R Packages are the most accessible way of extending the R language.
A data package is an R package that primarily provides data rather than code.
Adding data to a package is as easy as putting data into the data directory of a package’s source. Doing simply that however fails to inform users how those data were created, a critical component of reproducible research and information transparency.
DPR2 - DataPackageR 2 - is designed to make data packages that are reproducible and transparent, and a new implementation of the concepts and workflows found in the R package .
DPR2 offers:
- source data and processing script storage
- data object and vignette rendering
- data object documentation
The entire process from initializing a new data package, to processing data, to building the data package for sharing has been wrapped in convenient functions with a streamlined workflow.
Working as a team with data processing isolation
DPR2 lets data packages be worked on by teams developing different datasets at the same time using git branching.
Data processing scripts, which are stored in the package source, are built by running each script in its own R process by default, a good practice when making reproducible data. If desired, a shared processing environment can be used when configured in the DPR2 yaml configuration file.
Data versioning
DPR2 presents a data digest, an object that tracks the md5 checksums of the data being generated and shared.
When using git with DPR2, DPR2 offers functions that allow users to recall data objects from the git history. This allows users to easily compare datasets that may have changed throughout the data package development process.
Data documentation
Users can access a help file for data objects using the help operator ? on the object name, e.g. ?mtcars.
Like DataPackageR, DPR2 offers a convenient way to generate the necessary files for making data documentation that can be accessed using the help operator after the package is built.
Installation
You can install the development version of DPR2 from GitHub with:
# install.packages("remotes")
remotes::install_github("FredHutch/DPR2")Examples
For a full explanation of the DPR2 workflow, see the package vignettes.
Create a data package
Create a new empty data package with then package name “MyAnalysis”:
DPR2::dpr_create(desc = dpr_description_init(Package = "MyAnalysis"))Create a new data package in the current working directory using the directory name as the package name:
DPR2::dpr_init()