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< h1 > Guess antibiotic column< / h1 >
< 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 < code > < a href = 'antibiotics.html' > antibiotics< / a > < / code > data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the < code > data.frame< / code > for any column containing a name or ATC code of that antibiotic.< / p >
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< pre class = "usage" > < span class = 'fu' > guess_ab_col< / span > (< span class = 'kw' > tbl< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > col< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )< / pre >
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< th > tbl< / th >
< td > < p > a < code > data.frame< / code > < / p > < / td >
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< th > col< / th >
< td > < p > a character to look for< / p > < / td >
< / tr >
< tr >
< th > verbose< / th >
< td > < p > a logical to indicate whether additional info should be printed< / p > < / td >
< / tr >
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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 >
< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
< span class = 'no' > df< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/data.frame' > data.frame< / a > < / span > (< span class = 'kw' > amox< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > ,
< span class = 'kw' > tetr< / span > < span class = 'kw' > =< / span > < span class = 'st' > "R"< / span > )
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "amoxicillin"< / span > )
< span class = 'co' > # [1] "amox"< / span >
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "J01AA07"< / span > ) < span class = 'co' > # ATC code of Tetracycline< / span >
< span class = 'co' > # [1] "tetr"< / span >
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "J01AA07"< / span > , < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
< span class = 'co' > # using column `tetr` for col "J01AA07"< / span >
< span class = 'co' > # [1] "tetr"< / span >
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< span class = 'co' > # WHONET codes< / span >
< span class = 'no' > df< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/data.frame' > data.frame< / a > < / span > (< span class = 'kw' > AMP_ND10< / span > < span class = 'kw' > =< / span > < span class = 'st' > "R"< / span > ,
< span class = 'kw' > AMC_ED20< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > )
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "ampicillin"< / span > )
< span class = 'co' > # [1] "AMP_ND10"< / span >
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'st' > "J01CR02"< / span > )
< span class = 'co' > # [1] "AMC_ED20"< / span >
< span class = 'fu' > guess_ab_col< / span > (< span class = 'no' > df< / span > , < span class = 'fu' > < a href = 'as.atc.html' > as.atc< / a > < / span > (< span class = 'st' > "augmentin"< / span > ))
< span class = 'co' > # [1] "AMC_ED20"< / span >
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< span class = 'co' > # }< / span > < / pre >
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