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<h1>Get ATC Properties from WHOCC Website</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/atc_online.R'><code>R/atc_online.R</code></a></small>
<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>
<div class="hidden name"><code>atc_online.Rd</code></div>
</div>
@ -246,56 +161,42 @@
<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>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>atc_online_property</span><span class='op'>(</span>
<span class='va'>atc_code</span>,
<span class='va'>property</span>,
administration <span class='op'>=</span> <span class='st'>"O"</span>,
url <span class='op'>=</span> <span class='st'>"https://www.whocc.no/atc_ddd_index/?code=%s&amp;showdescription=no"</span>,
url_vet <span class='op'>=</span> <span class='st'>"https://www.whocc.no/atcvet/atcvet_index/?code=%s&amp;showdescription=no"</span>
<span class='op'>)</span>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">atc_online_property</span><span class="op">(</span>
<span class="va">atc_code</span>,
<span class="va">property</span>,
administration <span class="op">=</span> <span class="st">"O"</span>,
url <span class="op">=</span> <span class="st">"https://www.whocc.no/atc_ddd_index/?code=%s&amp;showdescription=no"</span>,
url_vet <span class="op">=</span> <span class="st">"https://www.whocc.no/atcvet/atcvet_index/?code=%s&amp;showdescription=no"</span>
<span class="op">)</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 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 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 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 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></code></pre></div>
<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></code></pre></div></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>atc_code</th>
<td><p>a <a href='https://rdrr.io/r/base/character.html'>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></td>
</tr>
<tr>
<th>property</th>
<td><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></td>
</tr>
<tr>
<th>administration</th>
<td><p>type of administration when using <code>property = "Adm.R"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>url</th>
<td><p>url of website of the WHOCC. The sign <code>%s</code> can be used as a placeholder for ATC codes.</p></td>
</tr>
<tr>
<th>url_vet</th>
<td><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></td>
</tr>
<tr>
<th>...</th>
<td><p>arguments to pass on to <code>atc_property</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p><a href='https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/'>https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/</a></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Options for argument <code>administration</code>:</p><ul>
<li><p><code>"Implant"</code> = Implant</p></li>
<div id="source">
<h2>Source</h2>
<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>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>atc_code</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>
<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>
<dd><p>type of administration when using <code>property = "Adm.R"</code>, see <em>Details</em></p></dd>
<dt>url</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>
<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>
<dd><p>arguments to pass on to <code>atc_property</code></p></dd>
</dl></div>
<div id="details">
<h2>Details</h2>
<p>Options for argument <code>administration</code>:</p><ul><li><p><code>"Implant"</code> = Implant</p></li>
<li><p><code>"Inhal"</code> = Inhalation</p></li>
<li><p><code>"Instill"</code> = Instillation</p></li>
<li><p><code>"N"</code> = nasal</p></li>
@ -305,10 +206,7 @@
<li><p><code>"SL"</code> = sublingual/buccal</p></li>
<li><p><code>"TD"</code> = transdermal</p></li>
<li><p><code>"V"</code> = vaginal</p></li>
</ul>
<p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul>
<li><p><code>"g"</code> = gram</p></li>
</ul><p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul><li><p><code>"g"</code> = gram</p></li>
<li><p><code>"mg"</code> = milligram</p></li>
<li><p>`"mcg"`` = microgram</p></li>
<li><p><code>"U"</code> = unit</p></li>
@ -316,63 +214,60 @@
<li><p><code>"MU"</code> = million units</p></li>
<li><p><code>"mmol"</code> = millimole</p></li>
<li><p><code>"ml"</code> = millilitre (e.g. eyedrops)</p></li>
</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>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
</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>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
</div>
<div id="read-more-on-our-website-">
<h2>Read more on Our Website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <a href="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <a href="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
</div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"curl"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"rvest"</span><span class='op'>)</span> <span class='op'>&amp;&amp;</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>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 class='co'># oral DDD (Defined Daily Dose) of amoxicillin</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 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>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</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">&amp;&amp;</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">&amp;&amp;</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 class="co"># oral DDD (Defined Daily Dose) of amoxicillin</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 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 class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</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 class="co"># parenteral DDD (Defined Daily Dose) of amoxicillin</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 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 class='op'>}</span>
<span class='co'># }</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 class="op">}</span>
<span class="co"># }</span>
</code></pre></div>
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