filter_ab_class.Rd
Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
filter_ab_class(x, ab_class, result = NULL, scope = "any", ...) filter_aminoglycosides(x, result = NULL, scope = "any", ...) filter_carbapenems(x, result = NULL, scope = "any", ...) filter_cephalosporins(x, result = NULL, scope = "any", ...) filter_1st_cephalosporins(x, result = NULL, scope = "any", ...) filter_2nd_cephalosporins(x, result = NULL, scope = "any", ...) filter_3rd_cephalosporins(x, result = NULL, scope = "any", ...) filter_4th_cephalosporins(x, result = NULL, scope = "any", ...) filter_5th_cephalosporins(x, result = NULL, scope = "any", ...) filter_fluoroquinolones(x, result = NULL, scope = "any", ...) filter_glycopeptides(x, result = NULL, scope = "any", ...) filter_macrolides(x, result = NULL, scope = "any", ...) filter_tetracyclines(x, result = NULL, scope = "any", ...)
x | a data set |
---|---|
ab_class | an antimicrobial class, like |
result | an antibiotic result: S, I or R (or a combination of more of them) |
scope | the scope to check which variables to check, can be |
... | parameters passed on to |
The group
column in antibiotics
data set will be searched for ab_class
(case-insensitive). If no results are found, the atc_group1
and atc_group2
columns will be searched. Next, x
will be checked for column names with a value in any abbreviations, codes or official names found in the antibiotics
data set.
library(dplyr) # filter on isolates that have any result for any aminoglycoside example_isolates %>% filter_aminoglycosides() # this is essentially the same as (but without determination of column names): example_isolates %>% filter_at(.vars = vars(c("GEN", "TOB", "AMK", "KAN")), .vars_predicate = any_vars(. %in% c("S", "I", "R"))) # filter on isolates that show resistance to ANY aminoglycoside example_isolates %>% filter_aminoglycosides("R") # filter on isolates that show resistance to ALL aminoglycosides example_isolates %>% filter_aminoglycosides("R", "all") # filter on isolates that show resistance to # any aminoglycoside and any fluoroquinolone example_isolates %>% filter_aminoglycosides("R") %>% filter_fluoroquinolones("R") # filter on isolates that show resistance to # all aminoglycosides and all fluoroquinolones example_isolates %>% filter_aminoglycosides("R", "all") %>% filter_fluoroquinolones("R", "all")