Dissemating citable, documented and quality assured model module libraries

ready4 supports tools to streamline the testing, description and distribution of computational model modules.

This below section renders a vignette article from the ready4pack library. You can use the following links to:

ready4pack is a toolkit for bundling collections of modules for computational health economic models authored with the ready4 framework as R packages that are:

  • Citable (with a Zenodo generated DOI and an algorithm generated CITATION file);
  • Community-minded (applying deprecation conventions supported by lifecycle);
  • Documented (applying a function self-documenting algorithm that extends sinew, deploying a GitHub pages hosted and pkgdown generated website and authoring PDF manuals stored in a GitHub Release via piggyback);
  • Internally consistent implementing automated checks to ensure consistency in naming conventions, etc;
  • Licensed (via a usethis generated GPL-3 license);
  • Quality assured (using continuous integration via GitHub actions and R-CMD-Check); and
  • Versioned (applying usethis version increments).

ready4pack extends ready4 framework tools for authoring module algorithms (ready4fun) and data structures (ready4class) and wraps functions from a number of third party R development workflow tools (such as devtools). ready4pack integrates these tools in a common workflow, while adding tools for authoring and documenting datasets to be shipped with model module R packages.

A combination of the ready4_pack_manifest class and author method are used to implement this workflow. This workflow has been used to author all public versions of the ready4 R packages available in the ready4 github repository.

Workflow

Manifest

The main class exported as part of ready4pack is readypack_manifest list based ready4 sub-module, that extends the ready4fun_manifest and ready4class_manifest sub-modules.

Typical usage

readypack_manifest sub-module is most efficiently created with the aid of the make_pt_ready4pack_manifest function and combines instances of the ready4fun_manifest and ready4class_constructor sub-modules.

x <- make_pt_ready4pack_manifest(ready4fun::ready4fun_manifest(),
                                 constructor_r3 = ready4class::ready4class_constructor()) %>%
  ready4pack_manifest()

The main method defined for readypack_manifest is author which extends the author method for ready4class_manifest to author a consistently documented R package.

## Not run
author(x)

Examples

Workflow example one

The program to author and document the ready4show package is relatively simple and authors:

Workflow example two

The program to author and document the youthvars package is a bit more complex as it includes syntax to create package datasets. In addition to the package datasets, the algorithm creates content corresponding to the previous example, specifically:

Future documentation

A more detailed guide to using ready4pack will be created in 2023.

Last modified February 2, 2024: more tidy-ups of model export (11ef896)