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Conduct AMR analysis
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Conduct principal component analysis for AMR
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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>Translate Strings from the AMR Package</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/translate.R" class="external-link"><code>R/translate.R</code></a></small>
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<div class="d-none name"><code>translate.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>For language-dependent output of AMR functions, like <code><a href="mo_property.html">mo_name()</a></code>, <code><a href="mo_property.html">mo_gramstain()</a></code>, <code><a href="mo_property.html">mo_type()</a></code> and <code><a href="ab_property.html">ab_name()</a></code>.</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">get_AMR_locale</span><span class="op">(</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="va">language</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">reset_AMR_locale</span><span class="op">(</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">translate_AMR</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu">get_AMR_locale</span><span class="op">(</span><span class="op">)</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="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>language</dt>
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<dd><p>language to choose. Use one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk).</p></dd>
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<dt>x</dt>
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<dd><p>text to translate</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>The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.</p>
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<p><strong>To silence language notes when this package loads</strong> on a non-English operating system, you can set the option <code>AMR_locale</code> in your <code>.Rprofile</code> file like this:</p>
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<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Open .Rprofile file</span></span>
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<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>
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<span></span>
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<span><span class="co"># Add e.g. Italian support to that file using:</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_locale <span class="op">=</span> <span class="st">"Italian"</span><span class="op">)</span></span></code></pre><p></p></div>
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<p>And then save the file.</p>
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<p>Please read about adding or updating a language in <a href="https://github.com/msberends/AMR/wiki/" class="external-link">our Wiki</a>.</p><div class="section">
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<h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3>
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<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the R option <code>AMR_locale</code>, either by using e.g. <code>set_AMR_locale("German")</code> or by running e.g. <code>options(AMR_locale = "German")</code>.</p>
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<p>Note that setting an <span style="R">R</span> option only works in the same session. Save the command <code>options(AMR_locale = "(your language)")</code> to your <code>.Rprofile</code> file to apply it for every session. Run <code>utils::file.edit("~/.Rprofile")</code> to edit your <code>.Rprofile</code> file.</p></li>
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<li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory.</p></li>
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</ol><p>Thus, if the R option <code>AMR_locale</code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
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</div>
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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"># Current settings (based on system language)</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ciprofloxacin"</span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># setting another language</span></span></span>
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<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Spanish"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using Spanish (Español) for the AMR package for this session.</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ciprofloxacina"</span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Staphylococcus coagulasa negativo (SCN)"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># setting yet another language</span></span></span>
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<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Greek"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using Greek (Ελληνικά) for the AMR package for this session.</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Σιπροφλοξασίνη"</span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Σταφυλόκοκκος με αρνητική πηκτικότητα (CoNS)"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># setting yet another language</span></span></span>
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<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Ukrainian"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using Ukrainian (Українська) for the AMR package for this session.</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"Ciprofloxacin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ципрофлоксацин"</span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Coagulase-negative Staphylococcus (CoNS)"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Коагулазонегативний стафілокок (КНС)"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1:</span></span></span>
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<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"Deutsch"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using German (Deutsch) for the AMR package for this session.</span>
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<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"German"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using German (Deutsch) for the AMR package for this session.</span>
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<span class="r-in"><span><span class="fu">set_AMR_locale</span><span class="op">(</span><span class="st">"de"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using German (Deutsch) for the AMR package for this session.</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># reset to system default</span></span></span>
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<span class="r-in"><span><span class="fu">reset_AMR_locale</span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using the English language (English) for the AMR package for this</span>
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<span class="r-msg co"><span class="r-pr">#></span> session.</span>
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</code></pre></div>
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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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