Superseding R packages - lessons learned from transitioning to {epichains} from {bpmodels}

R package

James M. Azam


July 17, 2023

This was a lightning talk at a workshop at the RSLondonSouthEast2023 workshop held at the Imperial College London’s South Kensington Campus. The talk was entitled: “Superseding R packages - lessons learned from transitioning to {epichains} from {bpmodels}”. The workshop brought together stakeholders who work with or are interested in research software including Research Software Engineers (RSEs), researchers, academics and individuals in a variety of related roles.


Occasionally, R package developers might decide to supersede their packages with a new implementation to reflect their evolved thinking and experiences in package design. Examples include {ggplot2} and {reshape2}. In multiple contributor projects, this often comes with non-trivial decisions, including name changes, deprecations, and the preservation of git histories. These decisions are non-trivial, especially in epidemiology and public health where reproducibility is a key consideration. {bpmodels}, an R package for analyzing infectious disease data, is currently in the same situation. {bpmodels} was independently developed in 2019, but the Epiverse-TRACE Initiative, which aims to develop an interoperable ecosystem for outbreak analytics, now provides the capacity to maintain it. This involves a re-imagination of the package, including a name change to {epichains}, planned integration of existing and new functionalities, and object-oriented programming. This talk will highlight some conundrums faced during this process, which is ongoing, and provide the opportunity for mutual learning.

Talk slides



BibTeX citation:
@online{m. azam2023,
  author = {M. Azam, James},
  title = {Superseding {R} Packages - Lessons Learned from Transitioning
    to \{Epichains\} from \{Bpmodels\}},
  date = {2023-07-17},
  url = {},
  langid = {en}
For attribution, please cite this work as:
M. Azam, James. 2023. “Superseding R Packages - Lessons Learned from Transitioning to {Epichains} from {Bpmodels}.” July 17, 2023.