R/test_cases_and_management.R

In ScottishCovidResponse/SCRCdata: Processing Scripts for the SCRC Data Pipeline

#' #' test_cases_and_management
#' #'
#' #' @param df dataframe
#' #'
#' test_cases_and_management <- function(df) {
#'   # Check column names match
#'   assertthat::assert_that(
#'     all(sort(unique(df$variable)) %in%
#'           c("Adult care homes - Adult care homes which submitted a return",
#'             "Adult care homes - Number of staff reported as absent",
#'             "Adult care homes - Response rate",
#'             "Adult care homes - Staff absence rate",
#'             "Adult care homes - Total number of staff in adult care homes which submitted a return",
#'             "Ambulance attendances - COVID-19 suspected",
#'             "Ambulance attendances - COVID-19 suspected patients taken to hospital",
#'             "Ambulance attendances - Total",
#'             "Calls - Coronavirus helpline",
#'             "Calls - NHS24 111",
#'             # "Care homes - Adult care homes - Number of homes with suspected cases",
#'             # "Care homes - Adult care homes - Proportion of homes with suspected cases",
#'             # "Care homes - All care homes - Residents - Weekly positive cases",
#'             "COVID-19 patients in hospital - Confirmed",
#'             # "COVID-19 patients in hospital - Confirmed - Length of stay 28 days or less",
#'             "COVID-19 patients in hospital - Confirmed (archived)",
#'             "COVID-19 patients in hospital - Suspected (archived)",
#'             "COVID-19 patients in hospital - Total (archived)",
#'             "COVID-19 patients in ICU - Confirmed",
#'             # "COVID-19 patients in ICU - Confirmed - Length of stay 28 days or less",
#'             # "COVID-19 patients in ICU - Confirmed - Length of stay more than 28 days",
#'             "COVID-19 patients in ICU - Confirmed (archived)",
#'             "COVID-19 patients in ICU - Suspected (archived)",
#'             "COVID-19 patients in ICU - Total (archived)",
#'             "Delayed discharges",
#'             "NHS workforce COVID-19 absences - All staff",
#'             "NHS workforce COVID-19 absences - Medical and dental staff",
#'             "NHS workforce COVID-19 absences - Nursing and midwifery staff",
#'             "NHS workforce COVID-19 absences - Other staff",
#'             "Number of COVID-19 confirmed deaths registered to date",
#'             # "Schools - Number of pupils absent due to COVID-19 related reasons",
#'             # "Schools - Percentage absence - Due to COVID-19 related reasons" ,
#'             # "Schools - Percentage absence - Not due to COVID-19 related reasons",
#'             # "Schools - Percentage attendance - All" ,
#'             # "Schools - Percentage attendance - Primary",
#'             # "Schools - Percentage attendance - Secondary",
#'             # "Schools - Percentage attendance - Special",
#'             "Testing - Cumulative people tested for COVID-19 - Negative",
#'             "Testing - Cumulative people tested for COVID-19 - Positive",
#'             "Testing - Cumulative people tested for COVID-19 - Total",
#'
#'             "Testing - New cases as percentage of people newly tested",
#'             "Testing - New cases reported",
#'             "Testing - People with first test results in last 7 days",
#'             "Testing - Positive cases reported in last 7 days",
#'             "Testing - Positive tests reported in last 7 days",
#'             "Testing - Test positivity (percent of tests that are positive)",
#'             "Testing - Test positivity rate in last 7 days",
#'             "Testing - Tests in last 7 days per 1000 population",
#'             "Testing - Tests reported in last 7 days",
#'             "Testing - Total daily number of positive tests reported",
#'             "Testing - Total daily tests reported",
#'             "Testing - Total number of COVID-19 tests reported by NHS Labs - Cumulative",
#'             "Testing - Total number of COVID-19 tests reported by NHS Labs - Daily",
#'             "Testing - Total number of COVID-19 tests reported by UK Gov testing programme - Cumulative",
#'             "Testing - Total number of COVID-19 tests reported by UK Gov testing programme - Daily"
#'             # "Vaccinations - By age group - Age 65 to 69 - Number vaccinated with first dose",
#'        #     "Vaccinations - By age group - Age 70 to 74 - Number vaccinated with first dose",
#'        #   "Vaccinations - By age group - Age 75 to 79 - Number vaccinated with first dose",
#'        #    "Vaccinations - By age group - Age 80 or over - Number vaccinated with first dose",
#'        #    "Vaccinations - By JCVI priority group - Care home residents - Number vaccinated with first dose",
#'        # "Vaccinations - By JCVI priority group - Care home residents - Number vaccinated with second dose",
#'        # "Vaccinations - By JCVI priority group - Care home staff - Number vaccinated with first dose",
#'        # "Vaccinations - By JCVI priority group - Clinically extremely vulnerable - Number vaccinated with first dose",
#'        # "Vaccinations - By JCVI priority group - Frontline health and social care workers - Number vaccinated with first dose",
#'        #   "Vaccinations - By JCVI priority group - Individuals aged 70 to 74 living in the community - Number vaccinated with first dose",
#'        #    "Vaccinations - By JCVI priority group - Individuals aged 75 to 79 living in the community - Number vaccinated with first dose",
#'        #   "Vaccinations - By JCVI priority group - Individuals aged 80 or over living in the community - Number vaccinated",
#'        #    "Vaccinations - Number of people who have received first dose",
#'        #   "Vaccinations - Number of people who have received second dose",
#'        #   "Vaccine supply - Total number of doses allocated",
#'        #   "Vaccine supply - Total number of doses delivered")
#'     ))
#' }