OJ247 / intro-to-rmarkdown

An intro crash course for using R-markdown

Intro to R Markdown for Data Science

An intro crash course for using R-markdown!

Feel free to post your questions in this Google Document!

Presentation Slides:

• IntroRMarkdown_NIAID_32421_PPT.zip [PowerPoint]
• IntroRMarkdown_NIAID_32421_PDF.zip [PDF]

Recommended Handouts: GitHub's Markdown Cheatsheet | R-Studio's RMarkdown Cheatsheet

Installation:

Looking to the run examples on your own machine? First install R-studio and then the latest versions of the following packages:

• dplyr
• knitr
• rmarkdown
• flexdashboard
• reticulate
• plotly
• kableExtra
• leaflet
• mapview

The following packages require a followup command to install software. These might need admin rights on your machine to install correctly! webshot <-- Installs PhantomJS - only needed if not already installed on machine Then run in R: webshot::install_phantomjs()

tinytex <-- Installs LaTeX - only needed if not already installed on machine Then run in R: tinytex::install_tinytex()

On the R Studio Server - you can use the preinstalled packages by typing the following in the console:

old_path <- Sys.getenv("PATH") Sys.setenv(PATH = paste(old_path, "/biocompace/bin", sep = ":"))

If you want to install the packages in your own local machine/directory, install the packages with the following line (and then run the install_tinytex function above): install.packages(c("dplyr","knitr","rmarkdown","kableExtra","flexdashboard","reticulate","plotly","leaflet","mapview"))

Note: If installing on your own machine, it might be easier on your machine to install LaTeX using a different installer rather than via TinyTex. See this page for more info!