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reference/antimicrobial_selectors.md
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@@ -669,10 +669,10 @@ example_isolates
# you can use the selectors separately to retrieve all possible antimicrobials:
carbapenems()
#> ℹ in `carbapenems()`: Imipenem/EDTA (`IPE`) and meropenem/nacubactam
#> (`MNC`) are not included since `only_treatable = TRUE`.
#> ℹ This 'ab' vector was retrieved using `carbapenems()`, which should
#> normally be used inside a `dplyr` verb or `data.frame` call, e.g.:
#> ℹ in `carbapenems()` (`?AMR::carbapenems()`): Imipenem/EDTA (`IPE`) and
#> meropenem/nacubactam (`MNC`) are not included since `only_treatable = TRUE`.
#> ℹ This <ab> vector was retrieved using `carbapenems()`, which should normally
#> be used inside a dplyr verb or <data.frame> call, e.g.:
#> • your_data %>% select(carbapenems())
#> • your_data %>% select(column_a, column_b, carbapenems())
#> • your_data %>% filter(any(carbapenems() == "R"))
@@ -795,8 +795,8 @@ example_isolates[, carbapenems()]
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())]
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 2,000 × 5
#> mo GEN TOB AMK KAN
#> <mo> <sir> <sir> <sir> <sir>
@@ -818,11 +818,10 @@ example_isolates[, administrable_per_os()]
#> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
#> (rifampicin)
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' (vancomycin),
#> 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' (erythromycin), 'CLI'
#> (clindamycin), 'AZM' (azithromycin), 'MTR' (metronidazole), 'CHL'
#> (chloramphenicol), 'COL' (colistin), and 'RIF' (rifampicin)
#> # A tibble: 2,000 × 23
#> OXA FLC AMX AMC AMP CXM KAN TMP NIT FOS LNZ CIP MFX
#> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -937,8 +936,8 @@ example_isolates[all(carbapenems()), ]
# filter with multiple antimicrobial selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 26 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -996,11 +995,10 @@ example_isolates[, penicillins() & administrable_per_os()]
#> (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#> 'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#> (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
#> (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
#> (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
#> (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
#> (rifampicin)
#> (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' (vancomycin),
#> 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' (erythromycin), 'CLI'
#> (clindamycin), 'AZM' (azithromycin), 'MTR' (metronidazole), 'CHL'
#> (chloramphenicol), 'COL' (colistin), and 'RIF' (rifampicin)
#> # A tibble: 2,000 × 5
#> OXA FLC AMX AMC AMP
#> <sir> <sir> <sir> <sir> <sir>
@@ -1067,7 +1065,7 @@ if (require("data.table")) {
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> Warning: It should never be needed to print an antimicrobial selector class. Are you
#> using data.table? Then add the argument `with = FALSE`, see our examples at
#> `?amr_selector`.
#> `amr_selector()` (`?AMR::amr_selector()`).
#> Class 'amr_selector'
#> [1] IPM MEM
if (require("data.table")) {
@@ -1093,8 +1091,8 @@ if (require("data.table")) {
if (require("data.table")) {
dt[, c("mo", aminoglycosides())]
}
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> mo GEN TOB AMK KAN
#> <mo> <sir> <sir> <sir> <sir>
#> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA>
@@ -1112,8 +1110,8 @@ if (require("data.table")) {
dt[, c(carbapenems(), aminoglycosides())]
}
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> IPM MEM GEN TOB AMK KAN
#> <sir> <sir> <sir> <sir> <sir> <sir>
#> 1: <NA> <NA> <NA> <NA> <NA> <NA>