data2019nCoV: Data on the COVID-19 Outbreak

# Documentation of Data Objects

## World

#' European Centre for Disease Control cases and deaths data
#'
#' A dataset containing the data reported by the ECDC, as curated and released
#' by Our World in Data. This object is in wide format with ISO 3-letter country
#' code variable names.
#'
#' @format A data frame with a row for each date
#' @source \url{https://ourworldindata.org/coronavirus-source-data}
"sarscov2_ecdc_2019"

#' European Centre for Disease Control cases and deaths data
#'
#' A dataset containing the data reported by the ECDC, as curated and released
#' by Our World in Data. This object is in long format as presented by OWiD.
#'
#' @format A data frame with a row for each date
#' @source \url{https://ourworldindata.org/coronavirus-source-data}
"ECDC_owid"

#' SARS-CoV-2 World Health Organization Situation Reports 2019 Outbreak (COVID-19)
#'
#' These data are transcribed from the WHO Situation Reports on the COVID-19
#' outbreak (SARS-CoV-2). Data was not available for all variables in all 
#' reports. For full details, see the original Situation Reports as published 
#' by WHO. Data were manually transcribed and errors are possible.
#' 
#' @docType data
#' @format A data frame where each row represents a new Situation Report
#'
#' @rdname sarscov2_who_2019
#'
#' @author Data from World Health Organization (WHO), published as Sitation
#' Reports. Transfer to R and documentation by Eric Brown.
#'
#' @source World Health Organization (2020)
#'
#' @references
#'
#' World Health Organization. 2020. <https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports>
#'
#' @examples
#' ## show global cases
#' sarscov2_who_2019$cases_global
#'
"sarscov2_who_2019"

#' World Health Organization situation reports data
#'
#' A dataset containing the data reported in the WHO COVID-19
#' situation reports.
#'
#' @format A data frame with a row for each situation report
#' @source \url{https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports}
"WHO_SR"


## Ontario

#' Ontario Ministry of Health Coronavirus Cumulative Case Totals
#'
#' A dataset containing the data reported online by the Ontario Ministry of 
#' Health. For verification purposes, the data is retrieved from the Internet
#' Archive web archives, with the URL of the snapshot provided.
#'
#' @source \url{https://www.ontario.ca/page/2019-novel-coronavirus}
#' @docType data
#' @format A data frame where each row represents a reporting time
#'  \describe{
#'     \item{URL}{Internet Archive snapshot of URL for source data}
#'     \item{AsOf}{The results are updated to this date}
#'     \item{LastUpdated}{The date the data were reported on the webpage}
#'     \item{Negative}{Negative tests.}
#'     \item{UnderInvestigation}{Number of current pending tests.}
#'     \item{PresumptivePositive}{Awaiting confirmation at national laboratory.}
#'     \item{Deceased}{Confirmed deceased cases.}
#'     \item{ConfirmedPositive}{"Patient still testing positive and has not had two consecutive negative results greater than 24 hours apart"}
#'     \item{Cases}{"Number of confirmed cases reported to date in iPHIS by 34 Public Health Units, including resolved and deceased cases"}
#'     \item{Resolved}{"Patient is no longer infectious based on two consecutive negative tests performed"}
#'     \item{TotalTested}{"Total number of patients approved for COVID-19 testing to date"}
#'     \item{TotalTests}{"Total number of tests completed by the COVID-19 Clinical Lab network"}
#'     \item{PreviousDayTests}{"Total number of tests completed in the previous day"}
#'     \item{Male}{"Male cases"}
#'     \item{Female}{"Female cases"}
#'     \item{X19andunder}{"Cases age 19 and under"} 
#'     \item{X20to64}{"Cases age 20 to 64"}
#'     \item{X65andover}{"Cases age 65 and over"}
#'     \item{X20to39}{"Cases age 20 to 39"}
#'     \item{X40to59}{"Cases age 40 to 59"}
#'     \item{X60to79}{"Cases age 60 to 79"}
#'     \item{X80andover}{"Cases age 80 and over"}
#'     \item{Hospitalized}{"Cases currently hospitalized"}
#'     \item{ICU}{"Cases currently in ICU"}
#'     \item{Ventilator}{"Cases currently in ICU and on ventilator"}
#'  }
"ON_cumulative"

#' Ontario Ministry of Health Epidemiologic Summaries (PDF reports)
#'
#' A dataset containing the data reported online by the Ontario Ministry of 
#' Health in its Epidemiologic Summary reports.
#'
#' @source \url{https://www.ontario.ca/page/2019-novel-coronavirus}
#' @docType data
#' @format A data frame where each row represents a report
"ON_mohreports"

#' Ontario Ministry of Health Status of COVID-19 cases in Ontario
#'
#' A dataset containing the data reported online by the Ontario Ministry of 
#' Health in its .csv file covidtesting.csv. Variable definitions from the
#' Ministry's provided data dictionary (covidtesting_data_dictionary.xlsx).
#'
#' @source \url{https://data.ontario.ca/dataset/status-of-covid-19-cases-in-ontario}
#' @docType data
#' @format A data frame where each row represents a date's data
#'  \describe{
#'     \item{date}{Reporting date of Ontario COVID-19 daily summary}
#'     \item{negative}{Patients tested negative based on testing performed at both Public Health Ontario (PHO) Laboratory and National Microbiology Lab (NML)}
#'     \item{negative_presumptive}{Patients tested negative at Public Health Ontario (PHO) Laboratory, but not yet tested by National Microbiology Lab (NML)}
#'     \item{positive}{Number of active confirmed positive COVID-19 cases in Ontario as measured on "Reported Date"}
#'     \item{positive_presumptive}{Patients tested positive at Public Health Ontario (PHO)  Laboratory, but not yet tested by National Microbiology Lab (NML)}
#'     \item{resolved}{Cumulative number of resolved cases as measured on "Reported Date"}
#'     \item{deaths}{Cumulative number of fatalities of people with COVID-19 as measured on "Reported Date"}
#'     \item{cases}{Cumulative number of confirmed cases reported to date in the Integrated Public Health Information System (iPHIS) by Ontario’s 34 Public Health Units (PHUs), including resolved and deceased cases as measured on "Reported Date"}
#'     \item{tested_patients}{Cumulative number of tests submitted to the COVID-19 Clinical Lab network (including PHO, hospital, academic and community laboratories) as measured on "Reported Date"}
#'     \item{tests_last_day}{Number of tests processed and completed during the day before the "Reported Date" (the 24-hour period from 12:00 a.m. – 11:59 p.m.)}
#'     \item{current_investigation}{Number of tests pending results as measured on "Reported Date"}
#'     \item{current_hospitalized}{Number of patients currently hospitalized with COVID-19 as measured on "Reported Date"}
#'     \item{current_ICU}{Number of patients currently in an Intensive Care Unit (ICU) with COVID-19 as measured on "Reported Date"}
#'     \item{current_ventilator}{Number of patients currently in an Intensive Care Unit (ICU), on a ventilator with COVID-19 as measured on "Reported Date"}
#'     \item{deaths_ltc_hcw}{"Cumulative deaths of Long Term Care home health care workers (HCW) as measured on "Reported Date""}
#'	   \item{deaths_ltc_residents}{"Cumulative number of resident deaths in Long Term Care homes as measured on "Reported Date"."} = Total.LTC.Resident.Deaths,
#'     \item{cases_ltc_hcw}{"Cumulative COVID-19 positive cases among Long Term Care home health care workers (HCW) as measured on "Reported Date"."}
#'     \item{cases_ltc_residents}{"Cumulative COVID-19 positive cases among residents of Long Term Care homes as measured on "Reported Date"."}
#'  }
"ON_status"

#' Ontario Ministry of Health Status of COVID-19 cases in Ontario
#'
#' A dataset containing the data reported online by the Ontario Ministry of 
#' Health in its .csv file conposcovidloc.csv. Variable definitions from the
#' Ministry's provided data dictionary (conposcovidloc_data_dictionary.xlsx).
#'
#' @source \url{https://data.ontario.ca/dataset/confirmed-positive-cases-of-covid-19-in-ontario}
#' @docType data
#' @format A data frame where each row confirmed case
#'  \describe{
#'     \item{id}{Identifier for each individual row/record within the dataset}
#'     \item{date}{A number of dates entered in the Integrated Public Health Information System (iPHIS) to provide an approximation of onset date}
#'     \item{age_group}{Age group of the patient}
#'     \item{gender}{Gender information of the patient}
#'     \item{exposure}{Suspected method of exposure to COVID-19, if known}
#'     \item{outcome}{Patient outcome}
#'     \item{phu}{Public Health Unit (PHU) where confirmed positive case occurred}
#'     \item{phu_address}{Official physical street address of Public Health Unit (PHU)}
#'     \item{phu_city}{Official city of Public Health Unit (PHU)}
#'     \item{phu_pc}{Official postal code of Public Health Unit (PHU)}
#'     \item{phu_website}{Official website of Public Health Unit (PHU)}
#'     \item{phu_lat}{Latitude of Public Health Unit (PHU) physical address for mapping purposes}
#'     \item{phu_long}{Longitude of Public Health Unit (PHU) physical address for mapping purposes}
#'     \item{Outbreak_Related}{"Cases related to a declared outbreak."}
#'     \item{date_case}{"The date that the case was reported to the local public health unit (PHU)."}
#'     \item{date_specimen}{"Set to the earliest specimen date on record for the case, as indicated on the laboratory slip."}
#'     \item{date_test}{"The test reported date as indicated on the laboratory slip."}
#'  }
"ON_linelist"


## Canada

#' Canada Public Health Coronavirus Cumulative Case Totals
#'
#' A dataset containing the data reported online by the Canadian government.
#' For verification purposes, the data is retrieved from the Internet
#' Archive web archives, with the URL of the snapshot provided.
#'
#' @source \url{https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection.html}
#' @docType data
#' @format A data frame where each row represents a reporting time
#'  \describe{
#'     \item{url}{Internet Archive snapshot of URL for source data}
#'     \item{date}{The date the of the data reported on the webpage}
#'     \item{bc_confirmed}{Confirmed cases in British Columbia}
#'     \item{bc_probable}{Probable cases in British Columbia}
#'     \item{bc_deaths}{Deaths in British Columbia}
#'     \item{ab_confirmed}{Confirmed cases in Alberta}
#'     \item{ab_probable}{Probable cases in Alberta}
#'     \item{ab_deaths}{Deaths in Alberta}
#'     \item{sk_confirmed}{Confirmed cases in Saskatchewan}
#'     \item{sk_probable}{Probable cases in Saskatchewan}
#'     \item{sk_deaths}{Deaths in Saskatchewan}
#'     \item{mb_confirmed}{Confirmed cases in Manitoba}
#'     \item{mb_probable}{Probable cases in Manitoba}
#'     \item{mb_deaths}{Deaths in Manitoba}
#'     \item{on_confirmed}{Confirmed cases in Ontario}
#'     \item{on_probable}{Probable cases in Ontario}
#'     \item{on_deaths}{Deaths in Ontario}
#'     \item{qc_confirmed}{Confirmed cases in Quebec}
#'     \item{qc_probable}{Probable cases in Quebec}
#'     \item{qc_deaths}{Deaths in Quebec}
#'     \item{nl_confirmed}{Confirmed cases in Newfoundland and Labrador}
#'     \item{nl_probable}{Probable cases in Newfoundland and Labrador}
#'     \item{nl_deaths}{Deaths in Newfoundland and Labrador}
#'     \item{nb_confirmed}{Confirmed cases in New Brunswick}
#'     \item{nb_probable}{Probable cases in New Brunswick}
#'     \item{nb_deaths}{Deaths in New Brunswick}
#'     \item{ns_confirmed}{Confirmed cases in Nova Scotia}
#'     \item{ns_probable}{Probable cases in Nova Scotia}
#'     \item{ns_deaths}{Deaths in Nova Scotia}
#'     \item{pe_confirmed}{Confirmed cases in Prince Edward Island}
#'     \item{pe_probable}{Probable cases in Prince Edward Island}
#'     \item{pe_deaths}{Deaths in Prince Edward Island}
#'     \item{yt_confirmed}{Confirmed cases in Yukon}
#'     \item{yt_probable}{Probable cases in Yukon}
#'     \item{yt_deaths}{Deaths in Yukon}
#'     \item{nt_confirmed}{Confirmed cases in Northwest Territories}
#'     \item{nt_probable}{Probable cases in Northwest Territories}
#'     \item{nt_deaths}{Deaths in Northwest Territories}
#'     \item{nu_confirmed}{Confirmed cases in Nunavut}
#'     \item{nu_probable}{Probable cases in Nunavut}
#'     \item{nu_deaths}{Deaths in Nunavut}
#'     \item{repatriated_confirmed}{Confirmed repatriated cases}
#'     \item{repatriated_probable}{Probable repatriated cases}
#'     \item{repatriated_deaths}{Deaths among repatriated cases}
#'     \item{total_confirmed}{Total confirmed cases}
#'     \item{total_probable}{Total probable cases}
#'     \item{total_deaths}{Total deaths}
#'     \item{proportion_female}{Proportion of cases that are female}
#'     \item{proportion_40plus}{Proportion of cases aged 40 and over}
#'     \item{proportion_60plus}{Proportion of cases aged 60 and over}
#'     \item{proportion_hospitalized}{Proportion of cases that are in hospital}
#'     \item{proportion_travellers}{Proportion of cases that are trevellers}
#'     \item{proportion_contactoftravellers}{Proportion of cases that are close contacts of travellers}
#'  }
"CAN_cumulative"

#' Canada Public Health Coronavirus Cumulative Case Totals
#'
#' A dataset containing the data reported online by the Canadian government,
#' which is published as a .csv file, titled covid19.csv. The data is
#' transformed into wide format.
#'
#' @source \url{https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection.html}
#' @docType data
#' @format A data frame where each row represents a reporting date
"CAN_govcsv"