class: center, middle, inverse, title-slide # R Markdown ## Communicate in a SMART way! ### Research Lounge Meet, University of Moratuwa ### <br/>Dr. Thiyanga S. Talagala ### October 18, 2022 --- class: middle center bg-main1 # Packages ## `install.packages("rmarkdown")` ## `install.packages("knitr")` -- <span><i class="fas fa-bell fa-5x faa-ring animated "></i></span> ## Additional packages ## `install.packages("tidyverse")` ## `install.packages("reticulate")` --- background-image:url("screenshots/1img.png") background-size: contain --- background-image:url("screenshots/2img.png") background-size: contain --- background-image:url("screenshots/3img.png") background-size: contain --- background-image:url("screenshots/4img.png") background-size: contain --- background-image:url("screenshots/5img.png") background-size: contain --- background-image:url("screenshots/6img.png") background-size: contain --- background-image:url("screenshots/7img.png") background-size: contain --- background-image:url("screenshots/8img.png") background-size: contain --- background-image:url("screenshots/9img.png") background-size: contain --- background-image:url("screenshots/10img.png") background-size: contain --- background-image:url("screenshots/11img.png") background-size: contain --- background-image:url("screenshots/12img.png") background-size: contain --- background-image:url("screenshots/13img.png") background-size: contain --- background-image:url("screenshots/14img.png") background-size: contain --- background-image:url("screenshots/15img.png") background-size: contain --- background-image:url("screenshots/16img.png") background-size: contain --- background-image:url("screenshots/17img.png") background-size: contain --- class: middle center bg-main1 <span><i class="fas fa-wrench fa-5x faa-flash animated "></i></span> # Creating an R Markdown document --- background-image: url(rmarkdown_step1.png) background-position: center background-size: contain --- background-image: url(rmarkdown_step2.png) background-position: center background-size: contain --- background-image: url(rmarkdown_step2_1.png) background-position: center background-size: contain --- background-image: url(rmarkdown_step3.png) background-position: center background-size: contain class: center, middle --- background-image: url(rmarkdown_step4.png) background-position: center background-size: contain class: center, middle --- # Select a folder to save the document  --- # Give a name to the document  --- background-image: url(rmarkdown_step5.png) background-position: center background-size: contain class: center, middle --- background-image: url(rmarkdown_step6.png) background-position: center background-size: contain class: center, middle --- background-image: url(rmarkdown_step7.png) background-position: center background-size: contain class: center, middle --- # Demo <video width="100%" height="100%" controls id="sc1"> <source src="media/1_media.mp4" type="video/mp4"> </video> --- <iframe width="860" height="315" src="media/1_media.mp4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> --- # R Markdown pipeline <img src="Rmarkdownpipeline.jpeg" width="100%" /> Image source: [here](https://rmarkdown.rstudio.com/authoring_quick_tour.html) --- background-image:url("anatomy.jpeg") background-size:contain --- class: middle center bg-main1 <span><i class="fas fa-leaf fa-5x faa-spin animated "></i></span> # Customizing your R Markdown document: text --- background-image:url("sc1/c1.png") background-size:contain --- background-image:url("sc1/c2.png") background-size:contain --- background-image:url("sc1/c3.png") background-size:contain --- background-image:url("sc1/c4.png") background-size:contain --- background-image:url("sc1/c5.png") background-size:contain --- background-image:url("sc1/c6.png") background-size:contain --- background-image:url("sc1/c7.png") background-size:contain --- background-image:url("sc1/c8.png") background-size:contain --- background-image:url("sc1/c9.png") background-size:contain --- background-image:url("sc1/c13.png") background-size:contain --- background-image:url("sc1/c14.png") background-size:contain --- background-image:url("sc1/c15.png") background-size:contain --- # Change Header .pull-left[ **Code** ```r # Header 1 ## Header 2 ### Header 3 ``` ] .pull-right[ **Output** # Header 1 ## Header 2 ### Header 3 ] --- # Add content .pull-left[ **Code** ```r # Header 1 This is section 1. ## Header 2 This is section 1.2 ### Header 3 This is section 1.2.1 ``` ] .pull-right[ **Output** # Header 1 This is section 1. ## Header 2 This is section 1.2 ### Header 3 This is section 1.2.1 ] --- # Text formatting .pull-left[ ## Code <img src="sc1/text.png" alt="text" width="300"/> ] .pull-right[ ## Output *M1: This text is in italics.* _M2: This is also italics._ **M3: This text is in bold.** __M4: This is also bold.__ ~~This text is strikethrough.~~ ] --- class: middle center bg-main1 <span><i class="fas fa-align-center fa-5x faa-pulse animated "></i></span> # Include R codes --- background-image:url("sc1/c17.png") background-size:contain --- background-image:url("sc1/inline-0.png") background-size:contain --- background-image:url("sc1/inline-1.png") background-size:contain --- background-image:url("sc1/inline-2.png") background-size:contain --- background-image:url("sc1/inline-3.png") background-size:contain --- background-image:url("sc1/inline-4.png") background-size:contain --- background-image:url("sc1/inline-5.png") background-size:contain --- class: middle center bg-main1 <span><i class="fas fa-exclamation-triangle fa-7x faa-flash animated "></i></span> # Anatomy of R Markdown --- class: middle center bg-main1 # Anatomy of R Markdown ## code chunk --- background-image:url("sc1/c18.png") background-size:contain --- class: middle center bg-main1 # Anatomy of R Markdown ## Text --- background-image:url("sc1/c20.png") background-size:contain --- class: middle center bg-main1 # Anatomy of R Markdown ## YAML ### HTML Document --- background-image:url("sc1/c19.png") background-size:contain --- class: middle center bg-main1 # Anatomy of R Markdown ## YAML ### PDF Document --- background-image:url("sc1/SC/s1.png") background-size:contain --- background-image:url("sc1/SC/s2.png") background-size:contain --- class: middle center bg-main1 # Anatomy of R Markdown ## YAML ### Word Document --- background-image:url("sc1/SC/s3.png") background-size:contain --- background-image:url("sc1/SC/s4.png") background-size:contain --- class: middle center bg-main1 <span><i class="fas fa-exclamation-circle fa-7x faa-bounce animated "></i></span> # Chunk options --- background-image:url("sc1/SC/s5.png") background-size:contain ## fig.width/ fig.height --- background-image:url("sc1/SC/s7.png") background-size:contain ## fig.width/ fig.height --- background-image:url("sc1/SC/s6.png") background-size:contain ## echo [TRUE/ FALSE] --- background-image:url("sc1/SC/s8.png") background-size:contain ## eval [TRUE/ FALSE] --- class: bg-main1 # Chunk options * `eval = FALSE` - prevent the code from being evaluated * `include = FALSE` - run the code but doesn't show it in the final document * `echo = FALSE` - prevent the code but not the results from appearing * `message = FALSE` - prevent messages from appearing in the finished file * `results = "hide"` - hide the printed output * `error = TRUE` - cause the render to continue even if the code returns an error * `comment=NA` - remove # from the output -- .pull-left[ Without `comment=NA` ```r a <- 1:5; a ``` ``` ## [1] 1 2 3 4 5 ``` ] .pull-right[ With `comment=NA` ```r a <- 1:5; a ``` ``` [1] 1 2 3 4 5 ``` ] --- background-image:url("sc1/equations.png") background-size:contain # Mathematical Equations --- class: middle center bg-main1 ## How to type Greek letters? Please read my blog post here: https://thiyanga.netlify.app/post/greekletters/ --- class: middle center bg-main1 # Styling your R Markdown document <span><i class="fas fa-thumbs-up fa-5x faa-float animated "></i></span> ## YAML --- background-image:url("sc1/SC/s9.png") background-size:contain ## toc: true --- background-image:url("sc1/SC/s10.png") background-size:contain ## toc_float: true --- background-image:url("sc1/SC/s11.png") background-size:contain --- background-image:url("sc1/SC/s12.png") background-size:contain --- background-image:url("sc1/SC/s13.png") background-size:contain --- background-image:url("sc1/SC/s14.png") background-size:contain ## number_sections --- background-image:url("sc1/SC/s15.png") background-size:contain --- background-image:url("sc1/SC/s16.png") background-size:contain --- class: middle center bg-main1 # Styling your R Markdown document <span><i class="fas fa-cogs fa-5x faa-vertical animated "></i></span> ## theme --- background-image:url("sc1/SC/s17.png") background-size:contain --- background-image:url("sc1/SC/s18.png") background-size:contain --- background-image:url("sc1/SC/s19.png") background-size:contain --- background-image:url("sc1/SC/s20.png") background-size:contain --- class: middle center bg-main1 # Styling your R Markdown document <span><i class="fas fa-cogs fa-5x faa-vertical animated "></i></span> ## highlight --- background-image:url("sc1/SC/s21.png") background-size:contain --- background-image:url("sc1/SC/s22.png") background-size:contain --- .pull-left[ ## Themes - default - cerulean - journal - flatly - darkly - readable - spacelab - united - cosmo - lumen - paper - sandstone - simplex - yeti ] .pull-right[ ## Highlight - default - tango - espresso - zenburn - haddock - breezedark - kate - monochrome ] --- class: middle center bg-main1 # Styling your R Markdown document <span><i class="fas fa-cogs fa-5x faa-vertical animated "></i></span> ## Tabbed Sections --- background-image:url("sc1/SC/s23.png") background-size:contain --- background-image:url("sc1/SC/s24.png") background-size:contain --- class: middle center bg-main1 # Include Latex tables <span><i class="fas fa-cogs fa-5x faa-spin animated "></i></span> --- background-image:url("sc1/SC/s39.png") background-size:contain --- background-image:url("sc1/courseoutline.png") background-size:contain --- class: middle center bg-main1 # Include images <span><i class="fas fa-cogs fa-5x faa-spin animated "></i></span> --- background-image:url("sc1/SC/s40.png") background-size:contain --- background-image:url("sc1/SC/s41.png") background-size:contain --- background-image:url("sc1/SC/s42.png") background-size:contain --- class: middle center bg-main1 # Python and R together ## `install.packages("reticulate")`  --- background-image:url("sc1/python1.png") background-size:contain --- background-image:url("sc1/python2.png") background-size:contain --- background-image:url("sc1/python3.png") background-size:contain --- class: middle center bg-main1 # Parameterized R Markdown <span><i class="fas fa-cogs fa-5x faa-spin animated "></i></span> --- background-image:url("sc1/param1.png") background-size:contain --- background-image:url("sc1/param2.png") background-size:contain --- background-image:url("sc1/param3.png") background-size:contain --- background-image:url("sc1/param4.png") background-size:contain --- background-image:url("sc1/param5.png") background-size:contain --- background-image:url("sc1/param6.png") background-size:contain --- background-image:url("sc1/param7.png") background-size:contain --- background-image:url("sc1/param8.png") background-size:contain --- background-image:url("sc1/param8-2.png") background-size:contain --- background-image:url("sc1/param9.png") background-size:contain --- background-image:url("screenshots/bookdown.png") background-size:contain --- background-image:url("screenshots/posterdown2.png") background-size:contain --- background-image:url("screenshots/powerpoint.png") background-size:contain --- background-image:url("screenshots/vitae.png") background-size:contain --- class: middle center bg-main1 # Acknowledgements: ## Yihui Xie, RStudio ## Emi Tanaka, Monash University, Australia ## All contributors --- class: middle center bg-main1 # Thank you <span><i class="fab fa-angellist fa-5x faa-shake animated "></i></span> ## <span class=" faa-flash animated " style=" display: -moz-inline-stack; display: inline-block; transform: rotate(0deg);">Make some VOICE using R Makrkdown!</span> Slides are available at [https://hellormd.netlify.app/](https://hellormd.netlify.app/) <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>.