This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
isolate_identifier(x, col_mo = NULL, cols_ab = NULL) # S3 method for isolate_identifier all.equal(target, current, ignore_empty_results = TRUE, ...)
Arguments
| x | data with antibiotic columns, such as |
|---|---|
| col_mo | column name of the IDs of the microorganisms (see |
| cols_ab | a character vector of column names of |
| target | R object. |
| current | other R object, to be compared with |
| ignore_empty_results | a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared |
| ... | column name of an antibiotic, see section Antibiotics below |
Experimental Lifecycle
The lifecycle of this function is experimental. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this AMR package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
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Examples
# automatic selection of microorganism and antibiotics (i.e., all <rsi> columns, see ?as.rsi) x <- isolate_identifier(example_isolates) # ignore microorganism codes, only use antimicrobial results x <- isolate_identifier(example_isolates, col_mo = FALSE, cols_ab = c("AMX", "TZP", "GEN", "TOB")) # select antibiotics from certain antibiotic classes x <- isolate_identifier(example_isolates, cols_ab = c(carbapenems(), aminoglycosides()))