To cite EpiStrainDynamics in publications please cite both the R package and the research publication:

Windecker S, McCaw J, Shearer F, Eales O (2025). Infer temporal trends of multiple pathogens. R package, https://github.com/ropensci/EpiStrainDynamics.

Eales O, Windecker S, McCaw J, Shearer F (2025). “Inferring temporal trends of multiple pathogens, variants, subtypes or serotypes from routine surveillance data.” American Journal of Epidemiology, kwaf119. doi:10.1093/aje/kwaf119.

Corresponding BibTeX entries:

  @Manual{EpiStrainDynamics,
    title = {Infer temporal trends of multiple pathogens},
    author = {Saras Windecker and James McCaw and Freya Shearer and
      Oliver Eales},
    note = {R package},
    year = {2025},
    url = {https://github.com/ropensci/EpiStrainDynamics},
  }

  @Article{EpiStrainDynamicspaper,
    title = {Inferring temporal trends of multiple pathogens, variants,
      subtypes or serotypes from routine surveillance data},
    author = {Oliver Eales and Saras Windecker and James McCaw and
      Freya Shearer},
    journal = {American Journal of Epidemiology},
    year = {2025},
    pages = {kwaf119},
    month = {06},
    doi = {10.1093/aje/kwaf119},
  }