R/syndrome_provider_country.R

In cturbelin/ifnBase: InfluenzaNet Data Analysis Base

# # symptoms
# 'no.sympt'='Q1_0',
# 'fever'='Q1_1',
# 'chills'='Q1_2',
# 'rhino'='Q1_3',
# 'sneeze'='Q1_4',
# 'sorethroat'='Q1_5',
# 'cough'='Q1_6',
# 'dyspnea'='Q1_7',
# 'headache'='Q1_8',
# 'pain'='Q1_9',
  # 'chestpain'='Q1_10',
  # 'asthenia'='Q1_11',
  # 'anorexia'='Q1_12',
  # 'sputum'='Q1_13',
  # 'wateryeye'='Q1_14',
  # 'nausea'='Q1_15',
  # 'vomiting'='Q1_16',
  # 'diarrhea'='Q1_17',
  # 'abdopain'='Q1_18',
  # 'sympt.other'='Q1_19',


#' Syndrome Provider
#'
#' @export
SyndromeProviderCountry <- R6Class("SyndromeProviderCountry",inherit=SyndromeProvider ,
public = list(

    #' @field pain.age.limit Age to take into account of pain. Under this age pain=TRUE (disabled if NA)
    pain.age.limit = NULL,

    #' @field country Country code
    country = NULL,

    #' @field season Season number \code{\link{concepts}}
    season = NULL,

    #' @field use.fever.level Use fever level when definition request a fever level or only the fever=TRUE
    use.fever.level=NULL,

    #' @field unknown.has.fever if TRUE consider that unknown fever status is fever=TRUE
    unknown.has.fever=NULL,

    #' @field min.syndrome.count Minimum syndrom count to take into account when definition doesnt say it
    min.syndrome.count=NULL,

    #' @description
    #' Instanciate
    #' @param country country code
    #' @param season season number
    #' @param use.fever.level logical use fever level variable
    #' @param unknown.has.fever unknown fever has fever
    #' @param min.syndrome.count count of symptom to take into account for some definition
    #' @param pain.age.limit age under wich to exclude pain from definition
    initialize = function(country, season, use.fever.level=T, unknown.has.fever=T, min.syndrome.count=1, pain.age.limit=NA) {
      self$pain.age.limit = pain.age.limit
      self$country = country
      self$season = season
      self$use.fever.level=use.fever.level
      self$unknown.has.fever=unknown.has.fever
      self$min.syndrome.count=min.syndrome.count
    },

    #' @description
    #' Compute definitions for all syndromes
    #' @param weekly weekly data
    #' @param intake intake data with at least 'person_id', 'age' column
    compute = function(weekly, intake) {
      country = self$country

      # Count
      at_least = function(d, columns, n=1) {
        apply(d[, columns, drop=FALSE], 1, function(r) { sum(r) >= n})
      }

      sudden = self$is_sudden(weekly)

      if(self$use.fever.level) {
        has_fever_38 = weekly$fever & ifelse(is.na(weekly$highest.temp), self$unknown.has.fever, weekly$highest.temp >= 3)
        has_fever_39 = weekly$fever & ifelse(is.na(weekly$highest.temp), self$unknown.has.fever, weekly$highest.temp >= 4)
      } else {
        has_fever_38 = weekly$fever
        has_fever_39 = weekly$fever
      }

      if(!is.na(self$pain.age.limit)) {
        weekly = self$compute_age(weekly, intake)
        weekly$has_pain = ifelse( !is.na(weekly$age) & weekly$age <= self$pain.age.limit, TRUE, weekly$pain)
      } else {
        weekly$has_pain = weekly$pain
      }

      ili = NULL

      if(country == "ES") {
        # The present definition of ILI case is the one proposed by the European Union:
        #
        #   - sudden onset of symptoms
        # - at least one of the four general symptoms: fever, malaise, headache, myalgia
        # - at least one of the three respiratory symptoms: cough, sore throat, dispnea
        # - lack of other suspected symptoms

        ili = sudden &
          at_least(weekly, c('fever', 'asthenia', 'headache', 'has_pain'), n=1) &
          at_least(weekly, c('cough', 'sorethroat', 'dyspnea'), n=1)

      }

      if(country == "IE") {
        # Influenza-like illness is characterised by the sudden onset of symptoms with a temperature of 38°C or more,
        # in the absence of any other disease, with at least two of the following: dry cough, headache, sore muscles and a sore throat.
        ili = has_fever_38 & sudden & at_least(weekly, c('cough', 'sorethroat', 'headache', 'has_pain'), n=2)

      }

      if(country == "IT") {
        # Since 2014-2015 the case definition has been modified to adapt it to the one used by ECDC:
        #   - sudden onset
        # - at least one of these general symptoms: fever, malaise, headache, muscle pain
        # - at least one of these respiratory symptoms: cough, sore throat, heavy breath
        #
        # Before 2014-2015 the definition would include the measurement of the fever:
        #   - sudden onset
        # - fever above 38 °C with at least one of the general symptoms: headache, malaise, chills, asthenia and at
        # least one of these respiratory symptoms: cough, sore throat, nasal congestion
        if(self$season >= 2014) {
          ili = sudden &
            at_least(weekly, c('fever', 'asthenia', 'headache', 'has_pain')) &
            at_least(weekly, c('cough','sorethroat','dyspnea'))
        } else {
          ili = sudden &
            has_fever_38 &
            at_least(weekly, c('headache', 'asthenia', 'chills', 'asthenia')) &
            at_least(weekly, c('cough','sorethroat','rhino'))
        }
      }

      if(country == "NL") {
        # Not the standardized WHO or EU case definition.
        # The case definition used according to the ‘PEL criteria': acute onset AND rectal temperature >38°C AND
        # at least one of the following symptoms: cough, coryza, sore throat, frontal headache, retrosternal pain, myalgia.
        # Provided by the Member State through a survey.

        ili = sudden &
          has_fever_38 &
          at_least(weekly, c('cough','rhino', 'sorethroat','headache','chestpain','has_pain'), n=1)
        # What about sneezing ?

      }

      if(country == "BE") {
        # Not the standardized WHO or EU ILI case definition. The case definition used is:
        # sudden onset of fever with respiratory symptoms AND general symptoms. Provided by the Member State through a survey
        ili =  sudden &
          at_least(weekly, c('headache',  'chills', 'asthenia','has_pain'), n=self$min.syndrome.count) &
          at_least(weekly, c('cough','sorethroat','rhino','dyspnea'), n=self$min.syndrome.count)
      }

      if(country == "PT") {
        #
        # Início súbito,
        #
        # + 1 dos seguintes sintomas sistémicos:
        # -Febre ou febrícula,
        # -Mal-estar, debilidade, prostração,
        # -Cefaleia,
        # -Mialgias ou dores generalizadas.
        #
        # + 1 dos seguintes sintomas respiratórios:
        # - Tosse,
        # - Dor de garganta ou inflamação da mucosa nasal ou faríngea sem sinais respiratórios relevantes,
        # - Dificuldade respiratória.
        ili = sudden &
          at_least(weekly, c('fever','chills','asthenia', 'headache','has_pain'), n=1) &
          at_least(weekly, c('cough','sorethroat','rhino', 'sneeze','dyspnea'), n=1)
      }

      if(country == "DK") {
        # “The Danish sentinel ILI case def. is;
        # sudden onset of fever or feverishness (chills) AND any symptom of malaise, headache or muscle pain
        # AND at least one of the following symptoms: cough, sore throat or shortness of breath”.

        ili = sudden &
          at_least(weekly, c('fever','chills')) & at_least(weekly, c('asthenia', 'headache','has_pain'), n=1) &
          at_least(weekly, c('cough','sorethroat','dyspnea'), n=1)
      }

      if(country == "FR") {
        # respi = r$sorethroat | r$cough | r$dyspnea
        # fever = r$fever & (!is.na(r$highest.temp) & r$highest.temp %in% c(3:5))
        # Not exact definition, but the one selected on french's data study

        ili = sudden &
          at_least(weekly, c('sorethroat','cough','dyspnea'), n=self$min.syndrome.count) &
          has_fever_39 &
          at_least(weekly, c('has_pain','headache'))

      }

      if(country %in% c("UK","SE")) {
        # No specific definition..By default use
        r = syndromes_influenzanet_2012(weekly, as.levels = TRUE)
        ili = r$status == "ili"
      }

      list(
        ili.country=ili,
        id=weekly$id
      )
    }
  )
)