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<!-- Generated by pkgdown: do not edit by hand --> < html lang = "en" > < head > < meta http-equiv = "Content-Type" content = "text/html; charset=UTF-8" > < meta charset = "utf-8" > < meta http-equiv = "X-UA-Compatible" content = "IE=edge" > < meta name = "viewport" content = "width=device-width, initial-scale=1.0" > < title > Antibiotic Selectors — antibiotic_class_selectors • AMR (for R)< / title > <!-- favicons --> < link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" > < link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "180x180" href = "../apple-touch-icon.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "120x120" href = "../apple-touch-icon-120x120.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "76x76" href = "../apple-touch-icon-76x76.png" > < link rel = "apple-touch-icon" type = "image/png" sizes = "60x60" href = "../apple-touch-icon-60x60.png" > <!-- jquery --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script > <!-- Bootstrap --> < link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" > < script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity = "sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin = "anonymous" > < / script > <!-- bootstrap - toc --> < link rel = "stylesheet" href = "../bootstrap-toc.css" > < script src = "../bootstrap-toc.js" > < / script > <!-- Font Awesome icons --> < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity = "sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin = "anonymous" > < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity = "sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin = "anonymous" > <!-- clipboard.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script > <!-- headroom.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity = "sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script > <!-- pkgdown --> < link href = "../pkgdown.css" rel = "stylesheet" > < script src = "../pkgdown.js" > < / script > < link href = "../extra.css" rel = "stylesheet" > < script src = "../extra.js" > < / script > < meta property = "og:title" content = "Antibiotic Selectors — antibiotic_class_selectors" > < meta property = "og:description" content = 'These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by cephalosporins().' > < meta property = "og:image" content = "https://msberends.github.io/AMR/logo.svg" > < meta name = "twitter:card" content = "summary_large_image" > < meta name = "twitter:creator" content = "@msberends" > < meta name = "twitter:site" content = "@univgroningen" > <!-- mathjax --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity = "sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity = "sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin = "anonymous" > < / script > <!-- [if lt IE 9]>
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< h1 > Antibiotic Selectors< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/ab_selectors.R" class = "external-link" > < code > R/ab_selectors.R< / code > < / a > < / small >
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< p > These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by < code > cephalosporins()< / code > .< / p >
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< / div >
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< div id = "ref-usage" >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "fu" > ab_class< / span > < span class = "op" > (< / span > < span class = "va" > ab_class< / span > , only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , only_treatable < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > ab_selector< / span > < span class = "op" > (< / span > < span class = "va" > filter< / span > , only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , only_treatable < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , only_treatable < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > aminopenicillins< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > antifungals< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > antimycobacterials< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > betalactams< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , only_treatable < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , only_treatable < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > cephalosporins< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > cephalosporins_1st< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > cephalosporins_2nd< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > cephalosporins_3rd< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > cephalosporins_4th< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > cephalosporins_5th< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > fluoroquinolones< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > glycopeptides< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > lincosamides< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > lipoglycopeptides< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > macrolides< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > oxazolidinones< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > penicillins< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > polymyxins< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , only_treatable < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > streptogramins< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > quinolones< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > tetracyclines< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > trimethoprims< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
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< span class = "fu" > ureidopenicillins< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
< span class = "fu" > administrable_per_os< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
< span class = "fu" > administrable_iv< / span > < span class = "op" > (< / span > only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > , < span class = "va" > ...< / span > < span class = "op" > )< / span >
< span class = "fu" > not_intrinsic_resistant< / span > < span class = "op" > (< / span >
only_rsi_columns < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > ,
col_mo < span class = "op" > =< / span > < span class = "cn" > NULL< / span > ,
version_expertrules < span class = "op" > =< / span > < span class = "fl" > 3.3< / span > ,
< span class = "va" > ...< / span >
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< span class = "op" > )< / span > < / code > < / pre > < / div >
< / div >
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< div id = "arguments" >
< h2 > Arguments< / h2 >
< dl > < dt > ab_class< / dt >
< dd > < p > an antimicrobial class or a part of it, such as < code > "carba"< / code > and < code > "carbapenems"< / code > . The columns < code > group< / code > , < code > atc_group1< / code > and < code > atc_group2< / code > of the < a href = "antibiotics.html" > antibiotics< / a > data set will be searched (case-insensitive) for this value.< / p > < / dd >
< dt > only_rsi_columns< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether only columns of class < code > < rsi> < / code > must be selected (defaults to < code > FALSE< / code > ), see < code > < a href = "as.rsi.html" > as.rsi()< / a > < / code > < / p > < / dd >
< dt > only_treatable< / dt >
< dd > < p > a < a href = "https://rdrr.io/r/base/logical.html" class = "external-link" > logical< / a > to indicate whether agents that are only for laboratory tests should be excluded (defaults to < code > TRUE< / code > ), such as gentamicin-high (< code > GEH< / code > ) and imipenem/EDTA (< code > IPE< / code > )< / p > < / dd >
< dt > ...< / dt >
< dd > < p > ignored, only in place to allow future extensions< / p > < / dd >
< dt > filter< / dt >
< dd > < p > an < a href = "https://rdrr.io/r/base/expression.html" class = "external-link" > expression< / a > to be evaluated in the < a href = "antibiotics.html" > antibiotics< / a > data set, such as < code > name %like% "trim"< / code > < / p > < / dd >
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< dt > col_mo< / dt >
< dd > < p > column name of the IDs of the microorganisms (see < code > < a href = "as.mo.html" > as.mo()< / a > < / code > ), defaults to the first column of class < code > < a href = "as.mo.html" > mo< / a > < / code > . Values will be coerced using < code > < a href = "as.mo.html" > as.mo()< / a > < / code > .< / p > < / dd >
< dt > version_expertrules< / dt >
< dd > < p > the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".< / p > < / dd >
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< / dl > < / div >
< div id = "value" >
< h2 > Value< / h2 >
< p > (internally) a < a href = "https://rdrr.io/r/base/character.html" class = "external-link" > character< / a > vector of column names, with additional class < code > "ab_selector"< / code > < / p >
< / div >
< div id = "details" >
< h2 > Details< / h2 >
< p > These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the < a href = "https://tidyselect.r-lib.org/reference/language.html" class = "external-link" > Tidyverse selection helpers< / a > such as < code > < a href = "https://tidyselect.r-lib.org/reference/everything.html" class = "external-link" > everything()< / a > < / code > , but also work in base < span style = "R" > R< / span > and not only in < code > dplyr< / code > verbs. Nonetheless, they are very convenient to use with < code > dplyr< / code > functions such as < code > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select()< / a > < / code > , < code > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter()< / a > < / code > and < code > < a href = "https://dplyr.tidyverse.org/reference/summarise.html" class = "external-link" > summarise()< / a > < / code > , see < em > Examples< / em > .< / p >
< p > All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the < a href = "antibiotics.html" > antibiotics< / a > data set. This means that a selector such as < code > aminoglycosides()< / code > will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.< / p >
< p > The < code > ab_class()< / code > function can be used to filter/select on a manually defined antibiotic class. It searches for results in the < a href = "antibiotics.html" > antibiotics< / a > data set within the columns < code > group< / code > , < code > atc_group1< / code > and < code > atc_group2< / code > .< / p >
< p > The < code > ab_selector()< / code > function can be used to internally filter the < a href = "antibiotics.html" > antibiotics< / a > data set on any results, see < em > Examples< / em > . It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.< / p >
< p > The < code > administrable_per_os()< / code > and < code > administrable_iv()< / code > functions also rely on the < a href = "antibiotics.html" > antibiotics< / a > data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the < a href = "antibiotics.html" > antibiotics< / a > data set.< / p >
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< p > The < code > not_intrinsic_resistant()< / code > function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of < em > E. coli< / em > and < em > K. pneumoniae< / em > and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies < a href = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class = "external-link" > 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3< / a > (2021) to determine intrinsic resistance, using the < code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > function internally. Because of this determination, this function is quite slow in terms of performance.< / p >
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< / div >
< div id = "full-list-of-supported-antibiotic-classes" >
< h2 > Full list of supported (antibiotic) classes< / h2 >
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< ul > < li > < p > < code > aminoglycosides()< / code > can select: < br > amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)< / p > < / li >
< li > < p > < code > aminopenicillins()< / code > can select: < br > amoxicillin (AMX) and ampicillin (AMP)< / p > < / li >
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< li > < p > < code > antifungals()< / code > can select: < br > 5-fluorocytosine (FCT), amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR)< / p > < / li >
< li > < p > < code > antimycobacterials()< / code > can select: < br > 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), prothionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO)< / p > < / li >
< li > < p > < code > betalactams()< / code > can select: < br > amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)< / p > < / li >
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< li > < p > < code > carbapenems()< / code > can select: < br > biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)< / p > < / li >
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< li > < p > < code > cephalosporins()< / code > can select: < br > cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)< / p > < / li >
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< li > < p > < code > cephalosporins_1st()< / code > can select: < br > cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)< / p > < / li >
< li > < p > < code > cephalosporins_2nd()< / code > can select: < br > cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)< / p > < / li >
< li > < p > < code > cephalosporins_3rd()< / code > can select: < br > cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO) and latamoxef (LTM)< / p > < / li >
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< li > < p > < code > cephalosporins_4th()< / code > can select: < br > cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)< / p > < / li >
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< li > < p > < code > cephalosporins_5th()< / code > can select: < br > ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT)< / p > < / li >
< li > < p > < code > fluoroquinolones()< / code > can select: < br > besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)< / p > < / li >
< li > < p > < code > glycopeptides()< / code > can select: < br > avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)< / p > < / li >
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< li > < p > < code > lincosamides()< / code > can select: < br > acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)< / p > < / li >
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< li > < p > < code > lipoglycopeptides()< / code > can select: < br > dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)< / p > < / li >
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< li > < p > < code > macrolides()< / code > can select: < br > acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)< / p > < / li >
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< li > < p > < code > oxazolidinones()< / code > can select: < br > cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)< / p > < / li >
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< li > < p > < code > penicillins()< / code > can select: < br > amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)< / p > < / li >
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< li > < p > < code > polymyxins()< / code > can select: < br > colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)< / p > < / li >
< li > < p > < code > quinolones()< / code > can select: < br > besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)< / p > < / li >
< li > < p > < code > streptogramins()< / code > can select: < br > pristinamycin (PRI) and quinupristin/dalfopristin (QDA)< / p > < / li >
< li > < p > < code > tetracyclines()< / code > can select: < br > cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), tetracycline (TCY) and tigecycline (TGC)< / p > < / li >
< li > < p > < code > trimethoprims()< / code > can select: < br > brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP) and trimethoprim/sulfamethoxazole (SXT)< / p > < / li >
< li > < p > < code > ureidopenicillins()< / code > can select: < br > azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)< / p > < / li >
< / ul > < / div >
< div id = "stable-lifecycle" >
< h2 > Stable Lifecycle< / h2 >
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< p > < img src = "figures/lifecycle_stable.svg" style = 'margin-bottom:"5"' > < br >
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The < a href = "lifecycle.html" > lifecycle< / a > of this function is < strong > stable< / strong > . In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.< / p >
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< p > If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.< / p >
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< / div >
< div id = "reference-data-publicly-available" >
< h2 > Reference Data Publicly Available< / h2 >
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< p > All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this < code > AMR< / code > package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find < a href = "https://msberends.github.io/AMR/articles/datasets.html" > all download links on our website< / a > , which is automatically updated with every code change.< / p >
< / div >
< div id = "read-more-on-our-website-" >
< h2 > Read more on Our Website!< / h2 >
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< p > On our website < a href = "https://msberends.github.io/AMR/" > https://msberends.github.io/AMR/< / a > you can find < a href = "https://msberends.github.io/AMR/articles/AMR.html" > a comprehensive tutorial< / a > about how to conduct AMR data analysis, the < a href = "https://msberends.github.io/AMR/reference/" > complete documentation of all functions< / a > and < a href = "https://msberends.github.io/AMR/articles/WHONET.html" > an example analysis using WHONET data< / a > .< / p >
< / div >
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< div id = "ref-examples" >
< h2 > Examples< / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "co" > # `example_isolates` is a data set available in the AMR package.< / span >
< span class = "co" > # See ?example_isolates.< / span >
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< span class = "co" > # base R ------------------------------------------------------------------< / span >
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< span class = "co" > # select columns 'IPM' (imipenem) and 'MEM' (meropenem)< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > , < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span >
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< span class = "co" > # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > , < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "mo"< / span > , < span class = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span >
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< span class = "co" > # select only antibiotic columns with DDDs for oral treatment< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > , < span class = "fu" > administrable_per_os< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span >
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< span class = "co" > # filter using any() or all()< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/any.html" class = "external-link" > any< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span >
< span class = "fu" > < a href = "https://rdrr.io/r/base/subset.html" class = "external-link" > subset< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > , < span class = "fu" > < a href = "https://rdrr.io/r/base/any.html" class = "external-link" > any< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/any.html" class = "external-link" > any< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/all.html" class = "external-link" > all< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span >
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< span class = "co" > # filter with multiple antibiotic selectors using c()< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/all.html" class = "external-link" > all< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span >
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< span class = "co" > # filter + select in one go: get penicillins in carbapenems-resistant strains< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/any.html" class = "external-link" > any< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > , < span class = "fu" > penicillins< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span >
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< span class = "co" > # You can combine selectors with '& ' to be more specific. For example,< / span >
< span class = "co" > # penicillins() would select benzylpenicillin ('peni G') and< / span >
< span class = "co" > # administrable_per_os() would select erythromycin. Yet, when combined these< / span >
< span class = "co" > # drugs are both omitted since benzylpenicillin is not administrable per os< / span >
< span class = "co" > # and erythromycin is not a penicillin:< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > , < span class = "fu" > penicillins< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > & < / span > < span class = "fu" > administrable_per_os< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span >
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< span class = "co" > # ab_selector() applies a filter in the `antibiotics` data set and is thus very< / span >
< span class = "co" > # flexible. For instance, to select antibiotic columns with an oral DDD of at< / span >
< span class = "co" > # least 1 gram:< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > , < span class = "fu" > ab_selector< / span > < span class = "op" > (< / span > < span class = "va" > oral_ddd< / span > < span class = "op" > > < / span > < span class = "fl" > 1< / span > < span class = "op" > & < / span > < span class = "va" > oral_units< / span > < span class = "op" > ==< / span > < span class = "st" > "g"< / span > < span class = "op" > )< / span > < span class = "op" > ]< / span >
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< span class = "co" > # dplyr -------------------------------------------------------------------< / span >
< span class = "co" > # \donttest{< / 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 >
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< span class = "co" > # get AMR for all aminoglycosides e.g., per hospital:< / span >
< span class = "va" > example_isolates< / 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/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > hospital_id< / span > < span class = "op" > )< / 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/summarise.html" class = "external-link" > summarise< / 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 = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > resistance< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # You can combine selectors with '& ' to be more specific:< / span >
< span class = "va" > example_isolates< / 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/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > penicillins< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > & < / span > < span class = "fu" > administrable_per_os< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # get AMR for only drugs that matter - no intrinsic resistance:< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "mo_property.html" > mo_genus< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://rdrr.io/r/base/match.html" class = "external-link" > %in%< / a > < / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Escherichia"< / span > , < span class = "st" > "Klebsiella"< / span > < span class = "op" > )< / span > < span class = "op" > )< / 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/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > hospital_id< / span > < span class = "op" > )< / 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/summarise.html" class = "external-link" > summarise< / 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 = "fu" > not_intrinsic_resistant< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "va" > resistance< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # get susceptibility for antibiotics whose name contains "trim":< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "first_isolate.html" > first_isolate< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / 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/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > hospital_id< / span > < span class = "op" > )< / 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/summarise.html" class = "external-link" > summarise< / 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 = "fu" > ab_selector< / span > < span class = "op" > (< / span > < span class = "va" > name< / span > < span class = "op" > < a href = "like.html" > %like%< / a > < / span > < span class = "st" > "trim"< / span > < span class = "op" > )< / span > , < span class = "va" > susceptibility< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
< span class = "co" > # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):< / span >
< span class = "va" > example_isolates< / 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/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':< / span >
< span class = "va" > example_isolates< / 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/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > , < span class = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # any() and all() work in dplyr's filter() too:< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/any.html" class = "external-link" > any< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > ,
< span class = "fu" > < a href = "https://rdrr.io/r/base/all.html" class = "external-link" > all< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > cephalosporins_2nd< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # also works with c():< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/any.html" class = "external-link" > any< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # not setting any/all will automatically apply all():< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > aminoglycosides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span >
< span class = "co" > #> i Assuming a filter on all 4 aminoglycosides.< / span >
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< span class = "co" > # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):< / span >
< span class = "va" > example_isolates< / 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/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > , < span class = "fu" > ab_class< / span > < span class = "op" > (< / span > < span class = "st" > "mycobact"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
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< span class = "co" > # get bug/drug combinations for only macrolides in Gram-positives:< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "mo_property.html" > mo_is_gram_positive< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / 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/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > , < span class = "fu" > macrolides< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span >
< span class = "fu" > < a href = "bug_drug_combinations.html" > bug_drug_combinations< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span >
< span class = "fu" > < a href = "https://rdrr.io/r/base/format.html" class = "external-link" > format< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > some_column < span class = "op" > =< / span > < span class = "st" > "some_value"< / span > ,
J01CA01 < span class = "op" > =< / span > < span class = "st" > "S"< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "co" > # ATC code of ampicillin< / span >
< span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > penicillins< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "co" > # only the 'J01CA01' column will be selected< / span >
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< span class = "co" > # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:< / span >
< span class = "va" > example_isolates< / span > < span class = "op" > [< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > , < span class = "op" > ]< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span >
< span class = "va" > example_isolates< / 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/filter.html" class = "external-link" > filter< / 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 = "fu" > carbapenems< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "op" > ~< / span > < span class = "va" > .x< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span >
< span class = "op" > }< / span >
< span class = "co" > # }< / span >
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< / code > < / pre > < / div >
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< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
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< nav id = "toc" data-toggle = "toc" class = "sticky-top" > < h2 data-toc-skip > Contents< / h2 >
< / nav > < / div >
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< footer > < div class = "copyright" >
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< p > < / p > < p > Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
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< div class = "pkgdown" >
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< p > < / p > < p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a >
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