Mid/long term development plans for {epiparameter}

[joshwlambert]

{epiparameter} is approaching the release of v0.1.0 after a full package review (PR #151).

Currently the development of {epiparameter} is in isolation of other packages. In other words, the library of parameters is being expanded but not linked to other databases, at present, and the functions are being refined in order to prevent breaking changes in future. The utility of {epiparameter} for other Epiverse-TRACE packages is being improved in the lead up to the first release.

The current scope of the package is to have the package be both a library of epidemiological and a set of classes, methods and functions for working with epidemiological parameters.

In the mid-term, the package will evolve more into a set of functions and data structures (S3 classes) for working parameters and distributions. The library of epidemiological parameters will move to the WHO Collaboratory (https://github.com/WorldHealthOrganization/collaboratory-epiparameter-community & https://worldhealthorganization.github.io/collaboratory-epiparameter-community/#/README). Epiverse-TRACE is working in collaboration with the WHO to develop this more comprehensive and sustainable database of epidemiological parameters and will eventually read in data from this source.

There is also concurrent work on epidemiological parameter collection and extraction from Imperial MRC-IDE (https://github.com/mrc-ide/epireview) with we will collaborate with them to avoid duplication of effort and combine the development of user-friendly and interoperable tooling with data collation.

The long term plans for {epiparameter} are yet to be defined but it is highly unlikely it will move away the mid term plans stated above. The package will develop and from v1.0.0 will be backwards compatible to work across scripts and pipelines.

As always feedback and suggestions are welcomed. Please file as issue on the github repo to request features or report a bug, as well as make contributions to the code via pull requests (see https://epiverse-trace.github.io/epiparameter/CONTRIBUTING.html).

[joshwlambert]

Update on this issue in August 2024 since it was originally posted September 2023.

The overall aims for the {epiparameter} package have not changed. The package still provides a library of epidemiological parameters. However, there is little active expansion of the epidemiological parameter database (although this may change if deemed useful, and the request for diseases/pathogens in #237 that are outside the priority pathogen scope of the {epireview}). Given the reasons outlined above there is a move to link up with other R packages and data resources that will contain a more comprehensive and well-designed database of epiparameters. The development focus that led to v0.2.0 of {epiparameter} was to create better interoperability with the {epireview} package, via the as_epiparameter() (formerly as_epidist()) function. Currently, the GREP database hosted by the WHO Collaboratory is not live, but once it is active {epiparameter} will be developed to allow users to read in parameters from this source and use them within R.

Development is continuing on making the <epiparameter> class a core data structure for working with epidemiological parameters. S3 methods are continuing to be added where requested or considered useful by the development team.

[joshwlambert]

Update January 2025

{epiparameter} (v0.3.0) was initially submitted to CRAN in November 2024, but was rejected due to the dual licensing (MIT & CC0) of the package.

A package can only be licensed as a whole. It can have a single license or a set of alternative licenes. If the data have to be licensed differently then the code, you have to provide the data in a separate data package with the other license.

Therefore the data was split from the code and stored in the {epiparameterDB} which is now hosted on CRAN.

The {epiparameter} (v0.4.0) without the epidemiological parameter library is now solely licensed as MIT and submitted to CRAN.

We will explore additionally hosting the epidemiological parameter library online with access with an API. This should enable quicker updates to database and not require a CRAN submission with each update. We are balancing this development with the knowledge that WHO are continuing to develop the Global Repository of Epidemiological Parameters (GREP) which is planned to be live later this year.

The {epiparameter} package will continue to receive active development over the next few months to improve functionality and user experience.