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 publishable/printable format, see Examples.

Usage,

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_AMR_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 == ",", ".", ","),
  ...
)

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/.

Arguments

x: data with antibiotic columns, such as amox, 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 codes, 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_AMR_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 argument combine_IR, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is TRUE.
combine_IR: a logical to indicate whether values R and I should be summed
add_ab_group: a logical to indicate where the group of the antimicrobials must be included as a first column
remove_intrinsic_resistant: logical to indicate that rows and columns 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.

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.

Stable Lifecycle

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

If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first 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
bug_drug_combinations(example_isolates, 
                      FUN = mo_gramstain)
                           
bug_drug_combinations(example_isolates,
                      FUN = function(x) ifelse(x == as.mo("E. coli"),
                                               "E. coli",
                                               "Others"))
# }