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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Add Custom Antimicrobials to This Package< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/add_custom_antimicrobials.R" class = "external-link" > < code > R/add_custom_antimicrobials.R< / code > < / a > < / small >
< div class = "d-none name" > < code > add_custom_antimicrobials.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
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< p > With < code > add_custom_antimicrobials()< / code > you can add your own custom antimicrobial codes to the < code > AMR< / code > package.< / 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" > add_custom_antimicrobials< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > clear_custom_antimicrobials< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > x< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > resembling the < a href = "antibiotics.html" > antibiotics< / a > data set, at least containing columns "ab" and "name"< / p > < / dd >
< / dl > < / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
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< p > Due to how < span style = "R" > R< / span > works, the < code > add_custom_antimicrobials()< / code > function has to be run in every < span style = "R" > R< / span > session - added antimicrobials are not stored between sessions and are thus lost when < span style = "R" > R< / span > is exited. It is possible to save the antimicrobial additions to your < code > .Rprofile< / code > file to circumvent this, although this requires to load the < code > AMR< / code > package at every start-up:< / p >
< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "co" > # Open .Rprofile file< / span > < / span >
< span > < span class = "fu" > utils< / span > < span class = "fu" > ::< / span > < span class = "fu" > < a href = "https://rdrr.io/r/utils/file.edit.html" class = "external-link" > file.edit< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "~/.Rprofile"< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "co" > # Add custom antibiotic codes:< / span > < / span >
< span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://msberends.github.io/AMR/" > AMR< / a > < / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "fu" > < a href = "../reference/add_custom_antimicrobials.html" > add_custom_antimicrobials< / a > < / span > < span class = "op" > (< / span > < / span >
< 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 > ab < span class = "op" > =< / span > < span class = "st" > "TEST"< / span > ,< / span >
< span > name < span class = "op" > =< / span > < span class = "st" > "Test Antibiotic"< / span > ,< / span >
< span > group < span class = "op" > =< / span > < span class = "st" > "Test Group"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div >
< p > Use < code > clear_custom_antimicrobials()< / code > to clear the previously added antimicrobials.< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
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< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # returns NA and throws a warning (which is now suppressed):< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/warning.html" class = "external-link" > suppressWarnings< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "as.ab.html" > as.ab< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "test"< / 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 > Class < ab> < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] < NA> < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # now add a custom entry - it will be considered by as.ab() and< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # all ab_*() functions< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > add_custom_antimicrobials< / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < 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 > ab < span class = "op" > =< / span > < span class = "st" > "TEST"< / span > ,< / span > < / span >
< span class = "r-in" > < span > name < span class = "op" > =< / span > < span class = "st" > "Test Antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # you can add any property present in the< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # 'antibiotics' data set, such as 'group':< / span > < / span > < / span >
< span class = "r-in" > < span > group < span class = "op" > =< / span > < span class = "st" > "Test Group"< / span > < span class = "op" > )< / 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 > ℹ < / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # "test" is now a new antibiotic:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "as.ab.html" > as.ab< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "test"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Class < ab> < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] TEST< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "test"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Antibiotic"< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_group< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "test"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Group"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_info< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "test"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ab< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "TEST"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $cid< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $name< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Antibiotic"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $group< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Test Group"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > NULL< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group1< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $atc_group2< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $tradenames< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > NULL< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $loinc< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > NULL< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$oral$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$amount< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ddd$iv$units< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # Add Co-fluampicil, which is one of the many J01CR50 codes, see< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # https://www.whocc.no/ddd/list_of_ddds_combined_products/< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > add_custom_antimicrobials< / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < 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 > ab < span class = "op" > =< / span > < span class = "st" > "COFLU"< / span > ,< / span > < / span >
< span class = "r-in" > < span > name < span class = "op" > =< / span > < span class = "st" > "Co-fluampicil"< / span > ,< / span > < / span >
< span class = "r-in" > < span > atc < span class = "op" > =< / span > < span class = "st" > "J01CR50"< / span > ,< / span > < / span >
< span class = "r-in" > < span > group < span class = "op" > =< / span > < span class = "st" > "Beta-lactams/penicillines"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_atc< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Co-fluampicil"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "J01CR50"< / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "ab_property.html" > ab_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "J01CR50"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Co-fluampicil"< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # even antibiotic selectors work< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / 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 > random_column < span class = "op" > =< / span > < span class = "st" > "test"< / span > ,< / span > < / span >
2022-10-14 13:08:40 +02:00
< span class = "r-in" > < span > coflu < span class = "op" > =< / span > < span class = "fu" > < a href = "as.rsi.html" > as.rsi< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > ampicillin < span class = "op" > =< / span > < span class = "fu" > < a href = "as.rsi.html" > as.rsi< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
2022-10-11 11:00:04 +02:00
< span class = "r-in" > < span > < span class = "va" > x< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > random_column coflu ampicillin< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 test S R< / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > [< / span > , < span class = "fu" > < a href = "antibiotic_class_selectors.html" > betalactams< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'ampicillin'< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > coflu ampicillin< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1 S R< / span >
2022-10-15 15:28:27 +02:00
< span class = "r-in" > < span > < span class = "co" > # }< / span > < / span > < / span >
2022-10-10 21:46:42 +02:00
< / code > < / pre > < / div >
2022-10-10 20:27:14 +02:00
< / div >
< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
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< footer > < div class = "pkgdown-footer-left" >
< p > < / p > < p > < code > AMR< / code > (for R). Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > in collaboration with non-profit organisations< br > < a target = "_blank" href = "https://www.certe.nl" class = "external-link" > Certe Medical Diagnostics and Advice Foundation< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > .< / p >
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