rmarkdown : : CHEAT SHEET

1 rmarkdown : : CHEAT SHEET SOURCE EDITOR. RENDERED output file path to output document What is rmarkdown ? 1. New File Write with .Rmd files Develop your code and ideas side-by-side in a single 5. Save and Render 6. Share find in document publish to , Markdown document. Run code as individual , The syntax on the le renders as the output on the right. chunks or as an entire document. set insert go to run code RStudio Connect Rmd preview code code chunk(s) Plain text. Plain text. Dynamic Documents Knit together location chunk chunk show End a line with two spaces to End a line with two spaces to plots, tables, and results with outline start a new paragraph.

2 Start a new paragraph. narrative text. Render to a variety of 4. Set output format (s) Also end with a backslash\ Also end with a backslash formats like HTML, PDF, MS Word, or and Options reload document to make a new line. to make a new line. MS Powerpoint. *italics* and **bold** italics and bold Reproducible Research Upload, link superscript^2^/subscript~2~ superscript2/subscript2. to, or attach your report to share. ~~strikethrough~~ strikethrough Anyone can read or run your code to 3. Write Text run all escaped: \* \_ \\ escaped: * _ \. reproduce your work. previous modify chunks endash: --, emdash: --- endash: , emdash: . chunk run options current # Header 1.

3 Header 1. Workflow 2. Embed Code chunk ## Header 2.. Header 2.. 11. Open a new .Rmd file in the RStudio IDE by ###### Header 6 Header 6. going to File > New File > R Markdown. unordered list - unordered list 22. Embed code in chunks. Run code by line, by - item 2 item 2. chunk, or all at once. - item 2a (indent 1 tab) item 2a (indent 1 tab). - item 2b item 2b 33. Write text and add tables, figures, images, and 1. ordered list 1. ordered list citations. format with Markdown syntax or the 2. item 2 2. item 2. RStudio Visual Markdown Editor. 44. Set output format (s) and options in the YAML. VISUAL EDITOR insert citations style options Insert Citations - item 2a (indent 1 tab).

4 - item 2b <link url>. item 2a (indent 1 tab). item 2b header. Customize themes or add parameters Create citations from a bibliography file, a Zotero library, to execute or add interactivity with Shiny. or from DOI references. [This is a link.](link url) This is a link. [This is another link][id]. This is another link. 55. Save and render the whole document. Knit BUILD YOUR BIBLIOGRAPHY. periodically to preview your work as you write. At the end of the document: add/edit Add BibTeX or CSL bibliographies to the YAML header. [id]: link url 66. Share your work! attributes --- . title: "My Document". bibliography: or ![Caption][id2]. link-citations: TRUE At the end of the document: Embed Code with knitr --- [id2]: Caption.

5 If Zotero is installed locally, your main library will `verbatim code` verbatim code automatically be available. ```. CODE CHUNKS OPTION DEFAULT EFFECTS. multiple lines multiple lines Surround code chunks with ```{r} and ``` or use echo TRUE display code in output document Add citations by DOI by searching "from DOI" in the of verbatim code of verbatim code the Insert Code Chunk button. Add a chunk label TRUE (display error messages in doc) Insert Citation dialog. ```. error FALSE FALSE (stop render when error occurs). and/or chunk options inside the curly braces a er r. > block quotes block quotes eval TRUE run code in chunk INSERT CITATIONS.

6 ```{r chunk-label, include=FALSE} include TRUE include chunk in doc a er running Access the Insert Citations dialog in the Visual Editor equation: $e^{i \pi} + 1 = 0$ equation: e i + 1 = 0. summary(mtcars) message TRUE display code messages in document by clicking the @ symbol in the toolbar or by clicking Insert > Citation. equation block: equation block: ``` warning TRUE display code warnings in document "asis" (passthrough results) $$E = mc^{2}$$ E = m c2. Add citations with markdown syntax by typing SET GLOBAL OPTIONS results "markup" "hide" (don't display results) or horizontal rule: horizontal rule: "hold" (put all results below all code) --- Set options for the entire document in the first chunk.

7 Insert Tables "default" "le ", "right", or "center". NULL alt text for a figure | Right | Le | Default | Center | Right Le Default Center ```{r include=FALSE} |-------:|:------|-----------|:--------- :|. knitr::opts_chunk$set(message = FALSE) NULL figure caption as a character string 12 12 12 12. output data frames as tables using | 12 | 12 | 12 | 12 |. ``` "figure/" prefix for generating figure file paths kable(data, caption). 123 123 123 123. | 123 | 123 | 123 | 123 |. & 1 1 1 1. 7 plot dimensions in inches |1|1|1|1|. INLINE CODE rescales output width, "75%", "300px" ```{r}. Insert `r <code>` into text sections. Code is evaluated collapse FALSE collapse all sources & output into a single block data <- faithful[1:4, ] HTML Tabsets at render and results appear as text.

8 Comment "##" prefix for each line of results knitr::kable(data, # Results {.tabset} Results ## Plots text "Built with `r getRversion()`" --> "Built with " child NULL files(s) to knit and then include caption = "Table with kable") text Plots Tables include or exclude a code chunk when ```. purl TRUE extracting source code with knitr::purl() ## Tables text See more options and defaults by running str(knitr::opts_chunk$get()) Other table packages include flextable, gt, and kableExtra. more text RStudio is a trademark of RStudio, PBC CC BY SA RStudio 844-448-1212 Learn more at rmarkdown Updated: 2021-08. ft ft ft ft ft ft Set output Formats and their Options in YAML Render MS Word MS PPT.

9 HTML. PDF. Use the document's YAML header to set an output IMPORTANT OPTIONS DESCRIPTION When you render a format and customize it with output options. anchor_sections Show section anchors on mouse hover (TRUE or FALSE) X document, rmarkdown : --- citation_package The LaTeX package to process citations ("default", "natbib", "biblatex") X 1. Runs the code and embeds title: "My Document" results and text into an .md author: "Author Name" code_download Give readers an option to download the .Rmd source code (TRUE or FALSE) X. file with knitr. output : code_folding Let readers to toggle the display of R code ("none", "hide", or "show") X. html_document: Indent format 2 characters, 2.

10 Converts the .md file into the output format with toc: TRUE css CSS or SCSS file to use to style document ( " ") X Pandoc. indent options 4 characters --- dev Graphics device to use for figure output ( "png", "pdf") X X HTML. knitr pandoc .Rmd .md PDF. df_print Method for printing data frames ("default", "kable", "tibble", "paged") X X X X DOC. output format CREATES. html_document .html fig_caption Should figures be rendered with captions (TRUE or FALSE) X X X X. Save, then Knit to preview the document output . pdf_document* .pdf highlight Syntax highlighting ("tango", "pygments", "kate", "zenburn", "textmate") X X X The resulting HTML/PDF/MS Word/etc.