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@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -87,7 +87,7 @@
<li>Peer-reviewed, used in over 175 countries, available in 28 languages</li>
<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
<li>Provides the <strong>full microbiological taxonomy</strong> of ~79 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
<li>Applies <strong>CLSI 2011-2025</strong> and <strong>EUCAST 2011-2025</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
<li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
<li>Corrects for duplicate isolates, <strong>calculates</strong> and <strong>predicts</strong> AMR per antimicrobial class</li>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</strong>
</li>
@@ -112,7 +112,7 @@
</h2>
<p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> 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. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) 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="./reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2025 and EUCAST 2011-2025 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 <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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 <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level3">
<h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a>
</h3>
@@ -142,14 +142,14 @@
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_fullname()`</span></span>
<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span></span>
<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_fullname()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_gram_negative()`</span></span>
<span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_intrinsic_resistant()`</span></span>
<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
<span><span class="co">#&gt; Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
<span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
<span><span class="co">#&gt; bacteria GEN TOB AMK KAN IPM MEM </span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
@@ -174,9 +174,9 @@
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></code></pre></div>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<colgroup>
<col width="14%">
@@ -425,15 +425,15 @@
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
<span><span class="co">#&gt; (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `polymyxins()` using column 'COL' (colistin)</span></span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span>
<span><span class="co">#&gt; ℹ For `polymyxins()` using column COL (colistin)</span></span>
<span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
<span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
<span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
<span><span class="co">#&gt; Caused by warning:</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward =</span></span>
<span><span class="co">#&gt; "Outpatient" (`minimum` = 30).</span></span>
<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"</span></span>
<span><span class="co">#&gt; (whilst `minimum = 30`).</span></span>
<span><span class="va">out</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward GEN TOB AMK KAN COL</span></span>