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(v2.1.1.9050) vctrs fix for sir, small documentation fixes

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dr. M.S. (Matthijs) Berends
2024-06-15 15:33:49 +02:00
parent 9bf7584d58
commit bdbf5198a2
15 changed files with 248 additions and 165 deletions
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97
man/antibiotic_class_selectors.Rd
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@ -185,59 +185,31 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR
example_isolates
# Examples sections below are split into 'base R', 'dplyr', and 'data.table':
# base R ------------------------------------------------------------------
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())]
# select only antibiotic columns with DDDs for oral treatment
example_isolates[, administrable_per_os()]
# filter using any() or all()
example_isolates[any(carbapenems() == "R"), ]
subset(example_isolates, any(carbapenems() == "R"))
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
example_isolates[all(carbapenems()), ]
# filter with multiple antibiotic selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
# filter + select in one go: get penicillins in carbapenem-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()]
# You can combine selectors with '&' to be more specific. For example,
# penicillins() would select benzylpenicillin ('peni G') and
# administrable_per_os() would select erythromycin. Yet, when combined these
# drugs are both omitted since benzylpenicillin is not administrable per os
# and erythromycin is not a penicillin:
example_isolates[, penicillins() & administrable_per_os()]
# ab_selector() applies a filter in the `antibiotics` data set and is thus
# very flexible. For instance, to select antibiotic columns with an oral DDD
# of at least 1 gram:
example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
# Examples sections below are split into 'dplyr', 'base R', and 'data.table':
\donttest{
# dplyr -------------------------------------------------------------------
if (require("dplyr")) {
tibble(kefzol = random_sir(5)) \%>\%
select(cephalosporins())
. example_isolates \%>\% select(carbapenems())
}
if (require("dplyr")) {
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates \%>\% select(mo, aminoglycosides())
}
if (require("dplyr")) {
# select only antibiotic columns with DDDs for oral treatment
. example_isolates \%>\% select(administrable_per_os())
}
if (require("dplyr")) {
# get AMR for all aminoglycosides e.g., per ward:
example_isolates \%>\%
group_by(ward) \%>\%
summarise(across(aminoglycosides(), resistance))
summarise(across(aminoglycosides(),
resistance))
}
if (require("dplyr")) {
# You can combine selectors with '&' to be more specific:
@ -249,7 +221,8 @@ if (require("dplyr")) {
example_isolates \%>\%
filter(mo_genus() \%in\% c("Escherichia", "Klebsiella")) \%>\%
group_by(ward) \%>\%
summarise(across(not_intrinsic_resistant(), resistance))
summarise_at(not_intrinsic_resistant(),
resistance)
}
if (require("dplyr")) {
# get susceptibility for antibiotics whose name contains "trim":
@ -315,6 +288,44 @@ if (require("dplyr")) {
}
# base R ------------------------------------------------------------------
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())]
# select only antibiotic columns with DDDs for oral treatment
example_isolates[, administrable_per_os()]
# filter using any() or all()
example_isolates[any(carbapenems() == "R"), ]
subset(example_isolates, any(carbapenems() == "R"))
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
example_isolates[all(carbapenems()), ]
# filter with multiple antibiotic selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
# filter + select in one go: get penicillins in carbapenem-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()]
# You can combine selectors with '&' to be more specific. For example,
# penicillins() would select benzylpenicillin ('peni G') and
# administrable_per_os() would select erythromycin. Yet, when combined these
# drugs are both omitted since benzylpenicillin is not administrable per os
# and erythromycin is not a penicillin:
example_isolates[, penicillins() & administrable_per_os()]
# ab_selector() applies a filter in the `antibiotics` data set and is thus
# very flexible. For instance, to select antibiotic columns with an oral DDD
# of at least 1 gram:
example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
# data.table --------------------------------------------------------------
# data.table is supported as well, just use it in the same way as with