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< title > Property of an antibiotic — ab_property • AMR (for R)< / title >
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< h1 > Property of an antibiotic< / h1 >
< div class = "hidden name" > < code > ab_property.Rd< / code > < / div >
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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_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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< 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 / >
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. We will strive to maintain backward compatibility, but the 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 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 = '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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< li > < a href = "#details" > Details< / a > < / li >
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< li > < a href = "#maturing-lifecycle" > Maturing lifecycle< / a > < / li >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
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