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(tbl, ab_class, result = NULL, scope = "any", ...) filter_aminoglycosides(tbl, result = NULL, scope = "any", ...) filter_carbapenems(tbl, result = NULL, scope = "any", ...) filter_cephalosporins(tbl, result = NULL, scope = "any", ...) filter_1st_cephalosporins(tbl, result = NULL, scope = "any", ...) filter_2nd_cephalosporins(tbl, result = NULL, scope = "any", ...) filter_3rd_cephalosporins(tbl, result = NULL, scope = "any", ...) filter_4th_cephalosporins(tbl, result = NULL, scope = "any", ...) filter_fluoroquinolones(tbl, result = NULL, scope = "any", ...) filter_glycopeptides(tbl, result = NULL, scope = "any", ...) filter_macrolides(tbl, result = NULL, scope = "any", ...) filter_tetracyclines(tbl, result = NULL, scope = "any", ...)
tbl | 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 antibiotics
data set will be searched for ab_class
in the columns atc_group1
and atc_group2
(case-insensitive). Next, tbl
will be checked for column names with a value in any abbreviations, codes or official names found in the antibiotics
data set.
# NOT RUN { library(dplyr) # filter on isolates that have any result for any aminoglycoside septic_patients %>% filter_aminoglycosides() # this is essentially the same as: septic_patients %>% filter_at(.vars = vars(c("gent", "tobr", "amik", "kana")), .vars_predicate = any_vars(. %in% c("S", "I", "R"))) # filter on isolates that show resistance to ANY aminoglycoside septic_patients %>% filter_aminoglycosides("R") # filter on isolates that show resistance to ALL aminoglycosides septic_patients %>% filter_aminoglycosides("R", "all") # filter on isolates that show resistance to # any aminoglycoside and any fluoroquinolone septic_patients %>% filter_aminoglycosides("R") %>% filter_fluoroquinolones("R") # filter on isolates that show resistance to # all aminoglycosides and all fluoroquinolones septic_patients %>% filter_aminoglycosides("R", "all") %>% filter_fluoroquinolones("R", "all") # }