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Check Organism-AST Consistency

Source: R/prep_ast.R
prep_check_organism_ast_consistency.Rd

Flags impossible/implausible AST results where a drug is inappropriate for the organism type (e.g., a Gram-positive organism tested against a Gram-negative-only drug).

Usage

prep_check_organism_ast_consistency(
  data,
  organism_col = "organism_normalized",
  antibiotic_col = "antibiotic_normalized"
)

Arguments

data

Data frame with organism and antibiotic columns.

organism_col

Character. Normalized organism column. Default "organism_normalized".

antibiotic_col

Character. Normalized antibiotic column. Default "antibiotic_normalized".

Value

Data frame with is_ast_inconsistent logical column added.

Details

Uses inst/extdata/Organism_AST_drugs.csv which maps organism groups to expected antibiotic panels.