Determine bug-drug combinations

Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples.

bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)

# S3 method for bug_drug_combinations
format(
  x,
  translate_ab = "name (ab, atc)",
  language = get_locale(),
  minimum = 30,
  combine_SI = TRUE,
  combine_IR = FALSE,
  add_ab_group = TRUE,
  remove_intrinsic_resistant = FALSE,
  decimal.mark = getOption("OutDec"),
  big.mark = ifelse(decimal.mark == ",", ".", ","),
  ...
)

Arguments

x	data with antibiotic columns, like e.g. `AMX` and `AMC`
col_mo	column name of the IDs of the microorganisms (see `as.mo()`), defaults to the first column of class `mo`. Values will be coerced using `as.mo()`.
FUN	the function to call on the `mo` column to transform the microorganism IDs, defaults to `mo_shortname()`
...	arguments passed on to `FUN`
translate_ab	a character of length 1 containing column names of the antibiotics data set
language	language of the returned text, defaults to system language (see `get_locale()`) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
minimum	the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
combine_SI	a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter `combine_IR`, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is `TRUE`.
combine_IR	logical to indicate whether values R and I should be summed
add_ab_group	logical to indicate where the group of the antimicrobials must be included as a first column
remove_intrinsic_resistant	logical to indicate that rows with 100% resistance for all tested antimicrobials must be removed from the table
decimal.mark	the character to be used to indicate the numeric decimal point.
big.mark	character; if not empty used as mark between every `big.interval` decimals before (hence `big`) the decimal point.

Source

M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition, 2014, Clinical and Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.

Value

The function bug_drug_combinations() returns a data.frame with columns "mo", "ab", "S", "I", "R" and "total".

Details

The function format() calculates the resistance per bug-drug combination. Use combine_IR = FALSE (default) to test R vs. S+I and combine_IR = TRUE to test R+I vs. S.

The language of the output can be overwritten with options(AMR_locale), please see translate.

Stable lifecycle

The lifecycle of this function is stable. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.

If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

Examples

# \donttest{
x <- bug_drug_combinations(example_isolates)
x
format(x, translate_ab = "name (atc)")

# Use FUN to change to transformation of microorganism codes
x <- bug_drug_combinations(example_isolates,
                           FUN = mo_gramstain)

x <- bug_drug_combinations(example_isolates,
                           FUN = function(x) ifelse(x == "B_ESCHR_COLI",
                                                    "E. coli",
                                                    "Others"))
# }