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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Transform Input to Disk Diffusion Diameters< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/main/R/disk.R" class = "external-link" > < code > R/disk.R< / code > < / a > < / small >
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< div class = "d-none name" > < code > as.disk.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
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< p > This transforms a vector to a new class < code > disk< / code > , which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50.< / p >
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< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > as.disk< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , na.rm < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "va" > NA_disk_< / span > < / span >
< span > < / span >
< span > < span class = "fu" > is.disk< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "format" > Format< a class = "anchor" aria-label = "anchor" href = "#format" > < / a > < / h2 >
< p > An object of class < code > disk< / code > (inherits from < code > integer< / code > ) of length 1.< / p >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
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< dl > < dt id = "arg-x" > x< a class = "anchor" aria-label = "anchor" href = "#arg-x" > < / a > < / dt >
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< dd > < p > vector< / p > < / dd >
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< dt id = "arg-na-rm" > na.rm< a class = "anchor" aria-label = "anchor" href = "#arg-na-rm" > < / a > < / dt >
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< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > indicating whether missing values should be removed< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "value" > Value< a class = "anchor" aria-label = "anchor" href = "#value" > < / a > < / h2 >
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< p > An < a href = "https://rdrr.io/r/base/integer.html" class = "external-link" > integer< / a > with additional class < code > disk< / code > < / p >
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< / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
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< p > Interpret disk values as SIR values with < code > < a href = "as.sir.html" > as.sir()< / a > < / code > . It supports guidelines from EUCAST and CLSI.< / p >
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< p > Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 0-50 range will return < code > NA< / code > .< / p >
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< p > < code > NA_disk_< / code > is a missing value of the new < code > disk< / code > class.< / p >
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< / div >
< div class = "section level2" >
< h2 id = "see-also" > See also< a class = "anchor" aria-label = "anchor" href = "#see-also" > < / a > < / h2 >
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< div class = "dont-index" > < p > < code > < a href = "as.sir.html" > as.sir()< / a > < / code > < / p > < / div >
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< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # transform existing disk zones to the `disk` class (using base R)< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > microorganism < span class = "op" > =< / span > < span class = "st" > "Escherichia coli"< / span > ,< / span > < / span >
< span class = "r-in" > < span > AMP < span class = "op" > =< / span > < span class = "fl" > 20< / span > ,< / span > < / span >
< span class = "r-in" > < span > CIP < span class = "op" > =< / span > < span class = "fl" > 14< / span > ,< / span > < / span >
< span class = "r-in" > < span > GEN < span class = "op" > =< / span > < span class = "fl" > 18< / span > ,< / span > < / span >
< span class = "r-in" > < span > TOB < span class = "op" > =< / span > < span class = "fl" > 16< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > [< / span > , < span class = "fl" > 2< / span > < span class = "op" > :< / span > < span class = "fl" > 5< / span > < span class = "op" > ]< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/lapply.html" class = "external-link" > lapply< / a > < / span > < span class = "op" > (< / span > < span class = "va" > df< / span > < span class = "op" > [< / span > , < span class = "fl" > 2< / span > < span class = "op" > :< / span > < span class = "fl" > 5< / span > < span class = "op" > ]< / span > , < span class = "va" > as.disk< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/str.html" class = "external-link" > str< / a > < / span > < span class = "op" > (< / span > < span class = "va" > df< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 'data.frame': 1 obs. of 5 variables:< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ microorganism: chr "Escherichia coli"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ AMP : 'disk' int 20< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ CIP : 'disk' int 14< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ GEN : 'disk' int 18< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ TOB : 'disk' int 16< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # transforming is easier with dplyr:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > , < span class = "va" > as.disk< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > microorganism AMP CIP GEN TOB< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 Escherichia coli 20 14 18 16< / span >
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # interpret disk values, see ?as.sir< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
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< span class = "r-in" > < span > x < span class = "op" > =< / span > < span class = "fu" > as.disk< / span > < span class = "op" > (< / span > < span class = "fl" > 18< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "Strep pneu"< / span > , < span class = "co" > # `mo` will be coerced with as.mo()< / span > < / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "ampicillin"< / span > , < span class = "co" > # and `ab` with as.ab()< / span > < / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "EUCAST"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2024...< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Class 'sir'< / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] R< / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # interpret whole data set, pretend to be all from urinary tract infections:< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "va" > df< / span > , uti < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: column 'AMP' (ampicillin), EUCAST< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 2024...< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: column 'CIP' (ciprofloxacin), EUCAST< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 2024...< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 2024...< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 2024...< / span >
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< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > microorganism AMP CIP GEN TOB< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 Escherichia coli S < NA> S S< / span >
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< p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
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