
to web or server
5
Reload document
Find in document
File path to
output document
Synch publish button
to accounts at
•rpubs.com,
•shinyapps.io
•RStudio Connect
Debug Mode
Interactive 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
