(v1.7.1.9024) unit tests

man/ab_property.Rd

@@ -5,11 +5,11 @@
 \alias{ab_name}
 \alias{set_ab_names}
 \alias{ATC}
-\alias{ab_atc}
 \alias{ab_cid}
 \alias{ab_synonyms}
 \alias{ab_tradenames}
 \alias{ab_group}
+\alias{ab_atc}
 \alias{ab_atc_group1}
 \alias{ab_atc_group2}
 \alias{ab_loinc}
@@ -28,8 +28,6 @@ set_ab_names(
   snake_case = property == "name"
 )
 
-ab_atc(x, ...)
-
 ab_cid(x, ...)
 
 ab_synonyms(x, ...)
@@ -38,6 +36,8 @@ ab_tradenames(x, ...)
 
 ab_group(x, language = get_locale(), ...)
 
+ab_atc(x, only_first = FALSE, ...)
+
 ab_atc_group1(x, language = get_locale(), ...)
 
 ab_atc_group2(x, language = get_locale(), ...)
@@ -69,6 +69,8 @@ ab_property(x, property = "name", language = get_locale(), ...)
 
 \item{snake_case}{a \link{logical} to indicate whether the names should be in so-called \href{https://en.wikipedia.org/wiki/Snake_case}{snake case}: in lower case and all spaces/slashes replaced with an underscore (\verb{_})}
 
+\item{only_first}{a \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)}
+
 \item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}
 
 \item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
@@ -122,7 +124,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 \examples{
 # all properties:
 ab_name("AMX")       # "Amoxicillin"
-ab_atc("AMX")        # J01CA04 (ATC code from the WHO)
+ab_atc("AMX")        # "J01CA04" (ATC code from the WHO)
 ab_cid("AMX")        # 33613 (Compound ID from PubChem)
 ab_synonyms("AMX")   # a list with brand names of amoxicillin
 ab_tradenames("AMX") # same

man/antibiotic_class_selectors.Rd

@@ -33,63 +33,63 @@
 \alias{ureidopenicillins}
 \title{Antibiotic Selectors}
 \usage{
-ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE)
+ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE)
+ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-administrable_per_os(only_rsi_columns = FALSE)
+administrable_per_os(only_rsi_columns = FALSE, ...)
 
-administrable_iv(only_rsi_columns = FALSE)
+administrable_iv(only_rsi_columns = FALSE, ...)
 
-aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE)
+aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-aminopenicillins(only_rsi_columns = FALSE)
+aminopenicillins(only_rsi_columns = FALSE, ...)
 
-antifungals(only_rsi_columns = FALSE)
+antifungals(only_rsi_columns = FALSE, ...)
 
-antimycobacterials(only_rsi_columns = FALSE)
+antimycobacterials(only_rsi_columns = FALSE, ...)
 
-betalactams(only_rsi_columns = FALSE, only_treatable = TRUE)
+betalactams(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE)
+carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-cephalosporins(only_rsi_columns = FALSE)
+cephalosporins(only_rsi_columns = FALSE, ...)
 
-cephalosporins_1st(only_rsi_columns = FALSE)
+cephalosporins_1st(only_rsi_columns = FALSE, ...)
 
-cephalosporins_2nd(only_rsi_columns = FALSE)
+cephalosporins_2nd(only_rsi_columns = FALSE, ...)
 
-cephalosporins_3rd(only_rsi_columns = FALSE)
+cephalosporins_3rd(only_rsi_columns = FALSE, ...)
 
-cephalosporins_4th(only_rsi_columns = FALSE)
+cephalosporins_4th(only_rsi_columns = FALSE, ...)
 
-cephalosporins_5th(only_rsi_columns = FALSE)
+cephalosporins_5th(only_rsi_columns = FALSE, ...)
 
-fluoroquinolones(only_rsi_columns = FALSE)
+fluoroquinolones(only_rsi_columns = FALSE, ...)
 
-glycopeptides(only_rsi_columns = FALSE)
+glycopeptides(only_rsi_columns = FALSE, ...)
 
-lincosamides(only_rsi_columns = FALSE)
+lincosamides(only_rsi_columns = FALSE, ...)
 
-lipoglycopeptides(only_rsi_columns = FALSE)
+lipoglycopeptides(only_rsi_columns = FALSE, ...)
 
-macrolides(only_rsi_columns = FALSE)
+macrolides(only_rsi_columns = FALSE, ...)
 
-oxazolidinones(only_rsi_columns = FALSE)
+oxazolidinones(only_rsi_columns = FALSE, ...)
 
-penicillins(only_rsi_columns = FALSE)
+penicillins(only_rsi_columns = FALSE, ...)
 
-polymyxins(only_rsi_columns = FALSE, only_treatable = TRUE)
+polymyxins(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
 
-streptogramins(only_rsi_columns = FALSE)
+streptogramins(only_rsi_columns = FALSE, ...)
 
-quinolones(only_rsi_columns = FALSE)
+quinolones(only_rsi_columns = FALSE, ...)
 
-tetracyclines(only_rsi_columns = FALSE)
+tetracyclines(only_rsi_columns = FALSE, ...)
 
-trimethoprims(only_rsi_columns = FALSE)
+trimethoprims(only_rsi_columns = FALSE, ...)
 
-ureidopenicillins(only_rsi_columns = FALSE)
+ureidopenicillins(only_rsi_columns = FALSE, ...)
 }
 \arguments{
 \item{ab_class}{an antimicrobial class, such as \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
@@ -98,6 +98,8 @@ ureidopenicillins(only_rsi_columns = FALSE)
 
 \item{only_treatable}{a \link{logical} to indicate whether agents that are only for laboratory tests should be excluded (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
 
+\item{...}{ignored, only in place to allow future extensions}
+
 \item{filter}{an \link{expression} to be evaluated in the \link{antibiotics} data set, such as \code{name \%like\% "trim"}}
 }
 \value{