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< meta property = "og:description" content = "Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()." / >
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< h1 > Property of an antibiotic< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://gitlab.com/msberends/AMR/blob/master/R/ab_property.R' > < code > R/ab_property.R< / code > < / a > < / small >
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< 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 < a href = 'antibiotics.html' > antibiotics< / a > 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_loinc< / span > (< span class = 'no' > x< / 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_url< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > open< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / 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 >
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< 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://rdrr.io/r/base/options.html' > getOption("AMR_locale")< / a > < / 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 >
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< td > < p > other parameters passed on to < code > < a href = 'as.ab.html' > as.ab()< / a > < / code > < / p > < / td >
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< / 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 >
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< td > < p > one of the column names of one of the < a href = 'antibiotics.html' > antibiotics< / a > data set< / p > < / td >
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< / tr >
< / table >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
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< ul >
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< li > < p > An < code > < a href = 'https://rdrr.io/r/base/integer.html' > integer< / a > < / code > in case of < code > ab_cid()< / code > < / p > < / li >
< li > < p > A named < code > < a href = 'https://rdrr.io/r/base/list.html' > list< / a > < / code > in case of < code > ab_info()< / code > and multiple < code > ab_synonyms()< / code > /< code > ab_tradenames()< / code > < / p > < / li >
< li > < p > A < code > < a href = 'https://rdrr.io/r/base/double.html' > double< / a > < / code > in case of < code > ab_ddd()< / code > < / p > < / li >
< li > < p > A < code > < a href = 'https://rdrr.io/r/base/character.html' > character< / a > < / code > in all other cases< / p > < / li >
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< / 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 >
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< p > The function < code > ab_url()< / code > will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.< / p >
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< h2 class = "hasAnchor" id = "maturing-lifecycle" > < a class = "anchor" href = "#maturing-lifecycle" > < / a > Maturing lifecycle< / h2 >
< p > < img src = 'figures/lifecycle_maturing.svg' style = margin-bottom:5px / > < br / >
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The < a href = 'lifecycle.html' > lifecycle< / a > of this function is < strong > maturing< / strong > . The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.< / p >
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< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
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< 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 >
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< 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 comprehensive 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 > < a href = 'antibiotics.html' > antibiotics< / a > < / 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' > # all properties:< / span >
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< 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 >
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< span class = 'fu' > ab_url< / span > (< span class = 'st' > "AMX"< / span > ) < span class = 'co' > # link to the official WHO page< / span >
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< span class = 'co' > # smart lowercase tranformation< / span >
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< span class = 'fu' > ab_name< / span > (< span class = 'kw' > x< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > 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://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "AMC"< / span > , < span class = 'st' > "PLB"< / span > ),
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< span class = 'kw' > tolower< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "amoxicillin/clavulanic acid" "polymyxin B"< / span >
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< span class = 'co' > # defined daily doses (DDD)< / span >
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< 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, so you can go from 'any' to 'any':< / span >
< span class = 'fu' > ab_atc< / span > (< span class = 'st' > "AMP"< / span > ) < span class = 'co' > # ATC code of AMP (ampicillin)< / span >
< span class = 'fu' > ab_group< / span > (< span class = 'st' > "J01CA01"< / span > ) < span class = 'co' > # Drug group of ampicillins ATC code< / span >
< span class = 'fu' > ab_loinc< / span > (< span class = 'st' > "ampicillin"< / span > ) < span class = 'co' > # LOINC codes of ampicillin< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'st' > "21066-6"< / span > ) < span class = 'co' > # "Ampicillin" (using LOINC)< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'fl' > 6249< / span > ) < span class = 'co' > # "Ampicillin" (using CID)< / span >
< span class = 'fu' > ab_name< / span > (< span class = 'st' > "J01CA01"< / span > ) < span class = 'co' > # "Ampicillin" (using ATC)< / span >
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< span class = 'co' > # spelling from different languages and dyslexia are no problem< / span >
< span class = 'fu' > ab_atc< / span > (< span class = 'st' > "ceftriaxon"< / span > )
< span class = 'fu' > ab_atc< / span > (< span class = 'st' > "cephtriaxone"< / span > )
< span class = 'fu' > ab_atc< / span > (< span class = 'st' > "cephthriaxone"< / span > )
< span class = 'fu' > ab_atc< / span > (< span class = 'st' > "seephthriaaksone"< / span > )< / pre >
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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/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.1.< / p >
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