Filter isolates on result in antibiotic class

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", ...)

Arguments

x	a data set
ab_class	an antimicrobial class, like "carbapenems", as can be found in AMR::antibiotics$group
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 "any" (default) or "all"
...	parameters passed on to filter_at

Details

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.

Examples

# NOT RUN {
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")
# }