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2026-06-23 18:00:14 +00:00
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commit 2a7bfb9ffb
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117
reference/antimicrobial_selectors.md
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@@ -18,8 +18,12 @@ pharmaceutical class, code or name: column names "cefazolin", "kefzol",
## Usage
``` r
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, ...)
@@ -27,41 +31,68 @@ 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, ...)
@@ -81,11 +112,19 @@ 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, ...)
@@ -95,25 +134,43 @@ 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