R/data.R

In bernadette-eu/Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics

#' Contact matrices per country
#'
#' A list of 16 by 16 contact matrices for 177 countries.
#' Row i of a column j of a contact matrix corresponds to the number of contacts
#' made by an individual in group i with an individual in group j.
#'
#' @format A list of 16 by 16 dataframes for 177 countries.
#'
#' @return A list object of 16 by 16 dataframes for 177 countries.
#'
#' @usage data(contact_matrices)
#'
#' @section References:
#' Prem, K., van Zandvoort, K., Klepac, P. et al (2020). Projecting contact matrices in 177 geographical regions: an update and comparison with empirical data for the COVID-19 era. medRxiv 2020.07.22.20159772; doi: https://doi.org/10.1101/2020.07.22.20159772
#'
"contact_matrices"

#' Age distribution of new reported deaths for Greece
#'
#' A dataset containing the age distribution of reported deaths in Greece from 2020-08-31 to 2021-03-28 (30 weeks).
#' The dataset has been extracted from the Hellenic National Public Health Organization database.
#'
#' @format A data frame with 210 rows and 8 variables:
#' \describe{
#'   \item{Index}{integer; a sequence of integer numbers from 1 to 210}
#'   \item{Right}{numeric; Index + 1}
#'   \item{Date}{Date, format; date in the format "2020-08-31"}
#'   \item{Week_ID}{numeric; index of the week that each day falls into. A week is assumed to have 7 days}
#'   \item{New_Deaths}{numeric; count of new total reported deaths on a given date}
#'   \item{0-39}{numeric; count of new reported deaths on a given date for the age group "0-39"}
#'   \item{40-64}{numeric; count of new reported deaths on a given date for the age group "40-64"}
#'   \item{65+}{numeric; count of new reported deaths on a given date for the age group "65+"}
#' }
#'
#' @return A data.frame object with 210 rows and 8 variables.
#'
#' @usage data(age_specific_mortality_counts)
#'
#' @section References:
#' Sandbird (2022). Daily regional statistics for covid19 cases in Greece.
#'
#' @source \url{https://github.com/Sandbird/covid19-Greece/}
#'
"age_specific_mortality_counts"

#' Age distribution of new reported infections for Greece
#'
#' A dataset containing the age distribution of new reported infections in Greece from 2020-08-31 to 2021-03-28 (30 weeks).
#' The dataset has been extracted from the Hellenic National Public Health Organization database.
#'
#' @format A data frame with 210 rows and 8 variables:
#' \describe{
#'   \item{Index}{integer; a sequence of integer numbers from 1 to 210}
#'   \item{Right}{numeric; Index + 1}
#'   \item{Date}{Date, format; date in the format "2020-08-31"}
#'   \item{Week_ID}{numeric; index of the week that each day falls into. A week is assumed to have 7 days}
#'   \item{Total_Cases}{numeric; count of total reported infections on a given date}
#'   \item{0-39}{numeric; count of reported infections on a given date for the age group "0-39"}
#'   \item{40-64}{numeric; count of reported infections on a given date for the age group "40-64"}
#'   \item{65+}{numeric; count of reported infections on a given date for the age group "65+"}
#' }
#'
#' @return A data.frame object with 210 rows and 8 variables.
#'
#' @usage data(age_specific_infection_counts)
#'
#' @section References:
#' Sandbird (2022). Daily regional statistics for covid19 cases in Greece.
#'
#' @source \url{https://github.com/Sandbird/covid19-Greece/}
#'
"age_specific_infection_counts"

#' Age distribution of cumulative reported infections for Greece
#'
#' A dataset containing the age distribution of cumulative reported infections in Greece from 2020-08-31 to 2021-03-28 (30 weeks).
#' The dataset has been extracted from the Hellenic National Public Health Organization database.
#'
#' @format A data frame with 210 rows and 5 variables:
#' \describe{
#'   \item{Date}{Date, format; date in the format "2020-08-31"}
#'   \item{Total_Cases}{numeric; count of total cumulative reported infections on a given date}
#'   \item{0-39}{numeric; count of cumulative reported infections on a given date for the age group "0-39"}
#'   \item{40-64}{numeric; count of cumulative reported infections on a given date for the age group "40-64"}
#'   \item{65+}{numeric; count of cumulative reported infections on a given date for the age group "65+"}
#' }
#'
#' @return A data.frame object with 210 rows and 5 variables.
#'
#' @usage data(age_specific_cusum_infection_counts)
#'
#' @section References:
#' Sandbird (2022). Daily regional statistics for covid19 cases in Greece.
#'
#' @source \url{https://github.com/Sandbird/covid19-Greece/}
#'
"age_specific_cusum_infection_counts"