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, ...)
-
-aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE,
+ aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
aminopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -142,6 +136,12 @@ my_data_with_all_these_columns %>%
ureidopenicillins(only_sir_columns = FALSE, 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, ...)
+
administrable_per_os(only_sir_columns = FALSE, return_all = TRUE, ...)
administrable_iv(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -154,11 +154,7 @@ my_data_with_all_these_columns %>%
Arguments
-- amr_class
-an antimicrobial class or a part of it, such as "carba" and "carbapenems". The columns group, atc_group1 and atc_group2 of the antibiotics data set will be searched (case-insensitive) for this value.
- only_sir_columns
+- only_sir_columns
a logical to indicate whether only columns of class sir must be selected (default is FALSE), see as.sir()
ignored, only in place to allow future extensions
- amr_class
+an antimicrobial class or a part of it, such as "carba" and "carbapenems". The columns group, atc_group1 and atc_group2 of the antibiotics data set will be searched (case-insensitive) for this value.
- filter
an expression to be evaluated in the antibiotics data set, such as name %like% "trim"
All selectors can also be used in tidymodels packages such as recipe and parsnip. See for more info our tutorial on using antimicrobial selectors for predictive modelling.
All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the antibiotics data set. This means that a selector such as aminoglycosides() will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
The amr_class() function can be used to filter/select on a manually defined antimicrobial class. It searches for results in the antibiotics data set within the columns group, atc_group1 and atc_group2.
-The amr_selector() function can be used to internally filter the antibiotics data set on any results, see Examples. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
The administrable_per_os() and administrable_iv() functions also rely on the antibiotics data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the antibiotics data set.
+The amr_selector() function can be used to internally filter the antibiotics data set on any results, see Examples. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
The not_intrinsic_resistant() function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of E. coli and K. pneumoniae and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021) to determine intrinsic resistance, using the eucast_rules() function internally. Because of this determination, this function is quite slow in terms of performance.
diff --git a/reference/as.ab.html b/reference/as.ab.html
index 38df67ade..e890a163f 100644
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9160
+
2.1.1.9163