R/data-davies-age-extended.R

In njtierney/conmat: Builds Contact Matrices using GAMs and Population Data

#' Susceptibility and clinical fraction parameters from Davies et al.
#'
#' A dataset containing data from  \url{https://www.nature.com/articles/s41591-020-0962-9#code-availability}
#' When using this data, ensure that you cite the original authors at:
#'
#' "Davies, N.G., Klepac, P., Liu, Y. et al. Age-dependent effects in the transmission and control of COVID-19 epidemics. Nat Med 26, 1205–1211 (2020). https://doi.org/10.1038/s41591-020-0962-9"
#'
#' @format A data frame of the probability of transmission from a case to a contact. There are 101 rows and 4 variables.
#' \describe{
#'   \item{age}{from 0 to 100}
#'   \item{clinical_fraction}{Estimate of fraction with clinical symptoms, or the age-specific proportion of infections resulting in clinical symptoms inferred by applying a smoothing spline to the mean estimates from Davies et al. }
#'   \item{davies_original}{Age specific parameters of the relative susceptibility to
#'     infection inferred from a smoothing-spline estimate of the mean relative susceptibility estimate from Davies et al.}
#'   \item{davies_updated}{Re-estimated parameter of the susceptibility profile for under-16s that is estimated in a similar way but to the age-distribution of infections in England from the UK ONS prevalence survey rather than case counts which may undercount children}
#' }
"davies_age_extended"