bug_drug_combinations {AMR}

Determine Bug-Drug Combinations

Description

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 class 'bug_drug_combinations'
format(
  x,
  translate_ab = "name (ab, atc)",
  language = get_AMR_locale(),
  minimum = 30,
  combine_SI = TRUE,
  add_ab_group = TRUE,
  remove_intrinsic_resistant = FALSE,
  decimal.mark = getOption("OutDec"),
  big.mark = ifelse(decimal.mark == ",", ".", ","),
  ...
)

Arguments

x

a data set with antibiotic columns, such as amox, AMX and AMC

col_mo

column name of the names or codes of the microorganisms (see as.mo()) - the default is 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 - the default is 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 - the default is the current system language (see get_AMR_locale()) and can also be set with the package option 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 values S and I should be summed, so resistance will be based on only R - the default is TRUE

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.

Details

The function format() calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use combine_SI = TRUE (default) to test R vs. S+I and combine_SI = FALSE to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. knitr::kable().

Value

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

Examples

# example_isolates is a data set available in the AMR package.
# run ?example_isolates for more info.
example_isolates


x <- bug_drug_combinations(example_isolates)
head(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("Escherichia coli"),
      "E. coli",
      "Others"
    )
  }
)