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orderly2

  1. an attendant in a hospital responsible for the non-medical care of patients and the maintenance of order and cleanliness.
  2. 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

Get started

Two vignettes provide an overview of the package, depending on your tastes:

Roadmap

This package is a ground-up rewrite of our orderly package, which is now ready for use on new projects or by adventurous users of the original package.

Over the next few months orderly will be renamed orderly1, and we will finalise the API for this package. Once stable, we will rename it back from orderly2 to orderly and release to CRAN to replace the existing package. A migration path for existing users is described in vignette("migrating") and will be updated based on our experience migrating people.

The web framework OrderlyWeb is being rewritten in parallel (to packit) and we will provide a migration path here too.

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")

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_server

For all tests we also require development versions of gert and jsonvalidate. These can be installed from the rOpenSci r-universe, with:

install.packages(
  c("gert", "jsonvalidate"),
  repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))

Without these, some tests will be skipped, but the suite will still run.

Licence

MIT © Imperial College of Science, Technology and Medicine