orderly

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.

orderly 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("orderly") describes the problem that orderly tries to solve (read on package website)
• vignette("introduction") describes orderly by example, walking through the basic features (read on package website)

There is also an orderly tutorial from a 3-hour interactive session.

Installation

Install orderly from CRAN with

install.packages("orderly")

To get the current development version, please install from our r-universe:

install.packages(
  "orderly",
  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/orderly", upgrade = FALSE)

History

This package is a ground-up rewrite of our original orderly version 1 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, though this version of the package is no longer available from CRAN.

A migration path for existing users is described in vignette("migrating").

The web framework OrderlyWeb has been rewritten as packit.

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

If you want to force validation of schemas during testing, set the R option orderly.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 orderly.schema_validate as FALSE to disable checking.

Licence

MIT © Imperial College of Science, Technology and Medicine