Quickly setup ‘SpaDES’ project directories, get modules, and deal with a number of issues related to reproducibility and reusabililty. This package was designed with a PERFICT approach in mind (See McIntire et al. 2022).
Achieving PERFICT in your projects can be challenging, but it becomes more accessible with the use of SpaDES
. The SpaDES.project
tool is designed to streamline the setup of SpaDES
projects. Complementing the R
scripting language, there are three valuable tools at your disposal:
SpaDES
supports version control through platforms like GitHub, giving you control over project history and collaboration.Our preferred toolset includes Posit (specifically, RStudio
), SpaDES
, and GitHub. While these are our recommendations, there are alternative options available. We acknowledge that not all users are familiar with Git, and that’s perfectly acceptable. SpaDES.project
has been designed to cater to all users, whether they choose to use a Git-controlled project or not.
Beyond these tools, our extensive experience in managing projects with diverse developers, operating systems, users, data sources, and packages has revealed various challenges. These challenges arise due to the nature of open, modular, and interoperable projects. As project complexity increases, typical reproducible workflows may falter. Issues include:
.Rprofile
files..GlobalEnv
, leading to undetected issues.Given these complexities, it’s not enough to create a “reproducible” script; it must be a “reusable” script that functions flawlessly on any machine, operating system, and for any user.
Users can certainly attempt to address these issues individually, but we’ve developed SpaDES.project
as a solution. It’s derived from our most intricate projects to date, yet it’s designed with beginners in mind. We’ve anticipated these challenges so that users won’t encounter them unexpectedly during their project journeys.
See this package readme and vignettes to get started.
Website: https://SpaDES.PredictiveEcology.org
Wiki: https://github.com/PredictiveEcology/SpaDES/wiki
install.packages("SpaDES.project", repos = c("predictiveecology.r-universe.dev", getOption("repos")))
setupProject(paths = list(projectPath = tempdir()),
modules = c("PredictiveEcology/Biomass_borealDataPrep@development",
"PredictiveEcology/Biomass_core@development"))
Please see CONTRIBUTING.md for information on how to contribute to this project.