R/data.R

In ImperialCollegeLondon/epidemia: Modeling of Epidemics using Hierarchical Bayesian Models

#' Covid-19 data for European countries
#' 
#' Contains a dataframe with recorded daily deaths from Covid-19 in 11 European countries up until 05/05/2020.
#' The dataframe includes variables representing different non-pharmaceutical interventions implemented by the 
#' countries considered. The data matches that used in \insertCite{Flaxman2020;textual}{epidemia}. Also 
#' includes empirical distributions for the serial interval and the time from infection to death.
#' 
#' @format A named list. The fields are:
#' \describe{
#'  \item{data}{A data frame giving indicators of certain non-pharmaceutical interventions in each country, along with death data and populations.
#'  The earliest date for each country in the dataframe is exactly 30 days before 10 cumulative deaths were observed in the country.}
#'  \item{inf2death}{A numeric vector representing the time distribution from infection to death assumed in \insertCite{Flaxman2020;textual}{epidemia}.}
#'  \item{si}{The serial interval of covid-19 assumed in \insertCite{Flaxman2020;textual}{epidemia}.}
#' }
#' @references
#' \insertAllCited{}
"EuropeCovid"



#' Covid-19 data for European countries
#' 
#' Similar to `EuropeCovid`, with the following exceptions. Daily death data is obtained from the WHO COVID-19 Explorer as of 05/01/2021. This differs 
#' from the data used in \insertCite{Flaxman2020;textual}{epidemia}, because counts were updated retrospectively by the WHO as new information came 
#' to light. Daily case data is also included from the same source. This data runs from 03/01/2020 until 30/06/2020.
#' 
#' @format A named list. The fields are:
#' \describe{
#'  \item{data}{A data frame giving indicators of certain non-pharmaceutical interventions in each country, along with death data and populations.}
#'  \item{inf2death}{A numeric vector representing the time distribution from infection to death.}
#'  \item{si}{The serial interval of covid-19 assumed in \insertCite{Flaxman2020;textual}{epidemia}.}
#' }
#' @references
#' \insertAllCited{}
"EuropeCovid2"


#' Covid-19 Case Counts for England
#' 
#' Contains case counts of SARS-CoV-2 in England from 30/01/2020 until 30/05/2021. Case counts correspond to 
#' 'New Cases by Specimen Date', as defined by Public Health England. The data was downloaded from 
#' \insertCite{PHE;textual}{epidemia} on 01/06/2021. Case counts in the last few days of May may be 
#' underreported as not all cases have been counted as of the download date.
#'
#' @format A dataframe with three columns, `date`, `region` and `cases`. Each row gives case counts for a given date in England.
#' 
#' @references
#' \insertAllCited{}
"EnglandNewCases"