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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 = 'ab_property.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 = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
< p > < img src = 'figures/logo.png' height = 40px style = margin-bottom:5px / > < br / >
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 omprehensive tutorial< / a > about how to conduct AMR analysis and find < a href = 'https://msberends.gitlab.io/AMR/reference' > the complete documentation of all functions< / a > , which reads a lot easier than in R.< / 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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