- an attendant in a hospital responsible for the non-medical care of patients and the maintenance of order and cleanliness.
- a soldier who carries orders or performs minor tasks for an officer.
orderly2 is a package designed to help make analysis more reproducible. Its principal aim is to automate a series of basic steps in the process of writing analyses, making it easy to:
- track all inputs into an analysis (packages, code, and data resources)
- store multiple versions of an analysis where it is repeated
- track outputs of an analysis
- create analyses that depend on the outputs of previous analyses
You can watch a short talk that describes the ideas in the package, and why it differs to other approaches to reproducibility and workflows.
Get started
Two vignettes provide an overview of the package, depending on your tastes:
-
vignette("orderly2")describes the problem thatorderly2tries to solve (read on package website) -
vignette("introduction")describesorderly2by example, walking through the basic features (read on package website)
There is also an orderly tutorial from a 3-hour interactive session.
Roadmap
This package is a ground-up rewrite of our original orderly package, which is now ready for use on all projects, including migrating projects created with the original package.
The original orderly package has now been renamed orderly1, and will be preserved and installable for use with historical projects without the need to migrate. We have stabilised the interface for orderly2 and will soon rename back to orderly and release on CRAN as version 2.0.x to replace the original version.
A migration path for existing users is described in vignette("migrating").
The web framework OrderlyWeb has been rewritten as packit.
Installation
Please install from our r-universe:
install.packages(
"orderly2",
repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))If you prefer, you can install from GitHub with remotes:
remotes::install_github("mrc-ide/orderly2", upgrade = FALSE)Testing
To run all tests, you need to have outpack_server available on your system path. One way to achieve this is to run
cargo install --git https://github.com/mrc-ide/outpack_serverIf you want to force validation of schemas during testing, set the R option outpack.schema_validate to TRUE. This will automatically be set on CI (as detected by the CI environment variable) and will be enabled if jsonvalidate is installed. Set the option outpack.schema_validate as FALSE to disable checking.