Using daedalus.data and daedalus

daedalus.data is a package to handle input data files to use in the DAEDALUS model. The idea behind the development of this package is to have the flexibility to * Update or otherwise modify the input data without needing to update the model package itself * Curate reference websites for the source data files and develop semi-automated workflows to maintain them up-to-date * Ensure compatibility of the input data with the working version of the daedalus model

This vignette demonstates how to use daedalus.data with the DAEDALUS model, as adapted from Haw et al. (2022) in R. The package provides data from Walker et al. (2020) on country demography, country workforce per economic sector, and social contacts between age groups in country_data. The package also provides data from Jarvis et al. (2024) on workplace contacts in economic sectors. Both datasets are accessed by internal functions to reduce the need for user input.

library(daedalus.data)
library(daedalus)

References

Haw, David J., Giovanni Forchini, Patrick Doohan, Paula Christen, Matteo Pianella, Robert Johnson, Sumali Bajaj, et al. 2022. “Optimizing Social and Economic Activity While Containing SARS-CoV-2 Transmission Using DAEDALUS.” Nature Computational Science 2 (4): 223–33. https://doi.org/10.1038/s43588-022-00233-0.

Jarvis, Christopher I., Pietro Coletti, Jantien A. Backer, James D. Munday, Christel Faes, Philippe Beutels, Christian L. Althaus, et al. 2024. “Social Contact Patterns Following the COVID-19 Pandemic: A Snapshot of Post-Pandemic Behaviour from the CoMix Study.” Epidemics 48 (September): 100778. https://doi.org/10.1016/j.epidem.2024.100778.

Walker, Patrick G. T., Charles Whittaker, Oliver J. Watson, Marc Baguelin, Peter Winskill, Arran Hamlet, Bimandra A. Djafaara, et al. 2020. “The Impact of COVID-19 and Strategies for Mitigation and Suppression in Low- and Middle-Income Countries.” Science 369 (6502): 413–22. https://doi.org/10.1126/science.abc0035.