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Flag Contaminant Organisms

Source: R/prep_contaminants.R
prep_flag_contaminants.Rd

Identifies likely contaminant organisms using multi-path logic (provided flags, device-based context, or heuristic organism+specimen matching).

Usage

prep_flag_contaminants(
  data,
  method = "auto",
  context = c("general", "icu_device"),
  organism_col = "organism_normalized",
  specimen_col = "specimen_type"
)

Arguments

data

Data frame.

method

Character. "auto" (try all methods), "device_based", "heuristic", or "provided". Default "auto".

context

Character. "general" or "icu_device". Default "general".

organism_col

Character. Normalized organism column. Default "organism_normalized".

specimen_col

Character. Specimen type column. Default "specimen_type".

Value

Data frame with is_contaminant, contaminant_confidence, and contaminant_method columns.

Details

When context = "icu_device" (AIIMS ICU BSI data), CoNS in blood with a central line present AND line in place > 2 days are classified as CLABSI pathogens rather than contaminants.