Extracts clean S/I/R values from messy antibiotic result columns.
Handles common patterns like "S (HIGH LEVEL)", "R Escherichia coli", etc.
Usage
clean_antibiotic_values(data, value_col = "antibiotic_value", strict = FALSE)
Arguments
- data
Data frame with antibiotic susceptibility data
- value_col
Character. Column name containing susceptibility values.
Default "antibiotic_value".
- strict
Logical. If TRUE, only accept S/I/R values. If FALSE, attempt
to parse from messy strings. Default FALSE.
Value
Data frame with cleaned antibiotic_value column
Examples
if (FALSE) { # \dontrun{
data <- data.frame(
antibiotic_value = c("S", "R E. coli", "S (HIGH LEVEL)", "I")
)
clean_antibiotic_values(data)
} # }