R/data.R

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

#' Delay between date of onset of symptoms of COVID-19 and date of case confirmation in Hong Kong
#'
#' A dataset compiling the delay (in days) between symptom onset and case report
#' for close to 3'000 individual cases.
#' This dataset is truncated in time latest and spans from January 2020 to July 2020.
#' This data was aggregated from the publicly-available linelist data for the COVID-19 epidemic in Hong Kong.
#' The linelist data is published by the Centre for Health Protection in Hong Kong.
#'
#' @format A data frame with 2,948 rows and 2 variables:
#' \describe{
#'   \item{event_date}{date of symptom onset in YYYY-mm-dd format}
#'   \item{report_delay}{number of days between symptom onset and case report}
#' }
#' @source \url{https://www.chp.gov.hk}
"HK_delay_data"


#' Incidence data for COVID-19 in Hong Kong
#'
#' A dataset containing aggregated incidence data for Hong Kong from January 2020 to July 2021.
#' This data was  put together by aggregating the publicly-available linelist data for SARS-CoV-2 in Hong Kong.
#' The linelist data is published by the Centre for Health Protection in Hong Kong.
#'
#' @format A data frame with 196 rows and 4 variables:
#' \describe{
#'   \item{date}{date of case reporting in YYYY-mm-dd format}
#'   \item{case_incidence}{total number of case confirmations
#'   reported on this date}
#'   \item{onset_incidence}{number of events of onset of symptoms
#'   occurring on this date}
#'   \item{report_incidence}{number of case confirmations reported on this date
#'   with no known date of onset of symptoms (or asymptomatoc cases)}
#' }
#' @source \url{https://www.chp.gov.hk}
"HK_incidence_data"

#' Incidence data for COVID-19 in Estonia
#'
#' A dataset containing aggregated incidence data for Estonia from February 2020 to May 2021.
#' The linelist data is published by the Estonian public health authorities.
#'
#' @format A data frame with 460 rows and 2 variables:
#' \describe{
#'   \item{date}{date of case reporting in YYYY-mm-dd format}
#'   \item{case_incidence}{number of cases reported on this date}
#' }
#' @source \url{https://opendata.digilugu.ee/opendata_covid19_tests_total.csv}
"EST_incidence_data"

#' Synthetic linelist of COVID-19 patients
#'
#' A synthetic dataset containing a simulated linelist of Swiss COVID-19 patients from February to June 2020.
#' The incidence that can be derived from aggregating this synthetic linelist
#' corresponds to or closely matches the
#' incidence numbers reported for Switzerland by the Federal Office of Public Health.
#'
#' In this simulated dataset, each row refers to a particular patient.
#' The 'confirmation_date' column refers to the date at which a positive COVID-19 test is reported.
#' For each patient, with a probability < 1, a date of onset of symptoms was drawn from a probability distribution.
#' Otherwise, the date of onset of symptoms was left as NA.
#'
#' @format A data frame with 31'950 rows and 2 columns:
#' \describe{
#'   \item{confirmation_date}{date of case confirmation in YYYY-mm-dd format}
#'   \item{symptom_onset_date}{If simulated, date of onset of symptoms in YYYY-mm-dd format}
#' }
"CH_simulated_linelist"