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(v1.7.1.9024) unit tests

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dr. M.S. (Matthijs) Berends committed 2021-08-17 14:34:11 +02:00
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man/ab_property.Rd
+6 -4
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@@ -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
+31 -29
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@@ -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{
man/eucast_rules.Rd
+1 -1
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@@ -101,7 +101,7 @@ To define antibiotics column names, leave as it is to determine it automatically
The following antibiotics are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
Amikacin (\code{AMK}, \link{NULL}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&showdescription=no)), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{c("J01MA12", "S01AE05")}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{c("J01CA01", "S01AA19")}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CA01",}{J01CA04}&showdescription=no)), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CA12}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01FA10",}{J01CR05}&showdescription=no)), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA13}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{c("A01AB22", "J01AA02")}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{c("J01FA10", "S01AA26")}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CE01",}{J01FA09}&showdescription=no)), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CR02}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{c("J01MA02", "S01AE03", "S02AA15", "S03AA07")}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{c("J01MA14", "S01AE07")}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{c("J01MA01", "S01AE01", "S02AA16")}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{c("A01AB23", "D10AF07", "J01AA08")}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01FA06}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CF04}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CF05}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{c("J01CE01", "S01AA14")}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01DC02",}{c("D06AX01", "D09AA02", "J01XC01", "S01AA13")}&showdescription=no)), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01FF02}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J04AB02}), chloramphenicol (\code{CHL}, \link{J01XX09}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), ciprofloxacin (\code{CIP}, \link{J01XX08}(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&showdescription=no)), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01DB04}), clindamycin (\code{CLI}, \link{J01DC01}(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&showdescription=no)), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A07AA10",}{c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")}&showdescription=no)), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01XE01}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A01AB22",}{J01AA12}&showdescription=no)), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{c("J01DC02", "S01AA27")}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{c("A07AA10", "J01XB01")}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD01}), fusidic acid (\code{FUS}, \link{J01DD04}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), gentamicin (\code{GEN}, \link{J01DF01}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")&showdescription=no)), hetacillin (\code{HET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA18&showdescription=no}{J01DH03}), imipenem (\code{IPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH51&showdescription=no}{J01EA01}), kanamycin (\code{KAN}, \link{J01XX01}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA08", "J01GB04", "S01AA24")&showdescription=no)), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01MA12",}{cLine truncated
Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{S01AE08}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01MA02}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01MA23}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01MA04}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01MA08}), arbekacin (\code{ARB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no}{J01MA19}), aspoxicillin (\code{APX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no}{J01MA16}), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01MA15}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01MA11}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01MA12}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01MA24}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01MA07}), bekanamycin (\code{BEK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no}{J01MA14}), benzathine benzylpenicillin (\code{BNB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no}{D10AF05}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no}{J01MA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01MA01}), besifloxacin (\code{BES}, \href{https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no}{J01MA18}), biapenem (\code{BIA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no}{J01MA03}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01MA17}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01MA10}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01MA21}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01MA09}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01MA05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{P01AA05}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01MA22}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01MA13}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01CA01}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01CA04}), cefcapene (\code{CCP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no}{J01CA12}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01CR05}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01CA13}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01AA02}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01FA10}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01FA09}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01CR02}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01AA08}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01FA06}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01CF04}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01CF05}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01CR01}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01CA19}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01CE04}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01CA09}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DF01}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?coLine truncated
}
\section{Stable Lifecycle}{
man/mdro.Rd
+1 -1
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@@ -166,7 +166,7 @@ To define antibiotics column names, leave as it is to determine it automatically
The following antibiotics are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
Amikacin (\code{AMK}, \link{NULL}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&showdescription=no)), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{c("J01MA12", "S01AE05")}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{c("J01CA01", "S01AA19")}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CA01",}{J01CA04}&showdescription=no)), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01CA12}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01FA10",}{J01CR05}&showdescription=no)), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01CA13}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{c("A01AB22", "J01AA02")}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{c("J01FA10", "S01AA26")}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01CE01",}{J01FA09}&showdescription=no)), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01CR02}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{c("J01MA02", "S01AE03", "S02AA15", "S03AA07")}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{c("J01MA14", "S01AE07")}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{c("J01MA01", "S01AE01", "S02AA16")}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{c("A01AB23", "D10AF07", "J01AA08")}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01FA06}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no}{J01CF04}), ceftazidime (\code{CAZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no}{J01CF05}), ceftriaxone (\code{CRO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no}{c("J01CE01", "S01AA14")}), cefuroxime (\code{CXM}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01DC02",}{c("D06AX01", "D09AA02", "J01XC01", "S01AA13")}&showdescription=no)), cephalexin (\code{LEX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no}{J01FF02}), cephalothin (\code{CEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no}{J04AB02}), chloramphenicol (\code{CHL}, \link{J01XX09}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&showdescription=no)), ciprofloxacin (\code{CIP}, \link{J01XX08}(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&showdescription=no)), clarithromycin (\code{CLR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no}{J01DB04}), clindamycin (\code{CLI}, \link{J01DC01}(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&showdescription=no)), colistin (\code{COL}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A07AA10",}{c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")}&showdescription=no)), daptomycin (\code{DAP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no}{J01XE01}), doxycycline (\code{DOX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("A01AB22",}{J01AA12}&showdescription=no)), epicillin (\code{EPC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no}{c("J01DC02", "S01AA27")}), ertapenem (\code{ETP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no}{c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")}), flucloxacillin (\code{FLC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no}{c("A07AA10", "J01XB01")}), fosfomycin (\code{FOS}, \href{https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no}{J01DD01}), fusidic acid (\code{FUS}, \link{J01DD04}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&showdescription=no)), gentamicin (\code{GEN}, \link{J01DF01}(https://www.whocc.no/atc_ddd_index/?code=c("D06AX07", "J01GB03", "S01AA11", "S02AA14", "S03AA06")&showdescription=no)), hetacillin (\code{HET}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA18&showdescription=no}{J01DH03}), imipenem (\code{IPM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH51&showdescription=no}{J01EA01}), kanamycin (\code{KAN}, \link{J01XX01}(https://www.whocc.no/atc_ddd_index/?code=c("A07AA08", "J01GB04", "S01AA24")&showdescription=no)), levofloxacin (\code{LVX}, \href{https://www.whocc.no/atc_ddd_index/?code=c("J01MA12",}{cLine truncated
Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no}{S01AE08}), amoxicillin (\code{AMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no}{J01MA02}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no}{J01MA23}), ampicillin (\code{AMP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no}{J01MA04}), ampicillin/sulbactam (\code{SAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no}{J01MA08}), arbekacin (\code{ARB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB12&showdescription=no}{J01MA19}), aspoxicillin (\code{APX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA19&showdescription=no}{J01MA16}), azidocillin (\code{AZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no}{J01MA15}), azithromycin (\code{AZM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no}{J01MA11}), azlocillin (\code{AZL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no}{J01MA12}), aztreonam (\code{ATM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no}{J01MA24}), bacampicillin (\code{BAM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no}{J01MA07}), bekanamycin (\code{BEK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB13&showdescription=no}{J01MA14}), benzathine benzylpenicillin (\code{BNB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no}{D10AF05}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no}{J01MA06}), benzylpenicillin (\code{PEN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no}{J01MA01}), besifloxacin (\code{BES}, \href{https://www.whocc.no/atc_ddd_index/?code=S01AE08&showdescription=no}{J01MA18}), biapenem (\code{BIA}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DH05&showdescription=no}{J01MA03}), carbenicillin (\code{CRB}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no}{J01MA17}), carindacillin (\code{CRN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no}{J01MA10}), cefacetrile (\code{CAC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no}{J01MA21}), cefaclor (\code{CEC}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no}{J01MA09}), cefadroxil (\code{CFR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no}{J01MA05}), cefaloridine (\code{RID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no}{P01AA05}), cefamandole (\code{MAN}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no}{J01MA22}), cefatrizine (\code{CTZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no}{J01MA13}), cefazedone (\code{CZD}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no}{J01CA01}), cefazolin (\code{CZO}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no}{J01CA04}), cefcapene (\code{CCP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD17&showdescription=no}{J01CA12}), cefdinir (\code{CDR}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no}{J01CR05}), cefditoren (\code{DIT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no}{J01CA13}), cefepime (\code{FEP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no}{J01AA02}), cefetamet (\code{CAT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no}{J01FA10}), cefixime (\code{CFM}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no}{J01FA09}), cefmenoxime (\code{CMX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no}{J01CR02}), cefmetazole (\code{CMZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no}{J01AA08}), cefodizime (\code{DIZ}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no}{J01FA06}), cefonicid (\code{CID}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no}{J01CF04}), cefoperazone (\code{CFP}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no}{J01CF05}), cefoperazone/sulbactam (\code{CSL}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no}{J01CR01}), ceforanide (\code{CND}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no}{J01CA19}), cefotaxime (\code{CTX}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no}{J01CE04}), cefotetan (\code{CTT}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no}{J01CA09}), cefotiam (\code{CTF}, \href{https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no}{J01DF01}), cefoxitin (\code{FOX}, \href{https://www.whocc.no/atc_ddd_index/?coLine truncated
}
\section{Interpretation of R and S/I}{