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Conduct principal component analysis for AMR
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Get properties of a microorganism
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Get properties of an antibiotic
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Get ATC Properties from WHOCC Website</h1>
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<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>
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<div class="d-none name"><code>atc_online.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">atc_online_property</span><span class="op">(</span></span>
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<span> <span class="va">atc_code</span>,</span>
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<span> <span class="va">property</span>,</span>
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<span> administration <span class="op">=</span> <span class="st">"O"</span>,</span>
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<span> url <span class="op">=</span> <span class="st">"https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no"</span>,</span>
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<span> url_vet <span class="op">=</span> <span class="st">"https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no"</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">atc_online_groups</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">atc_online_ddd</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">atc_online_ddd_units</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<p><a href="https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/" class="external-link">https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/</a></p>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>atc_code</dt>
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<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>
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<dt>property</dt>
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<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>
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<dt>administration</dt>
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<dd><p>type of administration when using <code>property = "Adm.R"</code>, see <em>Details</em></p></dd>
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<dt>url</dt>
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<dd><p>url of website of the WHOCC. The sign <code>%s</code> can be used as a placeholder for ATC codes.</p></dd>
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<dt>url_vet</dt>
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<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>
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<dt>...</dt>
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<dd><p>arguments to pass on to <code>atc_property</code></p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>Options for argument <code>administration</code>:</p><ul><li><p><code>"Implant"</code> = Implant</p></li>
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<li><p><code>"Inhal"</code> = Inhalation</p></li>
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<li><p><code>"Instill"</code> = Instillation</p></li>
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<li><p><code>"N"</code> = nasal</p></li>
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<li><p><code>"O"</code> = oral</p></li>
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<li><p><code>"P"</code> = parenteral</p></li>
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<li><p><code>"R"</code> = rectal</p></li>
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<li><p><code>"SL"</code> = sublingual/buccal</p></li>
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<li><p><code>"TD"</code> = transdermal</p></li>
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<li><p><code>"V"</code> = vaginal</p></li>
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</ul><p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul><li><p><code>"g"</code> = gram</p></li>
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<li><p><code>"mg"</code> = milligram</p></li>
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<li><p><code>"mcg"</code> = microgram</p></li>
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<li><p><code>"U"</code> = unit</p></li>
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<li><p><code>"TU"</code> = thousand units</p></li>
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<li><p><code>"MU"</code> = million units</p></li>
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<li><p><code>"mmol"</code> = millimole</p></li>
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<li><p><code>"ml"</code> = millilitre (e.g. eyedrops)</p></li>
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</ul><p><strong>N.B. This function requires an internet connection and only works if the following packages are installed: <code>curl</code>, <code>rvest</code>, <code>xml2</code>.</strong></p>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"curl"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"rvest"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"xml2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> </span></span>
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<span class="r-in"><span> <span class="co"># oral DDD (Defined Daily Dose) of amoxicillin</span></span></span>
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<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, <span class="st">"DDD"</span>, <span class="st">"O"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="fu">atc_online_ddd</span><span class="op">(</span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"amox"</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="co"># parenteral DDD (Defined Daily Dose) of amoxicillin</span></span></span>
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<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, <span class="st">"DDD"</span>, <span class="st">"P"</span><span class="op">)</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Loading required namespace: rvest</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" </span>
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<span class="r-out co"><span class="r-pr">#></span> [2] "ANTIBACTERIALS FOR SYSTEMIC USE" </span>
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<span class="r-out co"><span class="r-pr">#></span> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
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<span class="r-out co"><span class="r-pr">#></span> [4] "Penicillins with extended spectrum" </span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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<footer><div class="pkgdown-footer-left">
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.png" style="max-width: 200px;"></a></p>
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