A SIPS 2019 workshop on doing reproducible research with RMarkdown and Git

This workshop will be in room Maxima in the Engels Meeting and Conference Center Stationsplein 45, 3013 AK Rotterdam from 9:30 to 14:15 (with a break at 11:00-11:30 and 12:15-13:30) on July, 8, 2019.

This workshop will be hands-on and learn-by-doing and we will spend most of the time creating articles and slides using RMarkdown, and working with Git. I have some slides and notes, however.

• Workshop slides
• Introduction to Git
• In the workshop, one of the major aims will be to create an article like this from scratch
• And we’ll also try to make beamer slides like this and a papaja based manuscript likethis from scratch too

Anything else that is needed can be obtained by browsing through the GitHub repository or by downloading all of its content as a zip, or better yet, by cloning this repository.

git clone https://github.com/mark-andrews/sips2019.git

Preparing R/RStudio

You should have R and RStudio installed on your computer. It is not strictly necessary but it is best to have the latest version of both R and RStudio. You should also make sure your already installed R packages are up to date. In terms of the packages that you need for this workshop, which should ideally install before the workshop starts, the following (I think) covers everything. Unless otherwise stated, these packages are all on CRAN so be installed using the Install button in the Packages pane, or with install.packages.

• rmarkdown and knitr: These will probably be installed already.

• tinytex: If you have /installed and working on your machine, and have sucessfully got it working with rmarkdown and knitr, then you can skip this step. Otherwise, this is probably the single most important package for the workshop. It installs a subset of the /so that it can be used with rmarkdown and knitr. Although /is open-source and cross-platform software, installing and confguring it can be considerably more trouble than installing an R package. Therefore, tinytex is extremely welcome. Installing tinytex itself just takes a few seconds, but then you need to do tinytex::install_tinytex() to install and configure everything. That could take 10-20 minutes.

• tidyverse: This is a package of packages and installing tidyverse installs dozens of other packages like dplyr, tidyr, ggplot2, and so on.

• papaja: This must be installed from GitHub with devtools::install_github("crsh/papaja") (and so devtools must be installed first).

• cowplot: Just required for a few examples.

• kableExtra: Also, just required for a few examples.

• citr: A handy add-on to RStudio, but not vital.

Preparing Git

Git is available on macOS, Windows, Linux.

• For macOS, I believe git is pre-installed. For any Mac I’ve used, thus was the case, and it also says so here, but I could be wrong. In any case, there are many ways to install it on macOS. I’m not sure which is the best or easiest, but this advice looks good.

• For Windows, you want to use Git Bash. Install it from here. Here’s a helpful video.

• For Linux users, if you don’t have it already, you’ll need to do sudo apt-get install git or sudo pacman -S git, or some such. You know the drill.

Create a GitHub account

If you haven’t done so already, create a GitHub account. There’s no fee. That’s only if you want private repositories, etc.

GitHub resources

Further resources for this training course can be found on Github at mark-andrews/sips2019.