class: title-slide, left, top # Many faces of R Markdown: An introduction ## Dr. Selcan Aydin ??? Welcome! I want to thank Batool and R-ladies Dammam for organizing this series and for inviting me. Today we'll talk about Rmarkdown and its uses. --- name: hello class: middle, center ## Selcan Aydin, PhD <img style="border-radius: 50%;" src="images/avatar.jpg" width="200px"/> [<svg viewBox="0 0 496 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> @selcant](https://github.com/selcant) [<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg> @selcan_t](https://twitter.com/selcan_t) [<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"></path></svg> selcan-aydin.netlify.app/](https://selcan-aydin.netlify.app/) ??? My name is Selcan Aydin, and I'm a computational biologist. I really like teaching and talking about science. Got certified as a Software Carpentry and Rstudio instructor so I got to do it more! --- class: top, center background-image: url(images/rmarkdown_hedgehog_wide.png) background-size: center background-position: middle, center # R Markdown lets you make .footnote[Art by [Allison Horst](https://twitter.com/allison_horst?lang=en)] --- class: inverse, middle, center # But, **what** is R Markdown? --- background-image: url(images/rmarkdown_hedgehog.png) background-size: 25% background-position: 95% 90% # R Markdown is ... -- 1. ["An authoring framework for data science."](https://rmarkdown.rstudio.com/lesson-1.html) (✔️) -- 1. [A document format (`.Rmd`).](https://bookdown.org/yihui/rmarkdown/) (✔️) -- 1. [An R package named `rmarkdown`.](https://rmarkdown.rstudio.com/docs/) (✔️) -- 1. ["A file format for making dynamic documents with R."](https://rmarkdown.rstudio.com/articles_intro.html) (✔️) -- 1. ["A tool for integrating text, code, and results."](https://r4ds.had.co.nz/communicate-intro.html) (✔️) -- 1. ["A computational document."](http://radar.oreilly.com/2011/07/wolframs-computational-documen.html) (✔️) -- 1. Wizardry. (🧙♂️) --- class: inverse, middle, center # Why use R Markdown? -- ♻️ Make your work reproducible and reusable. -- 😎 Get confident about your work. -- 🌍 Easily share data, results and code. All together! ??? These are clearly not all advantages. But the ones I benefit the most. --- class: center, top background-image: url(images/rmarkdown_wizards.png) background-size: contain backgroun-position: top, center .footnote[Art by [Allison Horst](https://twitter.com/allison_horst?lang=en)] ??? What is IN Rmarkdown. --- class: inverse, center, middle background-image: url(images/rmarkdown_hedgehog.png) background-size: 25% background-position: 95% 95% # Let's knit an .Rmd to html! --- class: inverse, center, middle background-image: url(images/rmarkdown_hedgehog.png) background-size: 25% background-position: 95% 95% # Let's watch someone else knit first! --- class: inverse, top, center <video width="1530" height="610" controls> <source src="images/single-doc-knit.mp4" type="video/mp4"> </video> --- class: top, left .pull-left[ # metadata: YAML **Y(et) A(nother) M(arkup) L(anguage)** ```yaml --- author: Your name here title: Your title here output: html_document --- ``` ] .pull-right[ ![](images/orchestra.jpg) ] ??? Update your Rmd with your name + title. --- class: top, left .pull-left[ # Make it pretty! ```yaml --- author: Your name here title: Your title here output: html_document --- ``` ```yaml --- author: Your name here title: Your title here output: html_document: toc: true toc_float: true theme: flatly code_folding: hide code_download: true --- ``` ] .pull-right[ ![](images/orchestra.jpg) ] ??? Update your Rmd and re-knit! --- # 🧶 Knit to ... .pull-left[ ![](images/knit-dropdown.png) ] .pull-right[ ```yaml --- author: Your name here title: Your title here output: html_document: toc: true toc_float: true theme: flatly code_folding: hide code_download: true word_document: default pdf_document: default --- ``` ] ??? This is a great way to "control" your knit button! Notice that when you knit, it respects those output options in your YAML. This way you "save" your output options --- class: inverse, middle, center # Your turn! -- **Download the Rmd files if you haven't yet.** <https://github.com/selcant/Rladies_Dammam_042021/blob/main/_material.zip> -- 🧶 `test.Rmd` to html. -- Change theme and re-🧶! -- Change output and re-🧶! ??? Using what we learned so far. --- class: middle, center # Extension output formats <img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/flexdashboard.png" width="32%" /><img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/bookdown.png" width="32%" /><img src="https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/xaringan.png" width="32%" /> --- class: middle, center # Distill() <iframe src="https://rstudio.github.io/distill/" width="90%" height="400px"></iframe> --- class: middle .center[ # Use an extension package ] .pull-left[ ```yaml --- author: Your name here title: Your title here output: distill::distill_article: default bookdown::html_document2: default --- ``` ] .pull-right[ ```yaml --- author: Your name here title: Your title here output: distill::distill_article: toc: true bookdown::html_document2: toc: true theme: flatly toc_float: true --- ``` ] --- class: inverse, middle, center # Text in Rmarkdown Newest Rstudio comes with a visual editor! -- Here is a markdown tutorial 👇 https://commonmark.org/help/tutorial/ ??? Show it. --- class: inverse, middle, center # Code chunks -- Include code. -- Add plots. -- Add tables. -- and more ... ??? what to do with code chunks. --- class: top, left # Code chunks .pull-left[ ```` ```{r table, echo = TRUE, eval = FALSE } library(tidyverse) library(DT) library(palmerpenguins) # Making downloadable data tables create_dt <- function(x){ DT::datatable(x, extensions = 'Buttons', rownames = FALSE, filter="top", options = list(dom = 'Blfrtip', buttons = c('copy', 'csv', 'excel'), pageLength = 5, scrollX=T)) } create_dt(penguins) ``` ```` ] .pull-right[ What is the fate of this chunk? What happens when you change `eval = TRUE`? ] ??? evaluate = TRUE, it won't run when it is FALSE Tables you can search! -- DT package is very cool! Let's you share data easily. --- class: top, left # Chunk options for plots .pull-left[ You can adjust: + fig resolution + fig size + [fig "device"](https://r4ds.had.co.nz/graphics-for-communication.html#other-important-options) .footnote[https://yihui.name/knitr/options/#plots] ] .pull-right[ See also: + `fig.width` + `fig.height` + `fig.asp` .footnote[https://r4ds.had.co.nz/graphics-for-communication.html#figure-sizing] ] --- # Cache chunks You can cache code chunks that need: + long time + large resources ```` ```{r cache_example, cache =FALSE, eval = FALSE} mean_penguins <- summarize_if( penguins, is.numeric, mean, na.rm=TRUE ) ``` ```` After changing `eval = TRUE` and re-knitting, you should see a `*_cache` folder in your working directory. --- class: inverse, middle, center # Your turn! Knit test.Rmd to html. -- Change `eval = TRUE` and re-🧶! -- Check the tabs, anything new? 📈 -- How about your local directory, any new folders? 📂 ??? Tabs - plots will show up. This is a neat html trick that lets you organize things. cache - you can cache time consuming steps. --- class: inverse, top, left # Websites + Simple websites to share data, analysis using `rmarkdown()`. + For personal websites check out the `distill()` package. + There is also `blogdown()` and `bookdown()`available as more advanced options. <img src="https://github.com/rstudio/hex-stickers/blob/master/thumbs/rmarkdown.png?raw=true" width="15%" /><img src="https://github.com/rstudio/distill/blob/master/man/figures/logo.png?raw=true" width="15%" /><img src="https://github.com/rstudio/hex-stickers/blob/master/thumbs/blogdown.png?raw=true" width="15%" /><img src="https://github.com/rstudio/hex-stickers/blob/master/thumbs/bookdown.png?raw=true" width="15%" /> --- class: inverse, middle, center # Your turn! Download the example website here 👇 <https://github.com/selcant/Rladies_Dammam_042021/blob/main/_material.zip> -- ➡️ Click on website_ex.Rproj to start the Rstudio project. -- ➡️ Open _site.yml! -- ➡️ Do you see "Build" next to Environment/History/Connections? If not, go to Project Options > Build tools and choose website. -- ➡️ Build website! ??? build together + look through tabs. Change the author, add remove stuff. --- class: inverse, middle, left # Publish your website! 🌐 1. You can publish your website using netlify! Make a free account here: <https://www.netlify.com/> or login with other credentials. -- 1. Find the 📁 `_site` folder you just created and drag & drop into netlify! -- 1. Voila! Your website is live! 😎 --- class: inverse, middle, center # Resources... --- class: middle, center, inverse <span class="fa-stack fa-4x"> <i class="fa fa-circle fa-stack-2x" style="color: #fff;"></i> <strong class="fa-stack-1x" style="color:#2f5275;">!</strong> </span> # Cheatsheets! --- class: middle .left-column[ # 📌 ] .right-column[ _Help > Cheatsheets > RStudio IDE_ <a href="https://www.rstudio.com/resources/cheatsheets/#ide" target="_blank"><img src="https://d33wubrfki0l68.cloudfront.net/0dc0efccfaf638de8be4ce43e2bab8a91541d3d2/c4fdc/wp-content/uploads/2018/08/rstudio-ide.png" width="50%" /></a> ] .footnote[https://www.rstudio.com/resources/cheatsheets/#ide] --- class: middle .left-column[ # 📌 ] .right-column[ _Help > Cheatsheets > R Markdown Cheat Sheet_ <a href="https://www.rstudio.com/resources/cheatsheets/#rmarkdown" target="_blank"><img src="https://d33wubrfki0l68.cloudfront.net/65dffd1bdcaa0025006262164d98e8068e8b4387/c3895/wp-content/uploads/2018/08/rmarkdown-2.0.png" width="50%" /></a> ] .footnote[https://www.rstudio.com/resources/cheatsheets/#rmarkdown] --- class: middle .left-column[ # 📌 ] .right-column[ _Help > Cheatsheets > R Markdown Reference Guide_ <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf" target="_blank"><img src="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference-guide.png" width="40%" /></a> ] .footnote[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf] --- class: middle, center, inverse <span class="fa-stack fa-4x"> <i class="fa fa-circle fa-stack-2x" style="color: #fff;"></i> <strong class="fa-stack-1x" style="color:#2f5275;">!</strong> </span> # Book! --- class: middle .left-column[ # 📖 ] .right-column[ <a href="https://bookdown.org/yihui/rmarkdown/" target="_blank"><img src="https://bookdown.org/yihui/rmarkdown/images/cover.png" width="40%" /></a> ] .footnote[https://bookdown.org/yihui/rmarkdown/] --- class: left, middle, inverse # Thank you! 😄 + Special thanks to Rstudio Education, Dr. Alison Presmanes Hill and Dr. Allison Horst for making all of their teaching/talk materials available. I benefited from them greatly! + Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan). + The chakra comes from [remark.js](https://remarkjs.com), [**knitr**](https://yihui.org/knitr/), and [R Markdown](https://rmarkdown.rstudio.com). # References + https://rstd.io/rmd4cdc + https://rstudio-education.github.io/teaching-in-production/ ---