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@ -214,20 +214,17 @@ example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
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# dplyr -------------------------------------------------------------------
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\donttest{
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if (require("dplyr")) {
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# get AMR for all aminoglycosides e.g., per ward:
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example_isolates \%>\%
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group_by(ward) \%>\%
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summarise(across(aminoglycosides(), resistance))
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}
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if (require("dplyr")) {
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# You can combine selectors with '&' to be more specific:
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example_isolates \%>\%
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select(penicillins() & administrable_per_os())
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}
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if (require("dplyr")) {
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# get AMR for only drugs that matter - no intrinsic resistance:
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example_isolates \%>\%
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filter(mo_genus() \%in\% c("Escherichia", "Klebsiella")) \%>\%
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@ -235,7 +232,6 @@ if (require("dplyr")) {
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summarise(across(not_intrinsic_resistant(), resistance))
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}
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if (require("dplyr")) {
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# get susceptibility for antibiotics whose name contains "trim":
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example_isolates \%>\%
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filter(first_isolate()) \%>\%
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@ -243,19 +239,16 @@ if (require("dplyr")) {
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summarise(across(ab_selector(name \%like\% "trim"), susceptibility))
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}
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if (require("dplyr")) {
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# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
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example_isolates \%>\%
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select(carbapenems())
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}
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if (require("dplyr")) {
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# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
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example_isolates \%>\%
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select(mo, aminoglycosides())
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}
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if (require("dplyr")) {
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# any() and all() work in dplyr's filter() too:
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example_isolates \%>\%
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filter(
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@ -264,25 +257,21 @@ if (require("dplyr")) {
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)
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}
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if (require("dplyr")) {
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# also works with c():
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example_isolates \%>\%
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filter(any(c(carbapenems(), aminoglycosides()) == "R"))
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}
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if (require("dplyr")) {
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# not setting any/all will automatically apply all():
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example_isolates \%>\%
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filter(aminoglycosides() == "R")
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}
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if (require("dplyr")) {
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# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
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example_isolates \%>\%
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select(mo, ab_class("mycobact"))
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}
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if (require("dplyr")) {
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# get bug/drug combinations for only glycopeptides in Gram-positives:
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example_isolates \%>\%
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filter(mo_is_gram_positive()) \%>\%
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@ -298,7 +287,6 @@ if (require("dplyr")) {
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select(penicillins()) # only the 'J01CA01' column will be selected
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}
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if (require("dplyr")) {
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# with recent versions of dplyr this is all equal:
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x <- example_isolates[carbapenems() == "R", ]
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y <- example_isolates \%>\% filter(carbapenems() == "R")
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