.Rmd files Rmd Reproducible Research Dynamic Documents An R Markdown (.Rmd) file is a record of At the click of a button, or the type You can choose to export the R Markdown Cheat Sheet of a command, you can rerun the finished report as a html, pdf, your research. It contains the code that a Rmd learn more at rmarkdown.rstudio.com scientist needs to reproduce your work code in an R Markdown file to MS Word, ODT, RTF, or along with the narration that a reader reproduce your work and export markdown document; or as a needs to understand your work. the results as a finished report. html or pdf based slide show.
RStudioWorkflow Pro Features InteractiveDebug Documents Mode Open a new .Rmd file at File ▶ New File ▶ R Markdown. Write document Knit document to create report Preview Output Publish (optional) Turn your report into an interactive 1 Use the wizard that opens to pre-populate the file with a 2 by editing template 3 Use knit button or render() to knit 4 in IDE window 5 to web or server Shiny document in 4 steps template Synch publish button Open in Save Spell Find and Publish Show to accounts at Add runtime: shiny to the window Check replace outline • rpubs.com, YAML header. • shinyapps.io 1 • RStudio Connect Call Shiny input functions to embed Reload document 2 input objects. Find in document Call Shiny render functions to embed File path to reactive output. output document 3 Set Insert Go to Run .Rmd structure Examine build log Render with rmarkdown::run or click preview code code code Run Document in RStudio IDE YAML Header location chunk chunk chunk(s) 6 in R Markdown console 4 Optional section of render (e.g. pandoc) Use output file that is options written as 7 saved alongside .Rmd --- key:value pairs (YAML). output: html_document runtime: shiny • At start of file --- • Between lines of - - - Modify Run all Run render() chunk previous current ```{r, echo = FALSE} Text options chunks chunk Use rmarkdown::render() Narration formatted with to render/knit at cmd line. numericInput("n", "How many cars?", 5) markdown, mixed with: Important args: Code chunks input - file to render renderTable({ Chunks of embedded output_format head(cars, input$n) code. Each chunk: }) output_options - List of ``` • Begins with ```{r} render options (as in YAML) • ends with ``` output_file R Markdown will run the output_dir Embed a complete app into your document with code and append the shiny::shinyAppDir() results to the doc. params - list of params to use It will use the location of envir - environment to * Your report will rendered as a Shiny app, which means you the .Rmd file as the evaluate code chunks in must choose an html output format, like html_document, working directory encoding - of input file and serve it with an active R Session.
Embed codeDebug with Mode knitr syntax DebugParameters Mode Inline code Code chunks Global options Parameterize your documents to reuse with Insert with `r `. Results appear as text without code. One or more lines surrounded Set with knitr::opts_chunk$set(), e.g. different inputs (e.g., data sets, values, etc.) with ```{r} and ```. Place ```{r echo=TRUE} Built with getRversion() chunk options within curly ```{r include=FALSE} Add parameters --- `r getRversion()` ``` knitr::opts_chunk$set(echo = TRUE) Indent 2 braces, afer r. Insert with 1 Create and set params: spaces Important chunk options ``` parameters in the n: 100 header as sub-values d: !r Sys.Date() cache - cache results for future knits dependson - chunk dependencies for fig.align - 'lef', 'right', or 'center' (default message - display code messages in of params --- (default = FALSE) caching (default = NULL) = 'default') document (default = TRUE) Call parameters cache.path - directory to save cached echo - Display code in output document fig.cap - figure caption as character results (default = 'markup') Today’s date results in (default = "cache/") (default = TRUE) string (default = NULL) 'asis' - passthrough results 2 Call parameter values in code as is `r params$d` child - file(s) to knit and then include engine - code language used in chunk fig.height, fig.width - Dimensions of 'hide' - do not display results params$
RStudio® is a trademark of RStudio, Inc. • CC BY RStudio • [email protected] • 844-448-1212 • rstudio.com More cheat sheets at http://www.rstudio.com/resources/cheatsheets/ Learn more at rmarkdown.rstudio.com • RStudio IDE 0.99.879 • Updated: 02/16 Pandoc’sDebug Markdown Mode Set renderDebug options Mode with YAML Write with syntax on the lef to create effect on right (afer render) When you render, R Markdown 1. runs the R code, embeds results and text into .md file with knitr
sub-option description rtf md Plain text pdf odt 2. then converts the .md file into the finished format with pandoc html slidy word gituhb End a line with two spaces ioslides beamer to start a new paragraph. citation_package The LaTeX package to process citations, natbib, biblatex or none X X X *italics* and **bold** code_folding Let readers to toggle the display of R code, "none", "hide", or "show" X `verbatim code` colortheme Beamer color theme to use X sub/superscript^2^~2~ Set a document’s --- ~~strikethrough~~ default output format output: html_document css CSS file to use to style document X X X in the YAML header: escaped: \* \_ \\ --- dev Graphics device to use for figure output (e.g. "png") X X X X X X X endash: --, emdash: --- # Body duration Add a countdown timer (in minutes) to footer of slides X equation: $A = \pi*r^{2}$ output value creates fig_caption Should figures be rendered with captions? X X X X X X X equation block: html_document html fig_height, fig_width Default figure height and width (in inches) for document X X X X X X X X X X $$E = mc^{2}$$ pdf_document pdf (requires Tex ) highlight Syntax highlighting: "tango", "pygments", "kate","zenburn", "textmate" X X X X X > block quote word_document Microsof Word (.docx) includes File of content to place in document (in_header, before_body, after_body) X X X X X X X X # Header1 {#anchor} odt_document OpenDocument Text incremental Should bullets appear one at a time (on presenter mouse clicks)? X X X rtf_document Rich Text Format ## Header 2 {#css_id} keep_md Save a copy of .md file that contains knitr output X X X X X X md_document Markdown keep_tex Save a copy of .tex file that contains knitr output X X ### Header 3 {.css_class} github_document Github compatible markdown latex_engine Engine to render latex, "pdflatex", "xelatex", or "lualatex" X X #### Header 4 ioslides_presentation ioslides HTML slides lib_dir Directory of dependency files to use (Bootstrap, MathJax, etc.) X X X ##### Header 5 slidy_presentation slidy HTML slides mathjax Set to local or a URL to use a local/URL version of MathJax to render X X X ###### Header 6 beamer_presentation Beamer pdf slides (requires Tex) md_extensions Markdown extensions to add to default definition or R Markdown X X X X X X X X X X Customize output --- Indent 2 Indent 4 number_sections Add section numbering to headers X X output: spaces spaces \textbf{Tex ignored in HTML} with sub-options pandoc_args Additional arguments to pass to Pandoc X X X X X X X X X X HTML ignored in pdfs (listed at right): html_document: code_folding: hide preserve_yaml Preserve YAML front matter in final document? X