Recode Intermediate (I) Susceptibility Values

Converts "I" (Intermediate) values to either "S" or "R" based on antibiotic type. For Colistin: I -> S (following clinical guidelines) For all other antibiotics: I -> R (conservative approach for surveillance)

Usage

recode_intermediate(
  data,
  antibiotic_col = "antibiotic_name",
  value_col = "antibiotic_value",
  colistin_to_s = TRUE,
  others_to_r = TRUE
)

Arguments

data

Data frame with antibiotic susceptibility data

antibiotic_col

Character. Column name with antibiotic names. Default "antibiotic_name".

value_col

Character. Column name with S/I/R values. Default "antibiotic_value".

colistin_to_s

Logical. Convert Colistin I to S. Default TRUE.

others_to_r

Logical. Convert other antibiotics' I to R. Default TRUE.

Value

Data frame with recoded intermediate values

Examples

if (FALSE) { # \dontrun{
# Recode all I values according to standard rules
data <- recode_intermediate(data)

# Only recode Colistin
data <- recode_intermediate(data, others_to_r = FALSE)
} # }