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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -299,7 +299,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI 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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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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@ -350,13 +350,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<span class="r-msg co"><span class="r-pr">#></span> Staphylococcus aureus). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span> <span class="co"># Methicillin Resistant S. aureus</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span> <span class="co"># Vancomycin Intermediate S. aureus</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span> <span class="co"># Vancomycin Resistant S. aureus</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_AURS</span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span> <span class="co"># SNOMED CT code</span></span></span>
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@ -393,14 +393,14 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_GRPB</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span><span class="op">)</span> <span class="co"># will remain species: B_STPHY_EPDR</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_EPDR</span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STPHY_CONS</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STPHY_CONS</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span></span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span><span class="op">)</span> <span class="co"># will remain species: B_STRPT_PYGN</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <mo></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_PYGN</span>
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<span class="r-in"><span><span class="fu">as.mo</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># will not remain species: B_STRPT_GRPA</span></span></span>
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@ -408,11 +408,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<span class="r-out co"><span class="r-pr">#></span> [1] B_STRPT_GRPA</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># All mo_* functions use as.mo() internally too (see ?mo_property):</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Escherichia"</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Escherichia"</span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span> <span class="co"># returns "Gram negative"</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
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<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
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