Davis R Users Group

Discussion: software engineering practices in R

Wed, 12 Oct 2022 00:00:00 +0000

We discussed the value of and our experience with software engineering methods in R

The discussion was guided by our reading of a paper in The R Journal:

Software Engineering and R Programming: A Call for Research

As a group, we agreed that we are R users more than R developers. A few of us have written packages before, but we all recognize that we do the bad practices listed in the paper, like copying functions, naming files like xxx-analysis-final2.R, and commenting out blocks of code but never going back to clean them up, and making comments like #TODO: fix me.

Several folks are new to writing package documentation, and almost none of us have used unit tests. Nobody in the group has adopted a software development paradigm (Kanban, Extreme Programming, etc.) for their development process.

There was some debate over whether it is worth adopting best practices for code that is meant for our own personal use. We are going to make a series of this, reading the followup commentaries (there are four comments), and covering topics from the paper in our upcoming mini-workshops.

Liza Wood: Package creation using roxygen2

Wed, 05 Oct 2022 00:00:00 +0000

Liza shows us how to create an R package and write its documentation using Roxygen2

Live Code from presentation as separate script

Liza’s script shows how to make an R package for your favorite function(s) and distribute it via Github. The process, in brief:

Use the devtools package to create a blank project directory from a template.
Put each function into a script in the R folder of the project directory.
Decorate each function script with roxygen2-style documentation.
Run the devtools::document() function to generate the package documentation.
Fill in the template DESCRIPTION file
Create a Github repository and push the package to it.

Now anyone can load your package directly from Github and use the R functions you’ve created!

Liza Wood: Writing functions and iteration

Thu, 29 Sep 2022 00:00:00 +0000

Liza showed us her system of developing functions and using them with iteration to get more done with fewer lines of code.

Live Code from presentation as separate script

Taylor Reiter: Intro to ggplot2

Thu, 20 Feb 2020 12:00:00 +0000

Taylor continued an introductory ggplot lesson, going through titling plots, adding labels, and using plotly to make interactive plots.

Live Code from presentation as separate script

Link to the YouTube lesson recording

Taylor Reiter: Intro to ggplot2

Thu, 06 Feb 2020 12:00:00 +0000

Taylor gave us an introduction to ggplot, showing us the basic syntax of ggplot, how to modify plot elements like color or transparency, and how to try out different visualizations for your data.

Live Code from presentation as separate script

Link to the YouTube lesson recording