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<img src="../logo.svg" class="logo" alt=""><h1>Options for the AMR package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/aa_options.R" class="external-link"><code>R/aa_options.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/aa_options.R" class="external-link"><code>R/aa_options.R</code></a></small>
<div class="d-none name"><code>AMR-options.Rd</code></div>
</div>
@@ -166,7 +60,7 @@
<div class="section level2">
<h2 id="options">Options<a class="anchor" aria-label="anchor" href="#options"></a></h2>
<ul><li><p><code>AMR_breakpoint_type</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".</p></li>
<li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>
@@ -183,7 +77,7 @@
</ul></div>
<div class="section level2">
<h2 id="saving-settings-between-sessions">Saving Settings Between Sessions<a class="anchor" aria-label="anchor" href="#saving-settings-between-sessions"></a></h2>
<p>Settings in <span style="R">R</span> are not saved globally and are thus lost when <span style="R">R</span> is exited. You can save your options to your own <code>.Rprofile</code> file, which is a user-specific file. You can edit it using:</p>
<p></p><div class="sourceCode r"><pre><code><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></code></pre><p></p></div>
@@ -203,7 +97,7 @@
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The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><title>The AMR Package — AMR • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package.
After installing this package, R knows ~71 000 microorganisms (updated June 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><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="@msberends"><!-- 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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After installing this package, R knows ~71 000 microorganisms (updated June 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><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="@msberends"></head><body>
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<img src="../logo.svg" class="logo" alt=""><h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/aa_amr-package.R" class="external-link"><code>R/aa_amr-package.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/aa_amr-package.R" class="external-link"><code>R/aa_amr-package.R</code></a></small>
<div class="d-none name"><code>AMR.Rd</code></div>
</div>
@@ -180,7 +74,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
).</p>
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated January 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~71 000 microorganisms</strong></a> (updated June 2024) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>
@@ -206,7 +100,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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@@ -246,7 +140,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<li><p>Anita Williams (<a href="https://orcid.org/0000-0002-5295-8451" class="external-link">ORCID</a>) [contributor]</p></li>
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<img src="../logo.svg" class="logo" alt=""><h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/whocc.R" class="external-link"><code>R/whocc.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/whocc.R" class="external-link"><code>R/whocc.R</code></a></small>
<div class="d-none name"><code>WHOCC.Rd</code></div>
</div>
@@ -166,7 +60,7 @@
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://atcddd.fhi.no" class="external-link">https://atcddd.fhi.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
@@ -189,7 +83,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex" </span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 500 Isolates - WHONET Example</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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@@ -227,7 +121,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Carbapenemase &lt;lgl&gt;, `MRSA screening test` &lt;lgl&gt;, …</span></span>
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<img src="../logo.svg" class="logo" alt=""><h1>Retrieve Antimicrobial Drug Names and Doses from Clinical Text</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/ab_from_text.R" class="external-link"><code>R/ab_from_text.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/ab_from_text.R" class="external-link"><code>R/ab_from_text.R</code></a></small>
<div class="d-none name"><code>ab_from_text.Rd</code></div>
</div>
@@ -178,41 +72,39 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>text</dt>
<dl><dt id="arg-text">text<a class="anchor" aria-label="anchor" href="#arg-text"></a></dt>
<dd><p>text to analyse</p></dd>
<dt>type</dt>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></dd>
<dt>collapse</dt>
<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em></p></dd>
<dt>translate_ab</dt>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dt>thorough_search</dt>
<dt id="arg-thorough-search">thorough_search<a class="anchor" aria-label="anchor" href="#arg-thorough-search"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></dd>
<dt>info</dt>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> if <code>collapse</code> is not <code>NULL</code></p>
<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> if <code>collapse</code> is not <code>NULL</code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -310,7 +202,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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<img src="../logo.svg" class="logo" alt=""><h1>Get Properties of an Antibiotic</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/ab_property.R" class="external-link"><code>R/ab_property.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/ab_property.R" class="external-link"><code>R/ab_property.R</code></a></small>
<div class="d-none name"><code>ab_property.Rd</code></div>
</div>
@@ -204,49 +98,50 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>any (vector of) text that can be coerced to a valid antibiotic drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>language</dt>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>tolower</dt>
<dt id="arg-tolower">tolower<a class="anchor" aria-label="anchor" href="#arg-tolower"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the first <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of every output should be transformed to a lower case <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: columns to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>only_first</dt>
<dt id="arg-only-first">only_first<a class="anchor" aria-label="anchor" href="#arg-only-first"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)</p></dd>
<dt>administration</dt>
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></dd>
<dt>open</dt>
<dt id="arg-open">open<a class="anchor" aria-label="anchor" href="#arg-open"></a></dt>
<dd><p>browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code></p></dd>
<dt>property</dt>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>one of the column names of one of the <a href="antibiotics.html">antibiotics</a> data set: <code>vector_or(colnames(antibiotics), sort = FALSE)</code>.</p></dd>
<dt>data</dt>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> of which the columns need to be renamed, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector of column names</p></dd>
<dt>snake_case</dt>
<dt id="arg-snake-case">snake_case<a class="anchor" aria-label="anchor" href="#arg-snake-case"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the names should be in so-called <a href="https://en.wikipedia.org/wiki/Snake_case" class="external-link">snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>)</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>ab_cid()</code></p></li>
<li><p>A named <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>ab_info()</code> and multiple <code>ab_atc()</code>/<code>ab_synonyms()</code>/<code>ab_tradenames()</code></p></li>
@@ -262,14 +157,14 @@
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
@@ -530,7 +425,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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@@ -544,9 +439,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Add Custom Antimicrobials</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/custom_antimicrobials.R" class="external-link"><code>R/custom_antimicrobials.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/custom_antimicrobials.R" class="external-link"><code>R/custom_antimicrobials.R</code></a></small>
<div class="d-none name"><code>add_custom_antimicrobials.Rd</code></div>
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@@ -172,7 +66,9 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></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>
@@ -314,7 +210,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
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@@ -328,9 +224,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Add Custom Microorganisms</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/custom_microorganisms.R" class="external-link"><code>R/custom_microorganisms.R</code></a></small>
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@@ -172,7 +66,9 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="microorganisms.html">microorganisms</a> data set, at least containing column "genus" (case-insensitive)</p></dd>
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@@ -337,7 +233,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
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@@ -351,9 +247,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Age in Years of Individuals</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/age.R" class="external-link"><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/age.R" class="external-link"><code>R/age.R</code></a></small>
<div class="d-none name"><code>age.Rd</code></div>
</div>
@@ -170,31 +64,31 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>date(s), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dt>reference</dt>
<dt id="arg-reference">reference<a class="anchor" aria-label="anchor" href="#arg-reference"></a></dt>
<dd><p>reference date(s) (default is today), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dt>exact</dt>
<dt id="arg-exact">exact<a class="anchor" aria-label="anchor" href="#arg-exact"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of <a href="https://en.wikipedia.org/wiki/Year-to-date" class="external-link">year-to-date</a> (YTD) of <code>x</code> by the number of days in the year of <code>reference</code> (either 365 or 366).</p></dd>
<dt>na.rm</dt>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether missing values should be removed</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code>, such as <code>origin</code></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> (no decimals) if <code>exact = FALSE</code>, a <a href="https://rdrr.io/r/base/double.html" class="external-link">double</a> (with decimals) otherwise</p>
<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> (no decimals) if <code>exact = FALSE</code>, a <a href="https://rdrr.io/r/base/double.html" class="external-link">double</a> (with decimals) otherwise</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -222,19 +116,19 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.54918 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.31148 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.64208 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.35519 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.34153 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.45082 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.82240 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.40710 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.01639 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.86885 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.61202 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.37432 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.70492 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.41803 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.40437 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.51366 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.88525 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.46995 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.07923 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.93169 13</span>
</code></pre></div>
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@@ -248,9 +142,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Split Ages into Age Groups</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/age.R" class="external-link"><code>R/age.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/age.R" class="external-link"><code>R/age.R</code></a></small>
<div class="d-none name"><code>age_groups.Rd</code></div>
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@@ -170,25 +64,23 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>age, e.g. calculated with <code><a href="age.html">age()</a></code></p></dd>
<dt>split_at</dt>
<dt id="arg-split-at">split_at<a class="anchor" aria-label="anchor" href="#arg-split-at"></a></dt>
<dd><p>values to split <code>x</code> at - the default is age groups 0-11, 12-24, 25-54, 55-74 and 75+. See <em>Details</em>.</p></dd>
<dt>na.rm</dt>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate 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>
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></p>
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -263,7 +155,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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@@ -277,9 +169,9 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
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<img src="../logo.svg" class="logo" alt=""><h1>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/antibiogram.R" class="external-link"><code>R/antibiogram.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/antibiogram.R" class="external-link"><code>R/antibiogram.R</code></a></small>
<div class="d-none name"><code>antibiogram.Rd</code></div>
</div>
@@ -182,13 +76,13 @@
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for antibiogram</span></span>
<span><span class="co"># S3 method for class 'antibiogram'</span></span>
<span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for antibiogram</span></span>
<span><span class="co"># S3 method for class 'antibiogram'</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for antibiogram</span></span>
<span><span class="co"># S3 method for class 'antibiogram'</span></span>
<span><span class="fu">knit_print</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> italicise <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@@ -199,82 +93,84 @@
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<ul><li><p>Klinker KP <em>et al.</em> (2021). <strong>Antimicrobial stewardship and antibiograms: importance of moving beyond traditional antibiograms</strong>. <em>Therapeutic Advances in Infectious Disease</em>, May 5;8:20499361211011373; <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a></p></li>
<li><p>Barbieri E <em>et al.</em> (2021). <strong>Development of a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) to guide the choice of the empiric antibiotic treatment for urinary tract infection in paediatric patients: a Bayesian approach</strong> <em>Antimicrobial Resistance &amp; Infection Control</em> May 1;10(1):74; <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">doi:10.1186/s13756-021-00939-2</a></p></li>
<li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
<dt>antibiotics</dt>
<dt id="arg-antibiotics">antibiotics<a class="anchor" aria-label="anchor" href="#arg-antibiotics"></a></dt>
<dd><p>vector of any antibiotic name or code (will be evaluated with <code><a href="as.ab.html">as.ab()</a></code>, column name of <code>x</code>, or (any combinations of) <a href="antibiotic_class_selectors.html">antibiotic selectors</a> such as <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> or <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be set to values separated with <code>"+"</code>, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in <code>x</code>. See <em>Examples</em>.</p></dd>
<dt>mo_transform</dt>
<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt id="arg-mo-transform">mo_transform<a class="anchor" aria-label="anchor" href="#arg-mo-transform"></a></dt>
<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt>ab_transform</dt>
<dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt>
<dd><p>a character to transform antibiotic input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set: "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt>syndromic_group</dt>
<dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt>
<dd><p>a column name of <code>x</code>, or values calculated to split rows of <code>x</code>, e.g. by using <code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> or <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code>. See <em>Examples</em>.</p></dd>
<dt>add_total_n</dt>
<dt id="arg-add-total-n">add_total_n<a class="anchor" aria-label="anchor" href="#arg-add-total-n"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether total available numbers per pathogen should be added to the table (default is <code>TRUE</code>). This will add the lowest and highest number of available isolate per antibiotic (e.g, if for <em>E. coli</em> 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").</p></dd>
<dt>only_all_tested</dt>
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination antibiograms): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antibiotics, see <em>Details</em></p></dd>
<dt>digits</dt>
<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
<dd><p>number of digits to use for rounding</p></dd>
<dt>col_mo</dt>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is 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>language</dt>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language to translate text, which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dt>minimum</dt>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
<dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
<dt>combine_SI</dt>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (default is <code>TRUE</code>)</p></dd>
<dt>sep</dt>
<dt id="arg-sep">sep<a class="anchor" aria-label="anchor" href="#arg-sep"></a></dt>
<dd><p>a separating character for antibiotic columns in combination antibiograms</p></dd>
<dt>info</dt>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>when used in <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">R Markdown or Quarto</a>: arguments passed on to <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> (otherwise, has no use)</p></dd>
<dt>object</dt>
<dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
<dd><p>an <code>antibiogram()</code> object</p></dd>
<dt>italicise</dt>
<dt id="arg-italicise">italicise<a class="anchor" aria-label="anchor" href="#arg-italicise"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr</a> table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>.</p></dd>
<dt>na</dt>
<dt id="arg-na">na<a class="anchor" aria-label="anchor" href="#arg-na"></a></dt>
<dd><p>character to use for showing <code>NA</code> values</p></dd>
</dl></div>
@@ -370,7 +266,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CoNS (43-309) 0 86 52 0 52 22</span>
@@ -383,6 +279,8 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis (8-163) 0 79 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 51</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis (3-80) <span style="color: #BB0000;">NA</span> 92 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae (11-117) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
@@ -391,11 +289,13 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` J01GB01 J01GB03 J01GB04 J01GB06</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (35-686) 96 96 0 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (436-1170) 34 63 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
@@ -403,7 +303,7 @@
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` Imipenem Meropenem</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) (48-48) 52 52</span>
@@ -411,6 +311,8 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli (418-422) 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae (51-53) 100 100</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis (27-32) 94 <span style="color: #BB0000;">NA</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Combined antibiogram -------------------------------------------------</span></span></span>
@@ -420,11 +322,13 @@
<span class="r-in"><span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` TZP `TZP + GEN` `TZP + TOB`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 99 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 98 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># names of antibiotics do not need to resemble columns exactly:</span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
@@ -433,11 +337,13 @@
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" &amp; "</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Pathogen (N min-max)` Ciprofloxacin `Ciprofloxacin &amp; Gentamicin`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (684-694) 91 99</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (724-847) 77 93</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Syndromic antibiogram ------------------------------------------------</span></span></span>
@@ -450,7 +356,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical CoNS (23-205) <span style="color: #BB0000;">NA</span> 89 57 <span style="color: #BB0000;">NA</span> 57 26</span>
@@ -467,6 +373,8 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis (1-45) <span style="color: #BB0000;">NA</span> 96 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumoniae (5-78) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU S. pneumoniae (5-30) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now define a data set with only E. coli</span></span></span>
<span class="r-in"><span><span class="va">ex1</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</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">==</span> <span class="st">"Escherichia"</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -484,11 +392,13 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> No UCI E. coli (0-325) 100 98 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI E. coli (0-137) 100 99 96</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Weighted-incidence syndromic combination antibiogram (WISCA) ---------</span></span></span>
@@ -503,13 +413,15 @@
<span class="r-in"><span> <span class="st">"WISCA Group 1"</span>, <span class="st">"WISCA Group 2"</span></span></span>
<span class="r-in"><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">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 4 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Pathogen (N min-max)` AMC `AMC + CIP` TZP `TZP + TOB`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
@@ -563,7 +475,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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@@ -577,9 +489,9 @@
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@@ -1,163 +1,57 @@
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In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up by cephalosporins().'><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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><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 (according to the antibiotics data set), without the need to define the columns or antibiotic abbreviations.
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In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up by cephalosporins().'><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 (according to the antibiotics data set), without the need to define the columns or antibiotic abbreviations.
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "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="@msberends"></head><body>
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<img src="../logo.svg" class="logo" alt=""><h1>Antibiotic Selectors</h1>
<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>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/ab_selectors.R" class="external-link"><code>R/ab_selectors.R</code></a></small>
<div class="d-none name"><code>antibiotic_class_selectors.Rd</code></div>
</div>
@@ -240,41 +134,39 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>ab_class</dt>
<dl><dt id="arg-ab-class">ab_class<a class="anchor" aria-label="anchor" href="#arg-ab-class"></a></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_sir_columns</dt>
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></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>sir</code> must be selected (default is <code>FALSE</code>), see <code><a href="as.sir.html">as.sir()</a></code></p></dd>
<dt>only_treatable</dt>
<dt id="arg-only-treatable">only_treatable<a class="anchor" aria-label="anchor" href="#arg-only-treatable"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is <code>TRUE</code>), such as gentamicin-high (<code>GEH</code>) and imipenem/EDTA (<code>IPE</code>)</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>ignored, only in place to allow future extensions</p></dd>
<dt>filter</dt>
<dt id="arg-filter">filter<a class="anchor" aria-label="anchor" href="#arg-filter"></a></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>
<dt>col_mo</dt>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is 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>
<dt id="arg-version-expertrules">version_expertrules<a class="anchor" aria-label="anchor" href="#arg-version-expertrules"></a></dt>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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>
<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 class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -287,7 +179,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
</div>
<div class="section level2">
<h2 id="full-list-of-supported-antibiotic-classes">Full list of supported (antibiotic) classes<a class="anchor" aria-label="anchor" href="#full-list-of-supported-antibiotic-classes"></a></h2>
<ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), 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>
@@ -319,7 +211,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
</ul></div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
@@ -1165,7 +1057,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Transform Input to an Antibiotic ID</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/ab.R" class="external-link"><code>R/ab.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/ab.R" class="external-link"><code>R/ab.R</code></a></small>
<div class="d-none name"><code>as.ab.Rd</code></div>
</div>
@@ -172,31 +66,27 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector to determine to antibiotic ID</p></dd>
<dt>flag_multiple_results</dt>
<dt id="arg-flag-multiple-results">flag_multiple_results<a class="anchor" aria-label="anchor" href="#arg-flag-multiple-results"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a note should be printed to the console that probably more than one antibiotic drug code or name can be retrieved from a single input value.</p></dd>
<dt>info</dt>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to internal functions</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></p>
<p></p>
<p><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>ab</code></p>
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> <a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code>ab</code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -211,14 +101,14 @@
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://atcddd.fhi.no" class="external-link">https://atcddd.fhi.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
@@ -227,7 +117,7 @@
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
@@ -319,7 +209,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
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@@ -333,9 +223,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Transform Input to an Antiviral Drug ID</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/av.R" class="external-link"><code>R/av.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/av.R" class="external-link"><code>R/av.R</code></a></small>
<div class="d-none name"><code>as.av.Rd</code></div>
</div>
@@ -172,31 +66,27 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector to determine to antiviral drug ID</p></dd>
<dt>flag_multiple_results</dt>
<dt id="arg-flag-multiple-results">flag_multiple_results<a class="anchor" aria-label="anchor" href="#arg-flag-multiple-results"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a note should be printed to the console that probably more than one antiviral drug code or name can be retrieved from a single input value.</p></dd>
<dt>info</dt>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to internal functions</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a></p>
<p></p>
<p><a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code><a href="as.ab.html">ab</a></code></p>
<p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> <a href="https://rdrr.io/r/base/vector.html" class="external-link">vector</a> with additional class <code><a href="as.ab.html">ab</a></code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -210,14 +100,14 @@
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
<p>This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://atcddd.fhi.no" class="external-link">https://atcddd.fhi.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
@@ -226,7 +116,7 @@
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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@@ -281,7 +171,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Aciclovir"</span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Transform Input to Disk Diffusion Diameters</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/disk.R" class="external-link"><code>R/disk.R</code></a></small>
<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>
<div class="d-none name"><code>as.disk.Rd</code></div>
</div>
@@ -178,21 +72,19 @@
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>vector</p></dd>
<dt>na.rm</dt>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<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>
<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> with additional class <code>disk</code></p>
<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> with additional class <code>disk</code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -267,7 +159,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S &lt;NA&gt; S S</span>
</code></pre></div>
</div>
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@@ -281,9 +173,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Transform Input to Minimum Inhibitory Concentrations (MIC)</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/mic.R" class="external-link"><code>R/mic.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/mic.R" class="external-link"><code>R/mic.R</code></a></small>
<div class="d-none name"><code>as.mic.Rd</code></div>
</div>
@@ -173,41 +67,41 @@
<span></span>
<span><span class="fu">rescale_mic</span><span class="op">(</span><span class="va">x</span>, <span class="va">mic_range</span>, keep_operators <span class="op">=</span> <span class="st">"edges"</span>, as.mic <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mic</span></span>
<span><span class="co"># S3 method for class 'mic'</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels</a></span><span class="op">(</span><span class="va">x</span>, as.mic <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</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>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> or <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector</p></dd>
<dt>na.rm</dt>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<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>
<dt>keep_operators</dt>
<dt id="arg-keep-operators">keep_operators<a class="anchor" aria-label="anchor" href="#arg-keep-operators"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> specifying how to handle operators (such as <code>&gt;</code> and <code>&lt;=</code>) in the input. Accepts one of three values: <code>"all"</code> (or <code>TRUE</code>) to keep all operators, <code>"none"</code> (or <code>FALSE</code>) to remove all operators, or <code>"edges"</code> to keep operators only at both ends of the range.</p></dd>
<dt>mic_range</dt>
<dt id="arg-mic-range">mic_range<a class="anchor" aria-label="anchor" href="#arg-mic-range"></a></dt>
<dd><p>a manual range to limit the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to set no limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</p></dd>
<dt>as.mic</dt>
<dt id="arg-as-mic">as.mic<a class="anchor" aria-label="anchor" href="#arg-as-mic"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the <code>mic</code> class should be kept - the default is <code>FALSE</code></p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to methods</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with additional class <code>mic</code>, that in mathematical operations acts as a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector. Bear in mind that the outcome of any mathematical operation on MICs will return a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> value.</p>
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with additional class <code>mic</code>, that in mathematical operations acts as a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector. Bear in mind that the outcome of any mathematical operation on MICs will return a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> value.</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -275,7 +169,7 @@
<span class="r-in"><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="va">mic_data</span> <span class="op">&lt;</span> <span class="fl">512</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># limit MICs using rescale_mic()</span></span></span>
<span class="r-in"><span><span class="co"># rescale MICs using rescale_mic()</span></span></span>
<span class="r-in"><span><span class="fu">rescale_mic</span><span class="op">(</span><span class="va">mic_data</span>, mic_range <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="fl">4</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=16 &lt;=4 &lt;=4 &lt;=4 8 &lt;=4 8 &gt;=16 &gt;=16</span>
@@ -324,7 +218,7 @@
<span class="r-plt img"><img src="as.mic-4.png" alt="" width="700" height="433"></span>
</code></pre></div>
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@@ -338,9 +232,9 @@
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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, shrink-to-fit=no"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
<!-- 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, shrink-to-fit=no"><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.
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<img src="../logo.svg" class="logo" alt=""><h1>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/sir.R" class="external-link"><code>R/sir.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/sir.R" class="external-link"><code>R/sir.R</code></a></small>
<div class="d-none name"><code>as.sir.Rd</code></div>
</div>
@@ -191,7 +85,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span></span>
<span><span class="fu">is_sir_eligible</span><span class="op">(</span><span class="va">x</span>, threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for default</span></span>
<span><span class="co"># Default S3 method</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>,</span>
@@ -202,7 +96,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mic</span></span>
<span><span class="co"># S3 method for class 'mic'</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -220,7 +114,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for disk</span></span>
<span><span class="co"># S3 method for class 'disk'</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -237,7 +131,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for data.frame</span></span>
<span><span class="co"># S3 method for class 'data.frame'</span></span>
<span><span class="fu">as.sir</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> <span class="va">...</span>,</span>
@@ -267,85 +161,83 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>vector of values (for class <code><a href="as.mic.html">mic</a></code>: MIC values in mg/L, for class <code><a href="as.disk.html">disk</a></code>: a disk diffusion radius in millimetres)</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>for using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: names of columns to apply <code>as.sir()</code> on (supports tidy selection such as <code>column1:column4</code>). Otherwise: arguments passed on to methods.</p></dd>
<dt>threshold</dt>
<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
<dd><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em></p></dd>
<dt>S, I, R, NI, SDD</dt>
<dt id="arg-s-i-r-ni-sdd">S, I, R, NI, SDD<a class="anchor" aria-label="anchor" href="#arg-s-i-r-ni-sdd"></a></dt>
<dd><p>a case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters and whitespaces are removed from the input.</p></dd>
<dt>mo</dt>
<dt id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></dt>
<dd><p>a vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to valid microorganism codes with <code><a href="as.mo.html">as.mo()</a></code>, can be left empty to determine it automatically</p></dd>
<dt>ab</dt>
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
<dd><p>a vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>guideline</dt>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see <em>Details</em>.</p></dd>
<dt>uti</dt>
<dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt>
<dd><p>(Urinary Tract Infection) a vector (or column name) with <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.sir()</code> on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, this can also be a column containing <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
<dt>conserve_capped_values</dt>
<dt id="arg-conserve-capped-values">conserve_capped_values<a class="anchor" aria-label="anchor" href="#arg-conserve-capped-values"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that MIC values starting with <code>"&gt;"</code> (but not <code>"&gt;="</code>) must always return "R" , and that MIC values starting with <code>"&lt;"</code> (but not <code>"&lt;="</code>) must always return "S"</p></dd>
<dt>add_intrinsic_resistance</dt>
<dt id="arg-add-intrinsic-resistance">add_intrinsic_resistance<a class="anchor" aria-label="anchor" href="#arg-add-intrinsic-resistance"></a></dt>
<dd><p><em>(only useful when using a EUCAST guideline)</em> a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in <em>Klebsiella</em> species. Determination is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, that itself is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021).</p></dd>
<dt>reference_data</dt>
<dt id="arg-reference-data">reference_data<a class="anchor" aria-label="anchor" href="#arg-reference-data"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd>
<dt>include_screening</dt>
<dt id="arg-include-screening">include_screening<a class="anchor" aria-label="anchor" href="#arg-include-screening"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_screening</a></code>.</p></dd>
<dt>include_PKPD</dt>
<dt id="arg-include-pkpd">include_PKPD<a class="anchor" aria-label="anchor" href="#arg-include-pkpd"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
<dt>breakpoint_type</dt>
<dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
<dt>host</dt>
<dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt>
<dd><p>a vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s to indicate the host. Only useful for veterinary breakpoints, as it requires <code>breakpoint_type = "animal"</code>. The values can be any text resembling the animal species, even in any of the 20 supported languages of this package. For foreign languages, be sure to set the language with <code><a href="translate.html">set_AMR_locale()</a></code> (though it will be automatically guessed based on the system language).</p></dd>
<dt>verbose</dt>
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.</p></dd>
<dt>col_mo</dt>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is 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>clean</dt>
<dt id="arg-clean">clean<a class="anchor" aria-label="anchor" href="#arg-clean"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether previously stored results should be forgotten after returning the 'logbook' with results</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with new class <code>sir</code></p>
<p>Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with new class <code>sir</code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -421,7 +313,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
</div>
<div class="section level2">
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
@@ -434,7 +326,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
@@ -868,16 +760,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 59 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-23 <span style="color: #949494;">14:22:38</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-23 <span style="color: #949494;">14:22:44</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-23 <span style="color: #949494;">14:22:44</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-23 <span style="color: #949494;">14:22:44</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-23 <span style="color: #949494;">14:22:45</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-23 <span style="color: #949494;">14:22:38</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-23 <span style="color: #949494;">14:22:44</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-23 <span style="color: #949494;">14:22:44</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-23 <span style="color: #949494;">14:22:44</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-23 <span style="color: #949494;">14:22:45</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-07-16 <span style="color: #949494;">12:58:17</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-07-16 <span style="color: #949494;">12:58:23</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-07-16 <span style="color: #949494;">12:58:25</span> 4 genta Escheri… cattle GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-07-16 <span style="color: #949494;">12:58:17</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-07-16 <span style="color: #949494;">12:58:23</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-07-16 <span style="color: #949494;">12:58:24</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-07-16 <span style="color: #949494;">12:58:25</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 49 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
@@ -976,7 +868,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div>
@@ -990,9 +882,9 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
</footer></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Get ATC Properties from WHOCC Website</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/atc_online.R" class="external-link"><code>R/atc_online.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/atc_online.R" class="external-link"><code>R/atc_online.R</code></a></small>
<div class="d-none name"><code>atc_online.Rd</code></div>
</div>
@@ -186,27 +80,29 @@
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>atc_code</dt>
<dl><dt id="arg-atc-code">atc_code<a class="anchor" aria-label="anchor" href="#arg-atc-code"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) with ATC code(s) of antibiotics, will be coerced with <code><a href="as.ab.html">as.ab()</a></code> and <code><a href="ab_property.html">ab_atc()</a></code> internally if not a valid ATC code</p></dd>
<dt>property</dt>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>property of an ATC code. Valid values are <code>"ATC"</code>, <code>"Name"</code>, <code>"DDD"</code>, <code>"U"</code> (<code>"unit"</code>), <code>"Adm.R"</code>, <code>"Note"</code> and <code>groups</code>. For this last option, all hierarchical groups of an ATC code will be returned, see <em>Examples</em>.</p></dd>
<dt>administration</dt>
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>type of administration when using <code>property = "Adm.R"</code>, see <em>Details</em></p></dd>
<dt>url</dt>
<dt id="arg-url">url<a class="anchor" aria-label="anchor" href="#arg-url"></a></dt>
<dd><p>url of website of the WHOCC. The sign <code>%s</code> can be used as a placeholder for ATC codes.</p></dd>
<dt>url_vet</dt>
<dt id="arg-url-vet">url_vet<a class="anchor" aria-label="anchor" href="#arg-url-vet"></a></dt>
<dd><p>url of website of the WHOCC for veterinary medicine. The sign <code>%s</code> can be used as a placeholder for ATC_vet codes (that all start with "Q").</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments to pass on to <code>atc_property</code></p></dd>
</dl></div>
@@ -254,7 +150,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>Retrieve Antiviral Drug Names and Doses from Clinical Text</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/av_from_text.R" class="external-link"><code>R/av_from_text.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/av_from_text.R" class="external-link"><code>R/av_from_text.R</code></a></small>
<div class="d-none name"><code>av_from_text.Rd</code></div>
</div>
@@ -178,41 +72,39 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>text</dt>
<dl><dt id="arg-text">text<a class="anchor" aria-label="anchor" href="#arg-text"></a></dt>
<dd><p>text to analyse</p></dd>
<dt>type</dt>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></dd>
<dt>collapse</dt>
<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em></p></dd>
<dt>translate_av</dt>
<dt id="arg-translate-av">translate_av<a class="anchor" aria-label="anchor" href="#arg-translate-av"></a></dt>
<dd><p>if <code>type = "drug"</code>: a column name of the <a href="antibiotics.html">antivirals</a> data set to translate the antibiotic abbreviations to, using <code><a href="av_property.html">av_property()</a></code>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
<dt>thorough_search</dt>
<dt id="arg-thorough-search">thorough_search<a class="anchor" aria-label="anchor" href="#arg-thorough-search"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></dd>
<dt>info</dt>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to <code><a href="as.av.html">as.av()</a></code></p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> if <code>collapse</code> is not <code>NULL</code></p>
<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> if <code>collapse</code> is not <code>NULL</code></p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -249,7 +141,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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<img src="../logo.svg" class="logo" alt=""><h1>Get Properties of an Antiviral Drug</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/av_property.R" class="external-link"><code>R/av_property.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/av_property.R" class="external-link"><code>R/av_property.R</code></a></small>
<div class="d-none name"><code>av_property.Rd</code></div>
</div>
@@ -192,37 +86,38 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>any (vector of) text that can be coerced to a valid antiviral drug code with <code><a href="as.av.html">as.av()</a></code></p></dd>
<dt>language</dt>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>tolower</dt>
<dt id="arg-tolower">tolower<a class="anchor" aria-label="anchor" href="#arg-tolower"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the first <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of every output should be transformed to a lower case <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>.</p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>other arguments passed on to <code><a href="as.av.html">as.av()</a></code></p></dd>
<dt>administration</dt>
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></dd>
<dt>open</dt>
<dt id="arg-open">open<a class="anchor" aria-label="anchor" href="#arg-open"></a></dt>
<dd><p>browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code></p></dd>
<dt>property</dt>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>one of the column names of one of the <a href="antibiotics.html">antivirals</a> data set: <code>vector_or(colnames(antivirals), sort = FALSE)</code>.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>av_cid()</code></p></li>
<li><p>A named <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a> in case of <code>av_info()</code> and multiple <code>av_atc()</code>/<code>av_synonyms()</code>/<code>av_tradenames()</code></p></li>
@@ -236,14 +131,14 @@
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href="https://atcddd.fhi.no/atc_ddd_index/" class="external-link">https://atcddd.fhi.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<div class="section level2">
<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
</div>
@@ -365,7 +260,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Aciclovir"</span>
</code></pre></div>
</div>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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@@ -379,9 +274,9 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Check Availability of Columns</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/availability.R" class="external-link"><code>R/availability.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/availability.R" class="external-link"><code>R/availability.R</code></a></small>
<div class="d-none name"><code>availability.Rd</code></div>
</div>
@@ -170,19 +64,19 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>tbl</dt>
<dl><dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> or <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
<dt>width</dt>
<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a></dt>
<dd><p>number of characters to present the visual availability - the default is filling the width of the console</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with column names of <code>tbl</code> as row names</p>
<p><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with column names of <code>tbl</code> as row names</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -290,7 +184,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
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<img src="../logo.svg" class="logo" alt=""><h1>Determine Bug-Drug Combinations</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/bug_drug_combinations.R" class="external-link"><code>R/bug_drug_combinations.R</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/bug_drug_combinations.R" class="external-link"><code>R/bug_drug_combinations.R</code></a></small>
<div class="d-none name"><code>bug_drug_combinations.Rd</code></div>
</div>
@@ -167,7 +61,7 @@
<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">bug_drug_combinations</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, FUN <span class="op">=</span> <span class="va">mo_shortname</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for bug_drug_combinations</span></span>
<span><span class="co"># S3 method for class 'bug_drug_combinations'</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> translate_ab <span class="op">=</span> <span class="st">"name (ab, atc)"</span>,</span>
@@ -184,52 +78,54 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dt>col_mo</dt>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is 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>FUN</dt>
<dt id="arg-fun">FUN<a class="anchor" aria-label="anchor" href="#arg-fun"></a></dt>
<dd><p>the function to call on the <code>mo</code> column to transform the microorganism codes - the default is <code><a href="mo_property.html">mo_shortname()</a></code></p></dd>
<dt>...</dt>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to <code>FUN</code></p></dd>
<dt>translate_ab</dt>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antibiotics.html">antibiotics</a> data set</p></dd>
<dt>language</dt>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>minimum</dt>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
<dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
<dt>combine_SI</dt>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S and I should be summed, so resistance will be based on only R - the default is <code>TRUE</code></p></dd>
<dt>add_ab_group</dt>
<dt id="arg-add-ab-group">add_ab_group<a class="anchor" aria-label="anchor" href="#arg-add-ab-group"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate where the group of the antimicrobials must be included as a first column</p></dd>
<dt>remove_intrinsic_resistant</dt>
<dt id="arg-remove-intrinsic-resistant">remove_intrinsic_resistant<a class="anchor" aria-label="anchor" href="#arg-remove-intrinsic-resistant"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table</p></dd>
<dt>decimal.mark</dt>
<dt id="arg-decimal-mark">decimal.mark<a class="anchor" aria-label="anchor" href="#arg-decimal-mark"></a></dt>
<dd><p>the character to be used to indicate the numeric
decimal point.</p></dd>
<dt>big.mark</dt>
<dt id="arg-big-mark">big.mark<a class="anchor" aria-label="anchor" href="#arg-big-mark"></a></dt>
<dd><p>character; if not empty used as mark between every
<code>big.interval</code> decimals <em>before</em> (hence <code>big</code>) the
decimal point.</p></dd>
@@ -237,9 +133,7 @@
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>The function <code>bug_drug_combinations()</code> returns a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with columns "mo", "ab", "S", "SDD", "I", "R", and "total".</p>
<p>The function <code>bug_drug_combinations()</code> returns a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with columns "mo", "ab", "S", "SDD", "I", "R", and "total".</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -349,7 +243,7 @@
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
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@@ -363,9 +257,9 @@
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