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reference/antimicrobial_selectors.md
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@@ -669,7 +669,7 @@ 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
#> 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.:
@@ -777,7 +777,7 @@ identical(x, y) && identical(y, z)
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 2,000 × 2
#> IPM MEM
#> <sir> <sir>
@@ -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>
@@ -814,7 +814,7 @@ example_isolates[, c("mo", aminoglycosides())]
# select only antimicrobials with DDDs for oral treatment
example_isolates[, administrable_per_os()]
#> ℹ For `?administrable_per_os()` using columns OXA (oxacillin), FLC
#> ℹ For `administrable_per_os()` using columns OXA (oxacillin), FLC
#> (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), AMP
#> (ampicillin), CXM (cefuroxime), KAN (kanamycin), TMP (trimethoprim), NIT
#> (nitrofurantoin), FOS (fosfomycin), LNZ (linezolid), CIP (ciprofloxacin), MFX
@@ -840,7 +840,7 @@ example_isolates[, administrable_per_os()]
# filter using any() or all()
example_isolates[any(carbapenems() == "R"), ]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -862,7 +862,7 @@ example_isolates[any(carbapenems() == "R"), ]
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
subset(example_isolates, any(carbapenems() == "R"))
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 55 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
@@ -886,7 +886,7 @@ subset(example_isolates, any(carbapenems() == "R"))
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 962 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
@@ -909,7 +909,7 @@ example_isolates[any(carbapenems()), ]
#> # TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,
#> # IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …
example_isolates[all(carbapenems()), ]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 756 × 46
#> date patient age gender ward mo PEN OXA FLC AMX
@@ -934,9 +934,9 @@ 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 `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> 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>
@@ -960,8 +960,8 @@ example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
# filter + select in one go: get penicillins in carbapenem-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()]
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> # A tibble: 55 × 7
@@ -985,10 +985,10 @@ example_isolates[any(carbapenems() == "R"), penicillins()]
# drugs are both omitted since benzylpenicillin is not administrable per os
# and erythromycin is not a penicillin:
example_isolates[, penicillins() & administrable_per_os()]
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> ℹ For `penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> ℹ For `?administrable_per_os()` using columns OXA (oxacillin), FLC
#> ℹ For `administrable_per_os()` using columns OXA (oxacillin), FLC
#> (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid), AMP
#> (ampicillin), CXM (cefuroxime), KAN (kanamycin), TMP (trimethoprim), NIT
#> (nitrofurantoin), FOS (fosfomycin), LNZ (linezolid), CIP (ciprofloxacin), MFX
@@ -1014,7 +1014,7 @@ example_isolates[, penicillins() & administrable_per_os()]
# very flexible. For instance, to select antimicrobials with an oral DDD
# of at least 1 gram:
example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")]
#> ℹ For `?amr_selector(oral_ddd > 1 & oral_units == "g")` using columns OXA
#> ℹ For `amr_selector(oral_ddd > 1 & oral_units == "g")` using columns OXA
#> (oxacillin), FLC (flucloxacillin), AMX (amoxicillin), AMC
#> (amoxicillin/clavulanic acid), AMP (ampicillin), KAN (kanamycin), FOS
#> (fosfomycin), LNZ (linezolid), VAN (vancomycin), ERY (erythromycin), CLI
@@ -1058,17 +1058,17 @@ if (require("data.table")) {
#> The following objects are masked from ‘package:AMR’:
#>
#> %like%, like
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> 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()`.
#> Class <amr_selector>
#> [1] IPM MEM
if (require("data.table")) {
# so `with = FALSE` is required
dt[, carbapenems(), with = FALSE]
}
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> IPM MEM
#> <sir> <sir>
#> 1: <NA> <NA>
@@ -1087,8 +1087,8 @@ 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>
@@ -1105,9 +1105,9 @@ if (require("data.table")) {
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 `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> 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>
@@ -1126,7 +1126,7 @@ if (require("data.table")) {
if (require("data.table")) {
dt[any(carbapenems() == "S"), ]
}
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> date patient age gender ward mo PEN OXA FLC
#> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir>
#> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA>
@@ -1195,8 +1195,8 @@ if (require("data.table")) {
if (require("data.table")) {
dt[any(carbapenems() == "S"), penicillins(), with = FALSE]
}
#> ℹ For `?carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `?penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> ℹ For `penicillins()` using columns PEN (benzylpenicillin), OXA (oxacillin),
#> FLC (flucloxacillin), AMX (amoxicillin), AMC (amoxicillin/clavulanic acid),
#> AMP (ampicillin), and TZP (piperacillin/tazobactam)
#> PEN OXA FLC AMX AMC AMP TZP