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(v3.0.1.9059) Fix WISCA in vignette

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dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
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117
man/antimicrobial_selectors.Rd
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@@ -45,8 +45,12 @@
\alias{not_intrinsic_resistant}
\title{Antimicrobial Selectors}
\usage{
aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
aminoglycosides(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
aminopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -54,41 +58,68 @@ antifungals(only_sir_columns = FALSE, return_all = TRUE, ...)
antimycobacterials(only_sir_columns = FALSE, return_all = TRUE, ...)
betalactams(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
betalactams(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE,
...)
betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE, ...)
carbapenems(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
carbapenems(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
cephalosporins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
cephalosporins_1st(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_2nd(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_3rd(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
cephalosporins_3rd(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
cephalosporins_4th(only_sir_columns = FALSE, return_all = TRUE, ...)
cephalosporins_5th(only_sir_columns = FALSE, return_all = TRUE, ...)
fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
fluoroquinolones(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
isoxazolylpenicillins(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
lincosamides(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
lincosamides(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
lipoglycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -108,11 +139,19 @@ phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)
phosphonics(only_sir_columns = FALSE, return_all = TRUE, ...)
polymyxins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
polymyxins(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
quinolones(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
quinolones(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -122,25 +161,43 @@ streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)
sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)
tetracyclines(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
tetracyclines(
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
trimethoprims(only_sir_columns = FALSE, return_all = TRUE, ...)
ureidopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
amr_class(amr_class, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
amr_class(
amr_class,
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
amr_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
amr_selector(
filter,
only_sir_columns = FALSE,
only_treatable = TRUE,
return_all = TRUE,
...
)
administrable_per_os(only_sir_columns = FALSE, return_all = TRUE, ...)
administrable_iv(only_sir_columns = FALSE, return_all = TRUE, ...)
not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
version_expected_phenotypes = 1.2, ...)
not_intrinsic_resistant(
only_sir_columns = FALSE,
col_mo = NULL,
version_expected_phenotypes = 1.2,
...
)
}
\arguments{
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE}.}