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< h1 > Guess antibiotic column< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/guess_ab_col.R' > < code > R/guess_ab_col.R< / code > < / a > < / small >
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< div class = "hidden name" > < code > guess_ab_col.Rd< / code > < / div >
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< p > This tries to find a column name in a data set based on information from the < a href = 'antibiotics.html' > antibiotics< / a > data set. Also supports WHONET abbreviations.< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > guess_ab_col< / span > (x = < span class = 'kw' > NULL< / span > , search_string = < span class = 'kw' > NULL< / span > , verbose = < span class = 'fl' > FALSE< / 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 >
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< th > x< / th >
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< td > < p > a < code > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / code > < / p > < / td >
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< / tr >
< tr >
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< th > search_string< / th >
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< td > < p > a text to search < code > x< / code > for, will be checked with < code > < a href = 'as.ab.html' > as.ab()< / a > < / code > if this value is not a column in < code > x< / code > < / p > < / td >
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< / tr >
< tr >
< th > verbose< / th >
< td > < p > a logical to indicate whether additional info should be printed< / p > < / td >
< / tr >
< / table >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< p > A column name of < code > x< / code > , or < code > NULL< / code > when no result is found.< / p >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > You can look for an antibiotic (trade) name or abbreviation and it will search < code > x< / code > and the < a href = 'antibiotics.html' > antibiotics< / a > data set for any column containing a name or code of that antibiotic. < strong > Longer columns names take precendence over shorter column names.< / strong > < / 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. Since this function needs wider usage and more extensive testing, you are very welcome < a href = 'https://github.com/msberends/AMR/issues' > to suggest changes at our repository< / a > or < a href = 'AMR.html' > write us an email (see section 'Contact Us')< / 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.github.io/AMR' > https://msberends.github.io/AMR< / a > you can find < a href = 'https://msberends.github.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.github.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.github.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > . As we would like to better understand the backgrounds and needs of our users, please < a href = 'https://msberends.github.io/AMR/survey.html' > participate in our survey< / 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 = 'kw' > df< / span > < span class = 'op' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (amox = < span class = 'st' > "S"< / span > ,
tetr = < span class = 'st' > "R"< / span > )
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< span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > df< / span > , < span class = 'st' > "amoxicillin"< / span > )
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< span class = 'co' > # [1] "amox"< / span >
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< span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > df< / span > , < span class = 'st' > "J01AA07"< / span > ) < span class = 'co' > # ATC code of tetracycline< / span >
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< span class = 'co' > # [1] "tetr"< / span >
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< span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > df< / span > , < span class = 'st' > "J01AA07"< / span > , verbose = < span class = 'fl' > TRUE< / span > )
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< span class = 'co' > # NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).< / span >
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< span class = 'co' > # [1] "tetr"< / span >
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< span class = 'co' > # WHONET codes< / span >
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< span class = 'kw' > df< / span > < span class = 'op' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (AMP_ND10 = < span class = 'st' > "R"< / span > ,
AMC_ED20 = < span class = 'st' > "S"< / span > )
< span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > df< / span > , < span class = 'st' > "ampicillin"< / span > )
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< span class = 'co' > # [1] "AMP_ND10"< / span >
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< span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > df< / span > , < span class = 'st' > "J01CR02"< / span > )
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< span class = 'co' > # [1] "AMC_ED20"< / span >
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< span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > df< / span > , < span class = 'fu' > < a href = 'as.ab.html' > as.ab< / a > < / span > (< span class = 'st' > "augmentin"< / span > ))
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< span class = 'co' > # [1] "AMC_ED20"< / span >
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< span class = 'co' > # Longer names take precendence:< / span >
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< span class = 'kw' > df< / span > < span class = 'op' > < -< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / span > (AMP_ED2 = < span class = 'st' > "S"< / span > ,
AMP_ED20 = < span class = 'st' > "S"< / span > )
< span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > df< / span > , < span class = 'st' > "ampicillin"< / span > )
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< span class = 'co' > # [1] "AMP_ED20"< / 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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