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< h1 > Name of an antibiotic< / h1 >
< div class = "hidden name" > < code > abname.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > .< / p >
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< / div >
< pre class = "usage" > < span class = 'fu' > abname< / span > (< span class = 'no' > abcode< / span > , < span class = 'kw' > from< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "guess"< / span > , < span class = 'st' > "atc"< / span > , < span class = 'st' > "certe"< / span > , < span class = 'st' > "umcg"< / span > ),
< span class = 'kw' > to< / span > < span class = 'kw' > =< / span > < span class = 'st' > "official"< / span > , < span class = 'kw' > textbetween< / span > < span class = 'kw' > =< / span > < span class = 'st' > " + "< / span > , < span class = 'kw' > tolower< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )< / pre >
< 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 > abcode< / th >
< td > < p > a code or name, like < code > "AMOX"< / code > , < code > "AMCL"< / code > or < code > "J01CA04"< / code > < / p > < / td >
< / tr >
< tr >
< th > from, to< / th >
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< td > < p > type to transform from and to. See < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > for its column names. WIth < code > from = "guess"< / code > the from will be guessed from < code > "atc"< / code > , < code > "certe"< / code > and < code > "umcg"< / code > . When using < code > to = "atc"< / code > , the ATC code will be searched using < code > < a href = 'as.atc.html' > as.atc< / a > < / code > .< / p > < / td >
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< / tr >
< tr >
< th > textbetween< / th >
< td > < p > text to put between multiple returned texts< / p > < / td >
< / tr >
< tr >
< th > tolower< / th >
< td > < p > return output as lower case with function < code > < a href = 'https://www.rdocumentation.org/packages/base/topics/chartr' > tolower< / a > < / code > .< / p > < / td >
< / tr >
< / table >
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
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< p > < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > < / p >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > < strong > The < code > < a href = 'AMR-deprecated.html' > ab_property< / a > < / code > functions are faster and more concise< / strong > , but do not support concatenated strings, like < code > abname("AMCL+GENT"< / code > .< / p >
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< h2 class = "hasAnchor" id = "whocc" > < a class = "anchor" href = "#whocc" > < / a > WHOCC< / h2 >
< p > < img src = 'figures/logo_who.png' height = 60px style = margin-bottom:5px / > < br / >
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This package contains < strong > all ~500 antimicrobial drugs< / strong > and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, < a href = 'https://www.whocc.no' > https://www.whocc.no< / a > ) and the Pharmaceuticals Community Register of the European Commission (< 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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< p > These have become the gold standard for international drug utilisation monitoring and research.< / p >
< p > The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.< / 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 = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
< span class = 'fu' > abname< / span > (< span class = 'st' > "AMCL"< / span > )
< span class = 'co' > # "Amoxicillin and beta-lactamase inhibitor"< / span >
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< span class = 'co' > # It is quite flexible at default (having `from = "guess"`)< / span >
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< span class = 'fu' > abname< / span > (< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "amox"< / span > , < span class = 'st' > "J01CA04"< / span > , < span class = 'st' > "Trimox"< / span > , < span class = 'st' > "dispermox"< / span > , < span class = 'st' > "Amoxil"< / span > ))
< span class = 'co' > # "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"< / span >
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< span class = 'co' > # Multiple antibiotics can be combined with "+".< / span >
< span class = 'co' > # The second antibiotic will be set to lower case when `tolower` was not set:< / span >
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< span class = 'fu' > abname< / span > (< span class = 'st' > "AMCL+GENT"< / span > , < span class = 'kw' > textbetween< / span > < span class = 'kw' > =< / span > < span class = 'st' > "/"< / span > )
< span class = 'co' > # "amoxicillin and enzyme inhibitor/gentamicin"< / span >
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< span class = 'fu' > abname< / span > (< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "AMCL"< / span > , < span class = 'st' > "GENT"< / span > ))
< span class = 'co' > # "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"< / span >
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< span class = 'fu' > abname< / span > (< span class = 'st' > "AMCL"< / span > , < span class = 'kw' > to< / span > < span class = 'kw' > =< / span > < span class = 'st' > "trivial_nl"< / span > )
< span class = 'co' > # "Amoxicilline/clavulaanzuur"< / span >
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< span class = 'fu' > abname< / span > (< span class = 'st' > "AMCL"< / span > , < span class = 'kw' > to< / span > < span class = 'kw' > =< / span > < span class = 'st' > "atc"< / span > )
< span class = 'co' > # "J01CR02"< / span >
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< span class = 'co' > # specific codes for University Medical Center Groningen (UMCG):< / span >
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< span class = 'fu' > abname< / span > (< span class = 'st' > "J01CR02"< / span > , < span class = 'kw' > from< / span > < span class = 'kw' > =< / span > < span class = 'st' > "atc"< / span > , < span class = 'kw' > to< / span > < span class = 'kw' > =< / span > < span class = 'st' > "umcg"< / span > )
< span class = 'co' > # "AMCL"< / span >
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< span class = 'co' > # specific codes for Certe:< / span >
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< span class = 'fu' > abname< / span > (< span class = 'st' > "J01CR02"< / span > , < span class = 'kw' > from< / span > < span class = 'kw' > =< / span > < span class = 'st' > "atc"< / span > , < span class = 'kw' > to< / span > < span class = 'kw' > =< / span > < span class = 'st' > "certe"< / span > )
< span class = 'co' > # "amcl"< / span >
< span class = 'co' > # }< / 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/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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