Skip to contents

Derive Infection Type (HAI / CAI) per Patient

Source: R/burden.R
derive_infection_type.Rd

Classifies each row as HAI or CAI. Uses infection_type_col when it contains a valid value. For rows where that column is NA, "Not known", or "NULL", derives the classification from the gap between date_culture_col and date_admission_col:

  • gap <= hai_threshold_hours -> CAI

  • gap > hai_threshold_hours -> HAI

Usage

derive_infection_type(
  data,
  infection_type_col = "type_of_infection",
  date_admission_col = "date_of_admission",
  date_culture_col = "date_of_first_positive_culture",
  hai_threshold_hours = 48,
  patient_id_col = "PatientInformation_id"
)

Arguments

data

Data frame.

infection_type_col

Character. Raw infection type column. Default "type_of_infection".

date_admission_col

Character. Default "date_of_admission".

date_culture_col

Character. Date of first positive culture. Default "date_of_first_positive_culture".

hai_threshold_hours

Numeric. Gap threshold in hours. Default 48.

patient_id_col

Character. Unique patient identifier column. Default "PatientInformation_id".

Value

data with column infection_type_derived ("HAI" / "CAI" / "Unknown").