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2026-03-20 16:11:30 +00:00
parent ba003f3e23
commit 3560dfd611
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18
reference/interpretive_rules.md
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@@ -306,11 +306,10 @@ head(a)
# apply EUCAST rules: some results wil be changed
b <- eucast_rules(a, overwrite = TRUE)
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
#> class 'sir'. Transform them on beforehand, with e.g.:
#> - x %>% as.sir(CXM:AMX)
#> - x %>% mutate_if(is_sir_eligible, as.sir)
#> - x %>% mutate(across(where(is_sir_eligible), as.sir))
#> Warning: in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with
#> antimicrobial results are of class <sir>. Transform them on beforehand, e.g.: -
#> x %>% as.sir(CXM:AMX) - x %>% mutate_if(is_sir_eligible, as.sir) - x %>%
#> mutate(across(where(is_sir_eligible), as.sir))
head(b)
#> mo VAN AMX COL CAZ CXM PEN FOX
@@ -324,11 +323,10 @@ head(b)
# do not apply EUCAST rules, but rather get a data.frame
# containing all details about the transformations:
c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
#> Warning: in `eucast_rules()`: not all columns with antimicrobial results are of
#> class 'sir'. Transform them on beforehand, with e.g.:
#> - x %>% as.sir(CXM:AMX)
#> - x %>% mutate_if(is_sir_eligible, as.sir)
#> - x %>% mutate(across(where(is_sir_eligible), as.sir))
#> Warning: in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with
#> antimicrobial results are of class <sir>. Transform them on beforehand, e.g.: -
#> x %>% as.sir(CXM:AMX) - x %>% mutate_if(is_sir_eligible, as.sir) - x %>%
#> mutate(across(where(is_sir_eligible), as.sir))
head(c)
#> row col mo_fullname old new rule rule_group
#> 1 1 AMX Staphylococcus aureus - S Breakpoints