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< h1 > Property of an antibiotic< / h1 >
< div class = "hidden name" > < code > ab_property.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > Use these functions to return a specific property of an antibiotic from the < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > data set. All input values will be evaluated internally with < code > < a href = 'as.ab.html' > as.ab< / a > < / code > .< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > ab_name< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'kw' > tolower< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_atc< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_cid< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_synonyms< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_tradenames< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_group< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_atc_group1< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_atc_group2< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_ddd< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > administration< / span > < span class = 'kw' > =< / span > < span class = 'st' > "oral"< / span > , < span class = 'kw' > units< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_info< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > ab_property< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > property< / span > < span class = 'kw' > =< / span > < span class = 'st' > "name"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > x< / th >
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< td > < p > any (vector of) text that can be coerced to a valid microorganism code with < code > < a href = 'as.ab.html' > as.ab< / a > < / code > < / p > < / td >
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< / tr >
< tr >
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< th > language< / th >
< td > < p > language of the returned text, defaults to system language (see < code > < a href = 'translate.html' > get_locale< / a > < / code > ) and can also be set with < code > < a href = 'https://www.rdocumentation.org/packages/base/topics/options' > getOption< / a > ("AMR_locale")< / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / td >
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< / tr >
< tr >
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< th > tolower< / th >
< td > < p > logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
< td > < p > other parameters passed on to < code > < a href = 'as.ab.html' > as.ab< / a > < / code > < / p > < / td >
< / tr >
< tr >
< th > administration< / th >
< td > < p > way of administration, either < code > "oral"< / code > or < code > "iv"< / code > < / p > < / td >
< / tr >
< tr >
< th > units< / th >
< td > < p > a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples< / p > < / td >
< / tr >
< tr >
< th > property< / th >
< td > < p > one of the column names of one of the < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > data set< / p > < / td >
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< / tr >
< / table >
< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
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< ul >
< li > < p > An < code > integer< / code > in case of < code > ab_cid< / code > < / p > < / li >
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< li > < p > A named < code > list< / code > in case of < code > ab_info< / code > and multiple < code > ab_synonyms< / code > /< code > ab_tradenames< / code > < / p > < / li >
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< li > < p > A < code > double< / code > in case of < code > ab_ddd< / code > < / p > < / li >
< li > < p > A < code > character< / code > in all other cases< / p > < / li >
< / ul >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > All output will be < a href = 'translate.html' > translate< / a > d where possible.< / p >
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
< p > World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: < a href = 'https://www.whocc.no/atc_ddd_index/' > https://www.whocc.no/atc_ddd_index/< / a > < / p >
< p > WHONET 2019 software: < a href = 'http://www.whonet.org/software.html' > http://www.whonet.org/software.html< / a > < / p >
< p > European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: < a href = 'http://ec.europa.eu/health/documents/community-register/html/atc.htm' > http://ec.europa.eu/health/documents/community-register/html/atc.htm< / a > < / p >
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< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
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< p > On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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< h2 class = "hasAnchor" id = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
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< div class = 'dont-index' > < p > < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > < / p > < / div >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
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< span class = 'co' > # all properties:< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # "Amoxicillin"< / span >
< span class = 'fu' > ab_atc< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # J01CA04 (ATC code from the WHO)< / span >
< span class = 'fu' > ab_cid< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # 33613 (Compound ID from PubChem)< / span >
< span class = 'fu' > ab_synonyms< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # a list with brand names of amoxicillin< / span >
< span class = 'fu' > ab_tradenames< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # same< / span >
< span class = 'fu' > ab_group< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # "Beta-lactams/penicillins"< / span >
< span class = 'fu' > ab_atc_group1< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # "Beta-lactam antibacterials, penicillins"< / span >
< span class = 'fu' > ab_atc_group2< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # "Penicillins with extended spectrum"< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'kw' > x< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "AMC"< / span > , < span class = 'st' > "PLB"< / span > )) < span class = 'co' > # "Amoxicillin/clavulanic acid" "Polymyxin B"< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'kw' > x< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "AMC"< / span > , < span class = 'st' > "PLB"< / span > ),
< span class = 'kw' > tolower< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "amoxicillin/clavulanic acid" "polymyxin B"< / span >
< span class = 'fu' > ab_ddd< / span > (< span class = 'st' > "AMX"< / span > , < span class = 'st' > "oral"< / span > ) < span class = 'co' > # 1< / span >
< span class = 'fu' > ab_ddd< / span > (< span class = 'st' > "AMX"< / span > , < span class = 'st' > "oral"< / span > , < span class = 'kw' > units< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "g"< / span >
< span class = 'fu' > ab_ddd< / span > (< span class = 'st' > "AMX"< / span > , < span class = 'st' > "iv"< / span > ) < span class = 'co' > # 1< / span >
< span class = 'fu' > ab_ddd< / span > (< span class = 'st' > "AMX"< / span > , < span class = 'st' > "iv"< / span > , < span class = 'kw' > units< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "g"< / span >
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< span class = 'fu' > ab_info< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # all properties as a list< / span >
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< span class = 'co' > # all ab_* functions use as.ab() internally:< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'st' > "Fluclox"< / span > ) < span class = 'co' > # "Flucloxacillin"< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'st' > "fluklox"< / span > ) < span class = 'co' > # "Flucloxacillin"< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'st' > "floxapen"< / span > ) < span class = 'co' > # "Flucloxacillin"< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'fl' > 21319< / span > ) < span class = 'co' > # "Flucloxacillin" (using CID)< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'st' > "J01CF05"< / span > ) < span class = 'co' > # "Flucloxacillin" (using ATC)< / span >
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< span class = 'co' > # }< / span > < / pre >
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< li > < a href = "#details" > Details< / a > < / li >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > .< / p >
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