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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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12
man/antibiotic_class_selectors.Rd
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@ -214,20 +214,17 @@ example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
# dplyr -------------------------------------------------------------------
\donttest{
if (require("dplyr")) {
# get AMR for all aminoglycosides e.g., per ward:
example_isolates \%>\%
group_by(ward) \%>\%
summarise(across(aminoglycosides(), resistance))
}
if (require("dplyr")) {
# You can combine selectors with '&' to be more specific:
example_isolates \%>\%
select(penicillins() & administrable_per_os())
}
if (require("dplyr")) {
# get AMR for only drugs that matter - no intrinsic resistance:
example_isolates \%>\%
filter(mo_genus() \%in\% c("Escherichia", "Klebsiella")) \%>\%
@ -235,7 +232,6 @@ if (require("dplyr")) {
summarise(across(not_intrinsic_resistant(), resistance))
}
if (require("dplyr")) {
# get susceptibility for antibiotics whose name contains "trim":
example_isolates \%>\%
filter(first_isolate()) \%>\%
@ -243,19 +239,16 @@ if (require("dplyr")) {
summarise(across(ab_selector(name \%like\% "trim"), susceptibility))
}
if (require("dplyr")) {
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
example_isolates \%>\%
select(carbapenems())
}
if (require("dplyr")) {
# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
example_isolates \%>\%
select(mo, aminoglycosides())
}
if (require("dplyr")) {
# any() and all() work in dplyr's filter() too:
example_isolates \%>\%
filter(
@ -264,25 +257,21 @@ if (require("dplyr")) {
)
}
if (require("dplyr")) {
# also works with c():
example_isolates \%>\%
filter(any(c(carbapenems(), aminoglycosides()) == "R"))
}
if (require("dplyr")) {
# not setting any/all will automatically apply all():
example_isolates \%>\%
filter(aminoglycosides() == "R")
}
if (require("dplyr")) {
# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
example_isolates \%>\%
select(mo, ab_class("mycobact"))
}
if (require("dplyr")) {
# get bug/drug combinations for only glycopeptides in Gram-positives:
example_isolates \%>\%
filter(mo_is_gram_positive()) \%>\%
@ -298,7 +287,6 @@ if (require("dplyr")) {
select(penicillins()) # only the 'J01CA01' column will be selected
}
if (require("dplyr")) {
# with recent versions of dplyr this is all equal:
x <- example_isolates[carbapenems() == "R", ]
y <- example_isolates \%>\% filter(carbapenems() == "R")