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.

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"))
# }

Arguments

Source

Value

Details

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