From Scripts to Pipelines with Targets by Irena Papst
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Abstract: Do you ever find yourself starting with a simple analysis script only to end up wrangling a thousand line behemoth? Are you sick of wasting time re-running long scripts from start to finish, just to make sure everything is up-to-date? Are you haphazardly saving objects to file because they take a long time to generate? There’s got to be a better way! Enter targets, an R package used to build reproducible, efficient, and scalable pipelines. In this talk, I’ll introduce the targets package and share how I’ve used it to streamline my work modelling infectious disease spread at the Public Health Agency of Canada.
Bio: Irena is an applied mathematician and infectious disease modeller at the Public Health Agency of Canada (PHAC). She feels strongly about open source software and reproducible research, and she’s always on the hunt for tools, ideas, and workflows that will help her work smarter instead of harder. Irena has been using R for over a decade and has contributed to the macpan2 package, which is used to work with compartmental epidemic models, and the ern package, which is used to estimate the effective reproduction number of an infectious disease in real-time. Before joining PHAC, Irena was a postdoctoral fellow at McMaster University, where she used R Markdown to generate blog posts, like this and this, describing her research group’s COVID-19 forecasts to the public. Thanks to the 2022 R Gov conference, she is a Quarto convert. She also loves Github.
Twitter: https://twitter.com/irenapapst
Presented at the 2023 Government & Public Sector R Conference (October 19, 2023)