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Introduction to rmarkdown

This is a 1h-1h30 workshop given at UCSB (Eco-Data-Science Group and Center for Scientific Computing (CSC))

There are 2 main documents:

Preparing the workshop

Required software

We will primarily be using a web browser, R, RStudio. Please be sure these are all installed on your laptop, as follows:

  • R: We will use the lastest R version, which you can download and install from CRAN

  • RStudio: RStudio is an excellent front-end (IDE) for R with integrated graphics and coding tools and is recommended (read: required) for this course. It is free and available for both Windows, Mac OS X and Linux. To download RStudio, visit RStudio's download page. If you don't know how up to date your version of RStudio is, please download a recent version and install it

  • R packages: Please be sure you have installed or updated the following packages:

    • remotes (not needed, if you have devtools already installed)
    • knitr
    • rmarkdown
    • bookdown
    • DT
    • tidyverse
    • leaflet
    • captioner

There are several ways to install a R package:

  • In the R console, type: install.packages("package-name") Note that R is case sensitive, and that the package name should be in quotes.

  • In RStudio, click on the "Packages" tab in the bottom right quadrant of the interface, click Install, type the package name and click Istall or click Tools => Install Packages, type the package name and click Install

  • In R for Windows clients, go to the Packages menu => Install package(s).

  • In R for MacOS X clients, go to the Package & Data menu and click on Package Installer => CRAN (binaries) => Get list. Click on the box “install dependencies” in order to automatically install other necessary libraries while installing your R libraries.

In our case, you could type at the R console:

workshop_pkg <- c("remotes", "knitr", "rmarkdown", "bookdown", "DT", "tidyverse", "leaflet", "captioner")
install.packages(workshop_pkg)

PDF rendering

If you want to generate PDF output from Markdown (we will mainly focus on html files), you will need to install LaTeX. For R Markdown users who have not installed LaTeX before, we recommend to follow the recommendations of [Xie et al, 2018] and that you install TinyTeX (https://yihui.name/tinytex/):

install.packages("tinytex")
tinytex::install_tinytex()  # install TinyTeX