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>.

A BibTeX entry for LaTeX users is

  @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},
  }

  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
  <https://doi.org/10.1093/aje/kwaf119>.

A BibTeX entry for LaTeX users is

  @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},
  }