Enrich Infection Type

Infers Community-Acquired (CAI) vs Hospital-Acquired (HAI) infection using admission-culture date gap.

Usage

enrich_infection_type(
  data,
  infection_type_col = "infection_type",
  admission_col = "date_of_admission",
  culture_col = "date_of_culture",
  hai_cutoff = 2,
  overwrite = FALSE
)

Arguments

data

Data frame

infection_type_col

Character. Infection type column. Default "infection_type".

admission_col

Character. Admission date. Default "date_of_admission".

culture_col

Character. Culture date. Default "date_of_culture".

hai_cutoff

Numeric. Days after admission to classify as HAI. Default 2 (48 hours).

overwrite

Logical. Recalculate even if present. Default FALSE.

Value

Data frame with infection_type enriched

Examples

if (FALSE) { # \dontrun{
# Default 2-day cutoff
data_enriched <- enrich_infection_type(data)

# 3-day cutoff
data_enriched <- enrich_infection_type(data, hai_cutoff = 3)
} # }