.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$n) code. Each chunk: }) output_options - List of ``` • Begins with ```{r} render options (as in YAML) • ends with ``` output_file R Markdown will run the output_dir Embed a complete app into your document with code and append the shiny::shinyAppDir() results to the doc. params - list of params to use It will use the location of envir - environment to * Your report will rendered as a Shiny app, which means you the .Rmd file as the evaluate code chunks in must choose an html output format, like html_document, working directory encoding - of input file and serve it with an active R Session. Embed codeDebug with Mode knitr syntax DebugParameters Mode Inline code Code chunks Global options Parameterize your documents to reuse with Insert with `r <code>`. Results appear as text without code. One or more lines surrounded Set with knitr::opts_chunk$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$<name> (default = NULL) (default = 'R') plots in inches 'hold' - put all results below all code Set parameters collapse - collapse all output into single error - Display error messages in doc highlight - highlight source code tidy - tidy code for display (default = (TRUE) or stop render when errors occur FALSE) Set values wth Knit block (default = FALSE) (default = TRUE) 3 with parameters or (FALSE) (default = FALSE) warning - display code warnings in comment - prefix for each line of results eval - Run code in chunk (default = include - Include chunk in doc afer the params argument document (default = TRUE) of render(): (default = '##') TRUE) running (default = TRUE) 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, render("doc.Rmd", 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 params = list(n = 1, d = as.Date("2015-01-01")) 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 <!--Text comment--> 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 <em>HTML ignored in pdfs</em> (listed at right): html_document: code_folding: hide preserve_yaml Preserve YAML front matter in final document? X <http://www.rstudio.com> toc_float: TRUE reference_docx docx file whose styles should be copied when producing docx output X html tabsets --- [link](www.rstudio.com) self_contained Embed dependencies into the doc X X X Jump to [Header 1](#anchor) Use .tabset css class # Body slide_level The lowest heading level that defines individual slides X image: to place sub-headers into tabs 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 # Tabset {.tabset .tabset-fade .tabset-pills} * unordered list template Pandoc template to use when rendering file X X X X X + sub-item 1 ## Tab 1 + sub-item 2 text 1 theme Bootswatch or Beamer theme to use for page X X - sub-sub-item 1 ## Tab 2 toc Add a table of contents at start of document X X X X X X X text 2 toc_depth The lowest level of headings to add to table of contents X X X X X X * item 2 ### End tabset toc_float Float the table of contents to the lef of the main content X Continued (indent 4 spaces) Options not listed: extra_dependencies, fig_crop, fig_retina, font_adjustment, font_theme, footer, logo, html_preview, 1.