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 printable format, see Examples.

bug_drug_combinations(x, col_mo = NULL, minimum = 30)

Arguments

x	data with antibiotic columns, like e.g. AMX and AMC
col_mo	column name of the unique IDs of the microorganisms (see mo), defaults to the first column of class mo. Values will be coerced using as.mo.
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_RI	logical to indicate whether values R and I should be summed

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/.

Details

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

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

Examples

# NOT RUN {
x <- bug_drug_combinations(example_isolates)
x
format(x)
# }