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< title > Retrieve antimicrobial drugs from clinical text — ab_from_text • AMR (for R)< / title >
2020-06-25 17:34:50 +02:00
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< h1 > Retrieve antimicrobial drugs from clinical text< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://gitlab.com/msberends/AMR/blob/master/R/ab_from_text.R' > < code > R/ab_from_text.R< / code > < / a > < / small >
< div class = "hidden name" > < code > ab_from_text.Rd< / code > < / div >
< / div >
< div class = "ref-description" >
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< p > Use this function on e.g. clinical texts from health care records. It returns a < a href = 'https://rdrr.io/r/base/list.html' > list< / a > with all antimicrobial drugs found in the texts.< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > ab_from_text< / span > (< span class = 'no' > text< / span > , < span class = 'kw' > collapse< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > translate_ab< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / 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 > text< / th >
< td > < p > text to analyse< / p > < / td >
< / tr >
< tr >
< th > collapse< / th >
< td > < p > character to pass on to < code > < a href = 'https://rdrr.io/r/base/paste.html' > paste(..., collapse = ...)< / a > < / code > to only return one character per element of < code > text< / code > , see Examples< / p > < / td >
< / tr >
< tr >
< th > translate_ab< / th >
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< td > < p > a column name of the < a href = 'antibiotics.html' > antibiotics< / a > data set to translate the antibiotic abbreviations to, using < code > < a href = 'ab_property.html' > ab_property()< / a > < / code > . Defaults to < code > FALSE< / code > . Using < code > TRUE< / code > is equal to using "name".< / p > < / td >
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< / tr >
< tr >
< th > ...< / th >
< td > < p > parameters passed on to < code > < a href = 'as.ab.html' > as.ab()< / a > < / code > < / p > < / td >
< / tr >
< / table >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< p > A < a href = 'https://rdrr.io/r/base/list.html' > list< / a > , or a < a href = 'https://rdrr.io/r/base/character.html' > character< / a > if < code > collapse< / code > is not < code > NULL< / code > < / p >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > Without using < code > collapse< / code > , this function will return a < a href = 'https://rdrr.io/r/base/list.html' > list< / a > . This can be convenient to use e.g. inside a < code > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate()< / a > < / code > ):< br / >
< code > df %> % mutate(abx = ab_from_text(clinical_text))< / code > < / p >
< p > The returned AB codes can be transformed to official names, groups, etc. with all < code > < a href = 'ab_property.html' > ab_property()< / a > < / code > functions like < code > < a href = 'ab_property.html' > ab_name()< / a > < / code > and < code > < a href = 'ab_property.html' > ab_group()< / a > < / code > , or by using the < code > translate_ab< / code > parameter.< / p >
< p > With using < code > collapse< / code > , this function will return a < a href = 'https://rdrr.io/r/base/character.html' > character< / a > :< br / >
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< code > df %> % mutate(abx = ab_from_text(clinical_text, collapse = "|"))< / code > < / p >
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< p > This function is also internally used by < code > < a href = 'as.ab.html' > as.ab()< / a > < / code > , although it then only returns the first hit and will throw a note if more results could have been returned.< / p >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
< pre class = "examples" > < span class = 'co' > # mind the bad spelling of amoxicillin in this line, < / span >
< span class = 'co' > # straight from a true health care record:< / span >
< span class = 'fu' > ab_from_text< / span > (< span class = 'st' > "28/03/2020 regular amoxicilliin 500mg po tds"< / span > )
< span class = 'fu' > ab_from_text< / span > (< span class = 'st' > "administered amoxi/clav and cipro"< / span > )
< span class = 'fu' > ab_from_text< / span > (< span class = 'st' > "administered amoxi/clav and cipro"< / span > , < span class = 'kw' > collapse< / span > < span class = 'kw' > =< / span > < span class = 'st' > ", "< / span > )
< span class = 'co' > # if you want to know which antibiotic groups were administered, check it:< / span >
< span class = 'no' > abx< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > ab_from_text< / span > (< span class = 'st' > "administered amoxi/clav and cipro"< / span > )
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< span class = 'fu' > < a href = 'ab_property.html' > ab_group< / a > < / span > (< span class = 'no' > abx< / span > < span class = 'kw' > [[< / span > < span class = 'fl' > 1< / span > ]])
< span class = 'kw' > if< / span > (< span class = 'fu' > < a href = 'https://rdrr.io/r/base/library.html' > require< / a > < / span > (< span class = 'no' > dplyr< / span > )) {
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/reexports.html' > tibble< / a > < / span > (< span class = 'kw' > clinical_text< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://rdrr.io/r/base/c.html' > c< / a > < / span > (< span class = 'st' > "given cipro and mero"< / span > ,
< span class = 'st' > "started on doxy today"< / span > )) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > abx< / span > < span class = 'kw' > =< / span > < span class = 'fu' > ab_from_text< / span > (< span class = 'no' > clinical_text< / span > ),
< span class = 'kw' > abx2< / span > < span class = 'kw' > =< / span > < span class = 'fu' > ab_from_text< / span > (< span class = 'no' > clinical_text< / span > ,
< span class = 'kw' > collapse< / span > < span class = 'kw' > =< / span > < span class = 'st' > "|"< / span > ),
< span class = 'kw' > abx3< / span > < span class = 'kw' > =< / span > < span class = 'fu' > ab_from_text< / span > (< span class = 'no' > clinical_text< / span > ,
< span class = 'kw' > collapse< / span > < span class = 'kw' > =< / span > < span class = 'st' > "|"< / span > ,
< span class = 'kw' > translate_ab< / span > < span class = 'kw' > =< / span > < span class = 'st' > "name"< / span > ))
}< / pre >
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