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< title > Key antibiotics for first < em > weighted< / em > isolates — key_antibiotics • AMR (for R)< / title >
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< h1 > Key antibiotics for first < em > weighted< / em > isolates< / h1 >
< div class = "hidden name" > < code > key_antibiotics.Rd< / code > < / div >
< / div >
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< p > These function can be used to determine first isolates (see < code > < a href = 'first_isolate.html' > first_isolate< / a > < / code > ). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first < em > weighted< / em > isolates.< / p >
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< / div >
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< pre class = "usage" > < span class = 'fu' > key_antibiotics< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > universal_1< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "AMX"< / span > ),
< span class = 'kw' > universal_2< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "AMC"< / span > ), < span class = 'kw' > universal_3< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "CXM"< / span > ), < span class = 'kw' > universal_4< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "TZP"< / span > ),
< span class = 'kw' > universal_5< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "CIP"< / span > ), < span class = 'kw' > universal_6< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "SXT"< / span > ), < span class = 'kw' > GramPos_1< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "VAN"< / span > ),
< span class = 'kw' > GramPos_2< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "TEC"< / span > ), < span class = 'kw' > GramPos_3< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "TCY"< / span > ), < span class = 'kw' > GramPos_4< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "ERY"< / span > ),
< span class = 'kw' > GramPos_5< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "OXA"< / span > ), < span class = 'kw' > GramPos_6< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "RIF"< / span > ), < span class = 'kw' > GramNeg_1< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "GEN"< / span > ),
< span class = 'kw' > GramNeg_2< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "TOB"< / span > ), < span class = 'kw' > GramNeg_3< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "COL"< / span > ), < span class = 'kw' > GramNeg_4< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "CTX"< / span > ),
< span class = 'kw' > GramNeg_5< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > , < span class = 'st' > "CAZ"< / span > ), < span class = 'kw' > GramNeg_6< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (< span class = 'no' > x< / span > ,
< span class = 'st' > "MEM"< / span > ), < span class = 'kw' > warnings< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > key_antibiotics_equal< / span > (< span class = 'no' > y< / span > , < span class = 'no' > z< / span > , < span class = 'kw' > type< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "keyantibiotics"< / span > , < span class = 'st' > "points"< / span > ),
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< span class = 'kw' > ignore_I< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'kw' > points_threshold< / span > < span class = 'kw' > =< / span > < span class = 'fl' > 2< / span > , < span class = 'kw' > info< / 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 >
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< th > x< / th >
< td > < p > table with antibiotics coloms, like < code > AMX< / code > or < code > amox< / code > < / p > < / td >
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< / tr >
< tr >
< th > col_mo< / th >
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< td > < p > column name of the unique IDs of the microorganisms (see < code > < a href = 'as.mo.html' > mo< / a > < / code > ), defaults to the first column of class < code > mo< / code > . Values will be coerced using < code > < a href = 'as.mo.html' > as.mo< / a > < / code > .< / p > < / td >
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< / tr >
< tr >
< th > universal_1, universal_2, universal_3, universal_4, universal_5, universal_6< / th >
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< td > < p > column names of < strong > broad-spectrum< / strong > antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with < code > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / code > .< / p > < / td >
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< / tr >
< tr >
< th > GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6< / th >
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< td > < p > column names of antibiotics for < strong > Gram positives< / strong > , case-insensitive. At default, the columns containing these antibiotics will be guessed with < code > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / code > .< / p > < / td >
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< / tr >
< tr >
< th > GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6< / th >
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< td > < p > column names of antibiotics for < strong > Gram negatives< / strong > , case-insensitive. At default, the columns containing these antibiotics will be guessed with < code > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / code > .< / p > < / td >
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< / tr >
< tr >
< th > warnings< / th >
< td > < p > give warning about missing antibiotic columns, they will anyway be ignored< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
< td > < p > other parameters passed on to function< / p > < / td >
< / tr >
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< tr >
< th > y, z< / th >
< td > < p > characters to compare< / p > < / td >
< / tr >
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< tr >
< th > type< / th >
< td > < p > type to determine weighed isolates; can be < code > "keyantibiotics"< / code > or < code > "points"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > ignore_I< / th >
< td > < p > logical to determine whether antibiotic interpretations with < code > "I"< / code > will be ignored when < code > type = "keyantibiotics"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > points_threshold< / th >
< td > < p > points until the comparison of key antibiotics will lead to inclusion of an isolate when < code > type = "points"< / code > , see Details< / p > < / td >
< / tr >
< tr >
< th > info< / th >
< td > < p > print progress< / p > < / td >
< / tr >
< / table >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > The function < code > key_antibiotics< / code > returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using < code > key_antibiotics_equal< / code > , to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (< code > "."< / code > ). The < code > < a href = 'first_isolate.html' > first_isolate< / a > < / code > function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible < em > S. aureus< / em > (MSSA) found within the same episode (see < code > episode< / code > parameter of < code > < a href = 'first_isolate.html' > first_isolate< / a > < / code > ). Without key antibiotic comparison it would not.< / p >
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< p > At default, the antibiotics that are used for < strong > Gram positive bacteria< / strong > are (colum names): < br / >
< code > "amox"< / code > , < code > "amcl"< / code > , < code > "cfur"< / code > , < code > "pita"< / code > , < code > "cipr"< / code > , < code > "trsu"< / code > (until here is universal), < code > "vanc"< / code > , < code > "teic"< / code > , < code > "tetr"< / code > , < code > "eryt"< / code > , < code > "oxac"< / code > , < code > "rifa"< / code > .< / p >
< p > At default, the antibiotics that are used for < strong > Gram negative bacteria< / strong > are (colum names): < br / >
< code > "amox"< / code > , < code > "amcl"< / code > , < code > "cfur"< / code > , < code > "pita"< / code > , < code > "cipr"< / code > , < code > "trsu"< / code > (until here is universal), < code > "gent"< / code > , < code > "tobr"< / code > , < code > "coli"< / code > , < code > "cfot"< / code > , < code > "cfta"< / code > , < code > "mero"< / code > .< / p >
< p > The function < code > key_antibiotics_equal< / code > checks the characters returned by < code > key_antibiotics< / code > for equality, and returns a logical vector.< / p >
< h2 class = "hasAnchor" id = "key-antibiotics" > < a class = "anchor" href = "#key-antibiotics" > < / a > Key antibiotics< / h2 >
< p > There are two ways to determine whether isolates can be included as first < em > weighted< / em > isolates which will give generally the same results: < br / > < / p >
< p > < strong > 1. Using< / strong > < code > type = "keyantibiotics"< / code > < strong > and parameter< / strong > < code > ignore_I< / code > < br / >
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Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With < code > ignore_I = FALSE< / code > , also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the < code > key_antibiotics< / code > function. < br / > < / p >
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< p > < strong > 2. Using< / strong > < code > type = "points"< / code > < strong > and parameter< / strong > < code > points_threshold< / code > < br / >
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A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds < code > points_threshold< / code > , which default to < code > 2< / code > , an isolate will be (re)selected as a first weighted isolate.< / 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 = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
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< div class = 'dont-index' > < p > < code > < a href = 'first_isolate.html' > first_isolate< / a > < / code > < / p > < / div >
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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 = 'co' > # septic_patients is a dataset available in the AMR package< / span >
?< span class = 'no' > septic_patients< / span >
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/library' > library< / a > < / span > (< span class = 'no' > dplyr< / span > )
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< span class = 'co' > # set key antibiotics to a new variable< / span >
< span class = 'no' > my_patients< / span > < span class = 'kw' > < -< / span > < span class = 'no' > septic_patients< / span > < span class = 'kw' > %> %< / span >
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< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (< span class = 'kw' > keyab< / span > < span class = 'kw' > =< / span > < span class = 'fu' > key_antibiotics< / span > (< span class = 'no' > .< / span > )) < span class = 'kw' > %> %< / span >
< span class = 'fu' > < a href = 'https://dplyr.tidyverse.org/reference/mutate.html' > mutate< / a > < / span > (
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< span class = 'co' > # now calculate first isolates< / span >
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< span class = 'kw' > first_regular< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'first_isolate.html' > first_isolate< / a > < / span > (< span class = 'no' > .< / span > , < span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > ),
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< span class = 'co' > # and first WEIGHTED isolates< / span >
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< span class = 'kw' > first_weighted< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'first_isolate.html' > first_isolate< / a > < / span > (< span class = 'no' > .< / span > , < span class = 'kw' > col_keyantibiotics< / span > < span class = 'kw' > =< / span > < span class = 'st' > "keyab"< / span > )
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)
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< span class = 'co' > # Check the difference, in this data set it results in 7% more isolates:< / span >
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< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/sum' > sum< / a > < / span > (< span class = 'no' > my_patients< / span > $< span class = 'no' > first_regular< / span > , < span class = 'kw' > na.rm< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
< span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/sum' > sum< / a > < / span > (< span class = 'no' > my_patients< / span > $< span class = 'no' > first_weighted< / span > , < span class = 'kw' > na.rm< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
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< span class = 'co' > # output of the `key_antibiotics` function could be like this:< / span >
< span class = 'no' > strainA< / span > < span class = 'kw' > < -< / span > < span class = 'st' > "SSSRR.S.R..S"< / span >
< span class = 'no' > strainB< / span > < span class = 'kw' > < -< / span > < span class = 'st' > "SSSIRSSSRSSS"< / span >
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< span class = 'fu' > key_antibiotics_equal< / span > (< span class = 'no' > strainA< / span > , < span class = 'no' > strainB< / span > )
< span class = 'co' > # TRUE, because I is ignored (as well as missing values)< / span >
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< span class = 'fu' > key_antibiotics_equal< / span > (< span class = 'no' > strainA< / span > , < span class = 'no' > strainB< / span > , < span class = 'kw' > ignore_I< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
< span class = 'co' > # FALSE, because I is not ignored and so the 4th value differs< / span >
< span class = 'co' > # }< / span > < / pre >
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< h2 > Contents< / h2 >
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< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#details" > Details< / a > < / li >
< li > < a href = "#key-antibiotics" > Key antibiotics< / a > < / li >
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< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
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< li > < a href = "#see-also" > See also< / a > < / li >
< li > < a href = "#examples" > Examples< / a > < / li >
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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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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.3.0.< / p >
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