inst/referenceData/requiredColumns.R

In nextpagesoft/hivEstimatesAccuracyReloaded: Improves Accuracy of HIV Estimates in EU/EEA Countries

list(
  RecordId = list(
    desciption = 'Unique identifier for each record within and across the national surveillance system',
    type = 'character',
    defaultValue = NA_character_
  ),
  ReportingCountry = list(
    description = 'The country reporting the record',
    type = 'character',
    values = union('UNK', countryData$Code),
    defaultValue = NA_character_
  ),
  Age = list(
    description = 'Exact age at diagnosis of HIV. Age as a crude number is preferred',
    type = 'numeric',
    defaultValue = NA_real_
  ),
  Gender = list(
    description = 'Gender',
    type = 'character',
    values = c('', 'UNK', 'F', 'M', 'O'),
    defaultValue = NA_character_
  ),
  Transmission = list(
    description = 'Describes the most probable route of Transmission',
    type = 'character',
    values = c('', 'UNK', 'HAEMO', 'HETERO', 'IDU', 'MSM', 'MTCT', 'NOSO', 'TRANSFU'),
    defaultValue = NA_character_
  ),
  FirstCD4Count = list(
    description = 'CD4 cell count at time of diagnosis',
    type = 'numeric',
    defaultValue = NA_real_
  ),
  FirstCD4DateYear = list(
    description = 'Year of first CD4 cell count at time of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  FirstCD4DateQuarter = list(
    description = 'Quarter of first CD4 cell count at time of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  FirstCD4DateMonth = list(
    description = 'Month of first CD4 cell count at time of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  FirstCD4DateWeek = list(
    description = 'Week of first CD4 cell count at time of diagnosis',
    type = 'character',
    defaultValue = NA_character_
  ),
  FirstCD4DateDay = list(
    description = 'Day of first CD4 cell count at time of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfAIDSDiagnosisYear = list(
    description = 'Year of AIDS diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfAIDSDiagnosisQuarter = list(
    description = 'Quarter of AIDS diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfAIDSDiagnosisMonth = list(
    description = 'Month of AIDS diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfAIDSDiagnosisWeek = list(
    description = 'Week of AIDS diagnosis',
    type = 'character',
    defaultValue = NA_character_
  ),
  DateOfAIDSDiagnosisDay = list(
    description = 'Day of AIDS diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfDeathYear = list(
    description = 'Year of death',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfDiagnosisYear = list(
    description = 'Year of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_,
    restrictedValues = NA_integer_
  ),
  DateOfDiagnosisQuarter = list(
    description = 'Quarter of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfDiagnosisMonth = list(
    description = 'Month of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfDiagnosisWeek = list(
    description = 'Week of diagnosis',
    type = 'character',
    defaultValue = NA_character_
  ),
  DateOfDiagnosisDay = list(
    description = 'Day of diagnosis',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfNotificationYear = list(
    description = 'Year of notification',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  DateOfNotificationQuarter = list(
    description = 'Quarter of notification',
    type = 'integer',
    defaultValue = NA_integer_
  ),
  CountryOfBirth = list(
    description = 'Country of birth of patient',
    type = 'character',
    values = union(c('', 'UNK'), countryData$Code),
    defaultValue = NA_character_
  ),
  CountryOfNationality = list(
    description = 'Country of nationality of patient',
    type = 'character',
    values = union(c('', 'UNK'), countryData$Code),
    defaultValue = NA_character_
  ),
  RegionOfOrigin = list(
    description = 'Region of origin of patient.',
    type = 'character',
    values = c('', 'UNK', 'ABROAD', 'AUSTNZ', 'CAR', 'CENTEUR', 'EASTASIAPAC', 'EASTEUR', 'EUROPE',
               'LATAM', 'NORTHAFRMIDEAST', 'NORTHAM', 'REPCOUNTRY', 'SOUTHASIA', 'SUBAFR', 'WESTEUR'),
    defaultValue = NA_character_
  ),
  PlaceOfNotification = list(
    description = 'Place of notification',
    type = 'character',
    defaultValue = NA_character_
  ),
  PlaceOfResidence = list(
    description = 'Place of residence',
    type = 'character',
    defaultValue = NA_character_
  ),
  Outcome = list(
    description = 'Outcome of case',
    type = 'character',
    values = c('', 'UNK', 'A', 'D'),
    defaultValue = NA_character_
  )
)