Classify HAI/CAI Infection Type for the Mortality Cohort

Derives the healthcare-associated infection (HAI) vs community-acquired infection (CAI) classification for each patient record in the mortality cohort, using admission-to-culture date differences. Also performs a data-quality check for deceased patients missing an outcome date.

Usage

daly_derive_hai_cai_for_mortality(
  data,
  infection_type_col = "type_of_infection",
  date_admission_col = "date_of_admission",
  date_culture_col = "date_of_first_positive_culture",
  final_outcome_col = "final_outcome",
  final_outcome_date_col = "final_outcome_date",
  death_value = "Death",
  hai_threshold_hours = 48,
  patient_id_col = "PatientInformation_id"
)

Arguments

data

Data frame of patient-level records.

infection_type_col

Character. Column containing the raw infection type label. Default "type_of_infection".

date_admission_col

Character. Admission date column. Default "date_of_admission".

date_culture_col

Character. First positive culture date column. Default "date_of_first_positive_culture".

final_outcome_col

Character. Final outcome column. Default "final_outcome".

final_outcome_date_col

Character. Final outcome date column. Default "final_outcome_date".

death_value

Character. Value in final_outcome_col indicating a fatal outcome. Default "Death".

hai_threshold_hours

Numeric. Hours after admission at which a positive culture is classified as HAI. Default 48.

patient_id_col

Character. Patient identifier column. Default "PatientInformation_id".

Value

The input data frame with a derived infection_type column (values "HAI" or "CAI").