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new antibiotics
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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Get properties of an antibiotic
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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Get properties of an antibiotic
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<h1>How to import data from SPSS / SAS / Stata</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">05 April 2019</h4>
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<h4 class="date">10 May 2019</h4>
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<div class="hidden name"><code>SPSS.Rmd</code></div>
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<p>If you are working at a midsized or small company, you can save it tens of thousands of dollars by using R instead of e.g. SPSS - gaining even more functions and flexibility. And all R enthousiasts can do as much PR as they want (like I do here), because nobody is officially associated with or affiliated by R. It is really free.</p>
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<p>If you sometimes write syntaxes in SPSS to run a complete analysis or to ‘automate’ some of your work, you should perhaps do this in R. You will notice that writing syntaxes in R is a lot more nifty and clever than in SPSS.</p>
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<p>If you sometimes write syntaxes in SPSS to run a complete analysis or to ‘automate’ some of your work, you should perhaps do this in R. You will notice that writing syntaxes in R is a lot more nifty and clever than in SPSS. Still, as working with any statistical package, you will have to have knowledge about what you are doing (statistically) and what you are willing to accomplish.</p>
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<p>To demonstrate the first point:</p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="co"># not all values are valid MIC values:</span></a>
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<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="../reference/as.mic.html">as.mic</a></span>(<span class="fl">0.125</span>)</a>
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<a class="sourceLine" id="cb1-21" title="21"><span class="co">#> mo amox</span></a>
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<a class="sourceLine" id="cb1-22" title="22"><span class="co">#> 1 klebsiella R</span></a>
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<a class="sourceLine" id="cb1-23" title="23"></a>
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<a class="sourceLine" id="cb1-24" title="24"><span class="co"># hundreds of trade names can be translated to an ATC or name:</span></a>
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<a class="sourceLine" id="cb1-25" title="25"><span class="kw"><a href="../reference/atc_property.html">atc_name</a></span>(<span class="st">"floxapen"</span>)</a>
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<a class="sourceLine" id="cb1-24" title="24"><span class="co"># hundreds of trade names can be translated to a name, trade name or an ATC code:</span></a>
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<a class="sourceLine" id="cb1-25" title="25"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"floxapen"</span>)</a>
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<a class="sourceLine" id="cb1-26" title="26"><span class="co">#> [1] "Flucloxacillin"</span></a>
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<a class="sourceLine" id="cb1-27" title="27"><span class="kw"><a href="../reference/as.atc.html">as.atc</a></span>(<span class="st">"floxapen"</span>)</a>
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<a class="sourceLine" id="cb1-28" title="28"><span class="co">#> Class 'atc'</span></a>
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<a class="sourceLine" id="cb1-29" title="29"><span class="co">#> [1] J01CF05</span></a>
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<a class="sourceLine" id="cb1-30" title="30"><span class="kw"><a href="../reference/atc_property.html">atc_tradenames</a></span>(<span class="st">"floxapen"</span>)</a>
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<a class="sourceLine" id="cb1-31" title="31"><span class="co">#> [1] "Flopen" "Floxapen" "Fluclox" "Sesamol" "Softapen" "Staphylex"</span></a></code></pre></div>
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<a class="sourceLine" id="cb1-27" title="27"><span class="kw"><a href="../reference/ab_property.html">ab_tradenames</a></span>(<span class="st">"floxapen"</span>)</a>
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<a class="sourceLine" id="cb1-28" title="28"><span class="co">#> [1] "Floxacillin" "FLOXACILLIN" "Floxapen" </span></a>
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<a class="sourceLine" id="cb1-29" title="29"><span class="co">#> [4] "Floxapen sodium salt" "Fluclox" "Flucloxacilina" </span></a>
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<a class="sourceLine" id="cb1-30" title="30"><span class="co">#> [7] "Flucloxacillin" "Flucloxacilline" "Flucloxacillinum" </span></a>
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<a class="sourceLine" id="cb1-31" title="31"><span class="co">#> [10] "Fluorochloroxacillin"</span></a>
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<a class="sourceLine" id="cb1-32" title="32"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"floxapen"</span>)</a>
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<a class="sourceLine" id="cb1-33" title="33"><span class="co">#> Class 'atc'</span></a>
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<a class="sourceLine" id="cb1-34" title="34"><span class="co">#> [1] J01CF05</span></a></code></pre></div>
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<div id="import-data-from-spsssasstata" class="section level2">
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<h2 class="hasAnchor">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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</span>
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</a>
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<a href="../articles/Predict.html">
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<a href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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Predict antimicrobial resistance
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Work with WHONET data
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</a>
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<a href="../articles/SPSS.html">
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<span class="fa fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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</a>
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<a href="../articles/EUCAST.html">
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</a>
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<a href="../articles/mo_property.html">
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<a href="../reference/mo_property.html">
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Get properties of a microorganism
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</a>
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<a href="../articles/ab_property.html">
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Get properties of an antibiotic
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<h1>How to get properties of an antibiotic</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">09 February 2019</h4>
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<h4 class="date">10 May 2019</h4>
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<div class="hidden name"><code>ab_property.Rmd</code></div>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
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</span>
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</div>
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</a>
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<a href="../reference/ab_property.html">
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Get properties of an antibiotic
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<h1>Benchmarks</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">09 April 2019</h4>
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<h4 class="date">10 May 2019</h4>
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<div class="hidden name"><code>benchmarks.Rmd</code></div>
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<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
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<a class="sourceLine" id="cb2-10" title="10"><span class="co">#> Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb2-11" title="11"><span class="co">#> expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb2-12" title="12"><span class="co">#> as.mo("sau") 18 18.0 27 18.0 18.0 65 10</span></a>
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<a class="sourceLine" id="cb2-13" title="13"><span class="co">#> as.mo("stau") 48 48.0 56 48.0 48.0 130 10</span></a>
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<a class="sourceLine" id="cb2-14" title="14"><span class="co">#> as.mo("staaur") 18 18.0 24 18.0 18.0 76 10</span></a>
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<a class="sourceLine" id="cb2-15" title="15"><span class="co">#> as.mo("STAAUR") 18 18.0 27 18.0 19.0 63 10</span></a>
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<a class="sourceLine" id="cb2-16" title="16"><span class="co">#> as.mo("S. aureus") 28 28.0 33 28.0 29.0 72 10</span></a>
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<a class="sourceLine" id="cb2-17" title="17"><span class="co">#> as.mo("S. aureus") 28 29.0 38 29.0 31.0 76 10</span></a>
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<a class="sourceLine" id="cb2-18" title="18"><span class="co">#> as.mo("Staphylococcus aureus") 8 8.1 12 8.1 8.2 52 10</span></a></code></pre></div>
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<a class="sourceLine" id="cb2-11" title="11"><span class="co">#> expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb2-12" title="12"><span class="co">#> as.mo("sau") 18.0 18 23.0 18 18.0 65 10</span></a>
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<a class="sourceLine" id="cb2-13" title="13"><span class="co">#> as.mo("stau") 47.0 48 48.0 48 48.0 50 10</span></a>
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<a class="sourceLine" id="cb2-14" title="14"><span class="co">#> as.mo("staaur") 18.0 18 22.0 18 18.0 62 10</span></a>
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<a class="sourceLine" id="cb2-15" title="15"><span class="co">#> as.mo("STAAUR") 18.0 18 32.0 19 62.0 62 10</span></a>
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<a class="sourceLine" id="cb2-16" title="16"><span class="co">#> as.mo("S. aureus") 28.0 28 42.0 28 28.0 120 10</span></a>
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<a class="sourceLine" id="cb2-17" title="17"><span class="co">#> as.mo("S. aureus") 28.0 28 40.0 28 29.0 98 10</span></a>
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<a class="sourceLine" id="cb2-18" title="18"><span class="co">#> as.mo("Staphylococcus aureus") 7.9 8 9.2 8 8.1 20 10</span></a></code></pre></div>
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<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
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<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
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<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
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@@ -236,12 +236,12 @@
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<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
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<a class="sourceLine" id="cb3-8" title="8"><span class="co">#> Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb3-9" title="9"><span class="co">#> expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb3-10" title="10"><span class="co">#> as.mo("theisl") 460 480 490 500 510 510 10</span></a>
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<a class="sourceLine" id="cb3-11" title="11"><span class="co">#> as.mo("THEISL") 460 460 490 470 510 520 10</span></a>
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<a class="sourceLine" id="cb3-12" title="12"><span class="co">#> as.mo("T. islandicus") 72 73 88 75 110 120 10</span></a>
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<a class="sourceLine" id="cb3-13" title="13"><span class="co">#> as.mo("T. islandicus") 73 73 87 74 100 140 10</span></a>
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<a class="sourceLine" id="cb3-14" title="14"><span class="co">#> as.mo("Thermus islandicus") 72 73 90 75 120 130 10</span></a></code></pre></div>
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<p>That takes 8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
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<a class="sourceLine" id="cb3-10" title="10"><span class="co">#> as.mo("theisl") 470 470 490 470 520 520 10</span></a>
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<a class="sourceLine" id="cb3-11" title="11"><span class="co">#> as.mo("THEISL") 470 470 500 510 520 520 10</span></a>
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<a class="sourceLine" id="cb3-12" title="12"><span class="co">#> as.mo("T. islandicus") 76 76 81 76 77 120 10</span></a>
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<a class="sourceLine" id="cb3-13" title="13"><span class="co">#> as.mo("T. islandicus") 76 76 94 78 120 120 10</span></a>
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<a class="sourceLine" id="cb3-14" title="14"><span class="co">#> as.mo("Thermus islandicus") 74 74 96 77 120 150 10</span></a></code></pre></div>
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<p>That takes 8.2 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
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<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
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<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
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<a class="sourceLine" id="cb4-2" title="2"></a>
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@@ -253,7 +253,7 @@
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<a class="sourceLine" id="cb4-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
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<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>),</a>
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<a class="sourceLine" id="cb4-10" title="10"> <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"s"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>,</a>
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<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>, <span class="dt">ylim =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">0.5</span>),</a>
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<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>,</a>
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<a class="sourceLine" id="cb4-12" title="12"> <span class="dt">main =</span> <span class="st">"Benchmarks per prevalence"</span>)</a></code></pre></div>
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<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
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<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
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@@ -286,9 +286,9 @@
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<a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
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<a class="sourceLine" id="cb5-25" title="25"><span class="co">#> Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb5-26" title="26"><span class="co">#> expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb5-27" title="27"><span class="co">#> mo_fullname(x) 774 777 811 783 829 947 10</span></a></code></pre></div>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.78 seconds (783 ms). You only lose time on your unique input values.</p>
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<a class="sourceLine" id="cb5-26" title="26"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#> mo_fullname(x) 777 780 859 864 870 1080 10</span></a></code></pre></div>
|
||||
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.86 seconds (864 ms). You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@@ -300,11 +300,11 @@
|
||||
<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
|
||||
<a class="sourceLine" id="cb6-6" title="6"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#> A 12.000 12.100 12.500 12.400 12.800 13.20 10</span></a>
|
||||
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#> B 25.800 26.200 26.900 26.600 27.800 28.00 10</span></a>
|
||||
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#> C 0.476 0.691 0.758 0.812 0.848 1.03 10</span></a></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#> A 13.30 14.0 14.3 14.1 14.30 17.30 10</span></a>
|
||||
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#> B 25.20 25.5 36.5 26.5 39.60 71.30 10</span></a>
|
||||
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#> C 1.68 1.7 1.9 1.8 1.94 2.81 10</span></a></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0018 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
|
||||
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
|
||||
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
|
||||
@@ -317,14 +317,14 @@
|
||||
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
|
||||
<a class="sourceLine" id="cb7-11" title="11"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb7-12" title="12"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#> A 0.364 0.403 0.452 0.455 0.496 0.575 10</span></a>
|
||||
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#> B 0.478 0.533 0.566 0.565 0.594 0.645 10</span></a>
|
||||
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#> C 0.512 0.726 0.851 0.893 1.010 1.150 10</span></a>
|
||||
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#> D 0.409 0.460 0.490 0.507 0.530 0.544 10</span></a>
|
||||
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#> E 0.375 0.380 0.454 0.476 0.488 0.524 10</span></a>
|
||||
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#> F 0.395 0.411 0.463 0.442 0.522 0.587 10</span></a>
|
||||
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#> G 0.381 0.404 0.454 0.451 0.495 0.546 10</span></a>
|
||||
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#> H 0.232 0.268 0.304 0.297 0.336 0.391 10</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#> A 0.417 0.456 0.511 0.494 0.558 0.612 10</span></a>
|
||||
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#> B 0.416 0.555 0.620 0.614 0.658 0.837 10</span></a>
|
||||
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#> C 1.360 1.630 1.970 1.880 1.970 3.220 10</span></a>
|
||||
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#> D 0.435 0.519 0.671 0.665 0.734 1.120 10</span></a>
|
||||
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#> E 0.356 0.429 0.491 0.452 0.486 0.916 10</span></a>
|
||||
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#> F 0.384 0.450 0.559 0.502 0.543 1.180 10</span></a>
|
||||
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#> G 0.407 0.450 0.591 0.527 0.663 1.080 10</span></a>
|
||||
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#> H 0.219 0.272 0.295 0.276 0.311 0.420 10</span></a></code></pre></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
@@ -350,14 +350,14 @@
|
||||
<a class="sourceLine" id="cb8-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||||
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
|
||||
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#> en 18.37 19.07 19.98 19.22 19.41 27.24 10</span></a>
|
||||
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#> de 30.58 31.06 35.93 31.42 31.54 77.27 10</span></a>
|
||||
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#> nl 31.01 31.33 37.73 31.41 31.59 93.52 10</span></a>
|
||||
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#> es 31.38 31.45 36.30 31.81 32.53 76.12 10</span></a>
|
||||
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#> it 30.98 31.40 36.99 31.58 32.30 84.46 10</span></a>
|
||||
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#> fr 31.19 31.21 35.82 31.45 31.62 75.52 10</span></a>
|
||||
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#> pt 31.02 31.36 40.85 32.22 33.84 76.22 10</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#> en 18.34 18.37 23.22 18.54 19.53 63.17 10</span></a>
|
||||
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#> de 23.46 23.50 23.76 23.57 23.76 25.10 10</span></a>
|
||||
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#> nl 50.78 52.48 62.59 53.54 57.07 100.20 10</span></a>
|
||||
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#> es 23.53 23.59 28.70 23.76 24.17 68.55 10</span></a>
|
||||
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#> it 23.31 23.40 23.69 23.51 23.79 24.73 10</span></a>
|
||||
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#> fr 23.45 23.52 24.21 24.06 24.88 25.21 10</span></a>
|
||||
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#> pt 23.54 23.72 24.37 24.39 24.90 25.58 10</span></a></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 27 KiB After Width: | Height: | Size: 27 KiB |
@@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -143,7 +143,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -241,7 +241,7 @@
|
||||
<li><a href="G_test.html">How to use the *G*-test</a></li>
|
||||
<li><a href="SPSS.html">How to import data from SPSS / SAS / Stata</a></li>
|
||||
<li><a href="WHONET.html">How to work with WHONET data</a></li>
|
||||
<li><a href="atc_property.html">How to get properties of an antibiotic</a></li>
|
||||
<li><a href="ab_property.html">How to get properties of an antibiotic</a></li>
|
||||
<li><a href="benchmarks.html">Benchmarks</a></li>
|
||||
<li><a href="freq.html">How to create frequency tables</a></li>
|
||||
<li><a href="mo_property.html">How to get properties of a microorganism</a></li>
|
||||
|
||||
@@ -40,7 +40,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -105,7 +105,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -192,7 +192,7 @@
|
||||
<h1>How to predict antimicrobial resistance</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">27 March 2019</h4>
|
||||
<h4 class="date">10 May 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
|
||||
@@ -218,16 +218,16 @@
|
||||
<a href="#prediction-analysis" class="anchor"></a>Prediction analysis</h2>
|
||||
<p>Our package contains a function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>, which takes the same input as functions for <a href="./AMR.html">other AMR analysis</a>. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.</p>
|
||||
<p>It is basically as easy as:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># resistance prediction of piperacillin/tazobactam (pita):</span></a>
|
||||
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">tbl =</span> septic_patients, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"pita"</span>)</a>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># resistance prediction of piperacillin/tazobactam (TZP):</span></a>
|
||||
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">tbl =</span> septic_patients, <span class="dt">col_date =</span> <span class="st">"date"</span>, <span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-3" title="3"></a>
|
||||
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># or:</span></a>
|
||||
<a class="sourceLine" id="cb2-5" title="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb2-6" title="6"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"pita"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-6" title="6"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-7" title="7"></a>
|
||||
<a class="sourceLine" id="cb2-8" title="8"><span class="co"># to bind it to object 'predict_pita' for example:</span></a>
|
||||
<a class="sourceLine" id="cb2-9" title="9">predict_pita <-<span class="st"> </span>septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb2-10" title="10"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"pita"</span>)</a></code></pre></div>
|
||||
<a class="sourceLine" id="cb2-8" title="8"><span class="co"># to bind it to object 'predict_TZP' for example:</span></a>
|
||||
<a class="sourceLine" id="cb2-9" title="9">predict_TZP <-<span class="st"> </span>septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb2-10" title="10"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"TZP"</span>)</a></code></pre></div>
|
||||
<p>The function will look for a date column itself if <code>col_date</code> is not set.</p>
|
||||
<p>When running any of these commands, a summary of the regression model will be printed unless using <code><a href="../reference/resistance_predict.html">resistance_predict(..., info = FALSE)</a></code>.</p>
|
||||
<pre><code>#> NOTE: Using column `date` as input for `col_date`.
|
||||
@@ -240,62 +240,62 @@
|
||||
#>
|
||||
#> Deviance Residuals:
|
||||
#> Min 1Q Median 3Q Max
|
||||
#> -2.9224 -1.3120 0.0170 0.7586 3.1932
|
||||
#> -2.9203 -1.3066 0.0166 0.7641 3.1984
|
||||
#>
|
||||
#> Coefficients:
|
||||
#> Estimate Std. Error z value Pr(>|z|)
|
||||
#> (Intercept) -222.92857 45.93922 -4.853 1.22e-06 ***
|
||||
#> year 0.10994 0.02284 4.814 1.48e-06 ***
|
||||
#> (Intercept) -222.51053 45.94675 -4.843 1.28e-06 ***
|
||||
#> year 0.10973 0.02284 4.805 1.55e-06 ***
|
||||
#> ---
|
||||
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||||
#>
|
||||
#> (Dispersion parameter for binomial family taken to be 1)
|
||||
#>
|
||||
#> Null deviance: 59.794 on 14 degrees of freedom
|
||||
#> Residual deviance: 35.191 on 13 degrees of freedom
|
||||
#> AIC: 93.464
|
||||
#> Null deviance: 59.763 on 14 degrees of freedom
|
||||
#> Residual deviance: 35.261 on 13 degrees of freedom
|
||||
#> AIC: 93.537
|
||||
#>
|
||||
#> Number of Fisher Scoring iterations: 4</code></pre>
|
||||
<p>This text is only a printed summary - the actual result (output) of the function is a <code>data.frame</code> containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">predict_pita</a>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">predict_TZP</a>
|
||||
<a class="sourceLine" id="cb4-2" title="2"><span class="co">#> year value se_min se_max observations observed estimated</span></a>
|
||||
<a class="sourceLine" id="cb4-3" title="3"><span class="co">#> 1 2003 0.06250000 NA NA 32 0.06250000 0.06177594</span></a>
|
||||
<a class="sourceLine" id="cb4-4" title="4"><span class="co">#> 2 2004 0.08536585 NA NA 82 0.08536585 0.06846343</span></a>
|
||||
<a class="sourceLine" id="cb4-5" title="5"><span class="co">#> 3 2005 0.10000000 NA NA 60 0.10000000 0.07581637</span></a>
|
||||
<a class="sourceLine" id="cb4-6" title="6"><span class="co">#> 4 2006 0.05084746 NA NA 59 0.05084746 0.08388789</span></a>
|
||||
<a class="sourceLine" id="cb4-7" title="7"><span class="co">#> 5 2007 0.12121212 NA NA 66 0.12121212 0.09273250</span></a>
|
||||
<a class="sourceLine" id="cb4-8" title="8"><span class="co">#> 6 2008 0.04166667 NA NA 72 0.04166667 0.10240539</span></a>
|
||||
<a class="sourceLine" id="cb4-9" title="9"><span class="co">#> 7 2009 0.01639344 NA NA 61 0.01639344 0.11296163</span></a>
|
||||
<a class="sourceLine" id="cb4-10" title="10"><span class="co">#> 8 2010 0.09433962 NA NA 53 0.09433962 0.12445516</span></a>
|
||||
<a class="sourceLine" id="cb4-11" title="11"><span class="co">#> 9 2011 0.18279570 NA NA 93 0.18279570 0.13693759</span></a>
|
||||
<a class="sourceLine" id="cb4-12" title="12"><span class="co">#> 10 2012 0.30769231 NA NA 65 0.30769231 0.15045682</span></a>
|
||||
<a class="sourceLine" id="cb4-13" title="13"><span class="co">#> 11 2013 0.08620690 NA NA 58 0.08620690 0.16505550</span></a>
|
||||
<a class="sourceLine" id="cb4-14" title="14"><span class="co">#> 12 2014 0.15254237 NA NA 59 0.15254237 0.18076926</span></a>
|
||||
<a class="sourceLine" id="cb4-15" title="15"><span class="co">#> 13 2015 0.27272727 NA NA 55 0.27272727 0.19762493</span></a>
|
||||
<a class="sourceLine" id="cb4-16" title="16"><span class="co">#> 14 2016 0.25000000 NA NA 84 0.25000000 0.21563859</span></a>
|
||||
<a class="sourceLine" id="cb4-17" title="17"><span class="co">#> 15 2017 0.16279070 NA NA 86 0.16279070 0.23481370</span></a>
|
||||
<a class="sourceLine" id="cb4-18" title="18"><span class="co">#> 16 2018 0.25513926 0.2228376 0.2874409 NA NA 0.25513926</span></a>
|
||||
<a class="sourceLine" id="cb4-19" title="19"><span class="co">#> 17 2019 0.27658825 0.2386811 0.3144954 NA NA 0.27658825</span></a>
|
||||
<a class="sourceLine" id="cb4-20" title="20"><span class="co">#> 18 2020 0.29911630 0.2551715 0.3430611 NA NA 0.29911630</span></a>
|
||||
<a class="sourceLine" id="cb4-21" title="21"><span class="co">#> 19 2021 0.32266085 0.2723340 0.3729877 NA NA 0.32266085</span></a>
|
||||
<a class="sourceLine" id="cb4-22" title="22"><span class="co">#> 20 2022 0.34714076 0.2901847 0.4040968 NA NA 0.34714076</span></a>
|
||||
<a class="sourceLine" id="cb4-23" title="23"><span class="co">#> 21 2023 0.37245666 0.3087318 0.4361815 NA NA 0.37245666</span></a>
|
||||
<a class="sourceLine" id="cb4-24" title="24"><span class="co">#> 22 2024 0.39849187 0.3279750 0.4690088 NA NA 0.39849187</span></a>
|
||||
<a class="sourceLine" id="cb4-25" title="25"><span class="co">#> 23 2025 0.42511415 0.3479042 0.5023241 NA NA 0.42511415</span></a>
|
||||
<a class="sourceLine" id="cb4-26" title="26"><span class="co">#> 24 2026 0.45217796 0.3684992 0.5358568 NA NA 0.45217796</span></a>
|
||||
<a class="sourceLine" id="cb4-27" title="27"><span class="co">#> 25 2027 0.47952757 0.3897276 0.5693275 NA NA 0.47952757</span></a>
|
||||
<a class="sourceLine" id="cb4-28" title="28"><span class="co">#> 26 2028 0.50700045 0.4115444 0.6024565 NA NA 0.50700045</span></a>
|
||||
<a class="sourceLine" id="cb4-29" title="29"><span class="co">#> 27 2029 0.53443111 0.4338908 0.6349714 NA NA 0.53443111</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb4-3" title="3"><span class="co">#> 1 2003 0.06250000 NA NA 32 0.06250000 0.06179057</span></a>
|
||||
<a class="sourceLine" id="cb4-4" title="4"><span class="co">#> 2 2004 0.08536585 NA NA 82 0.08536585 0.06846623</span></a>
|
||||
<a class="sourceLine" id="cb4-5" title="5"><span class="co">#> 3 2005 0.10000000 NA NA 60 0.10000000 0.07580483</span></a>
|
||||
<a class="sourceLine" id="cb4-6" title="6"><span class="co">#> 4 2006 0.05084746 NA NA 59 0.05084746 0.08385921</span></a>
|
||||
<a class="sourceLine" id="cb4-7" title="7"><span class="co">#> 5 2007 0.12121212 NA NA 66 0.12121212 0.09268356</span></a>
|
||||
<a class="sourceLine" id="cb4-8" title="8"><span class="co">#> 6 2008 0.04166667 NA NA 72 0.04166667 0.10233276</span></a>
|
||||
<a class="sourceLine" id="cb4-9" title="9"><span class="co">#> 7 2009 0.01639344 NA NA 61 0.01639344 0.11286156</span></a>
|
||||
<a class="sourceLine" id="cb4-10" title="10"><span class="co">#> 8 2010 0.09433962 NA NA 53 0.09433962 0.12432363</span></a>
|
||||
<a class="sourceLine" id="cb4-11" title="11"><span class="co">#> 9 2011 0.18279570 NA NA 93 0.18279570 0.13677030</span></a>
|
||||
<a class="sourceLine" id="cb4-12" title="12"><span class="co">#> 10 2012 0.30769231 NA NA 65 0.30769231 0.15024926</span></a>
|
||||
<a class="sourceLine" id="cb4-13" title="13"><span class="co">#> 11 2013 0.08620690 NA NA 58 0.08620690 0.16480299</span></a>
|
||||
<a class="sourceLine" id="cb4-14" title="14"><span class="co">#> 12 2014 0.15000000 NA NA 60 0.15000000 0.18046706</span></a>
|
||||
<a class="sourceLine" id="cb4-15" title="15"><span class="co">#> 13 2015 0.27272727 NA NA 55 0.27272727 0.19726831</span></a>
|
||||
<a class="sourceLine" id="cb4-16" title="16"><span class="co">#> 14 2016 0.25000000 NA NA 84 0.25000000 0.21522295</span></a>
|
||||
<a class="sourceLine" id="cb4-17" title="17"><span class="co">#> 15 2017 0.16279070 NA NA 86 0.16279070 0.23433471</span></a>
|
||||
<a class="sourceLine" id="cb4-18" title="18"><span class="co">#> 16 2018 0.25459302 0.2223385 0.2868476 NA NA 0.25459302</span></a>
|
||||
<a class="sourceLine" id="cb4-19" title="19"><span class="co">#> 17 2019 0.27597143 0.2381174 0.3138255 NA NA 0.27597143</span></a>
|
||||
<a class="sourceLine" id="cb4-20" title="20"><span class="co">#> 18 2020 0.29842630 0.2545398 0.3423128 NA NA 0.29842630</span></a>
|
||||
<a class="sourceLine" id="cb4-21" title="21"><span class="co">#> 19 2021 0.32189595 0.2716308 0.3721611 NA NA 0.32189595</span></a>
|
||||
<a class="sourceLine" id="cb4-22" title="22"><span class="co">#> 20 2022 0.34630028 0.2894072 0.4031934 NA NA 0.34630028</span></a>
|
||||
<a class="sourceLine" id="cb4-23" title="23"><span class="co">#> 21 2023 0.37154107 0.3078773 0.4352048 NA NA 0.37154107</span></a>
|
||||
<a class="sourceLine" id="cb4-24" title="24"><span class="co">#> 22 2024 0.39750288 0.3270414 0.4679643 NA NA 0.39750288</span></a>
|
||||
<a class="sourceLine" id="cb4-25" title="25"><span class="co">#> 23 2025 0.42405472 0.3468903 0.5012191 NA NA 0.42405472</span></a>
|
||||
<a class="sourceLine" id="cb4-26" title="26"><span class="co">#> 24 2026 0.45105237 0.3674044 0.5347004 NA NA 0.45105237</span></a>
|
||||
<a class="sourceLine" id="cb4-27" title="27"><span class="co">#> 25 2027 0.47834130 0.3885523 0.5681303 NA NA 0.47834130</span></a>
|
||||
<a class="sourceLine" id="cb4-28" title="28"><span class="co">#> 26 2028 0.50576012 0.4102900 0.6012302 NA NA 0.50576012</span></a>
|
||||
<a class="sourceLine" id="cb4-29" title="29"><span class="co">#> 27 2029 0.53314434 0.4325600 0.6337287 NA NA 0.53314434</span></a></code></pre></div>
|
||||
<p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(predict_pita)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(predict_TZP)</a></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
|
||||
<p>This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.</p>
|
||||
<p>We also support the <code>ggplot2</code> package with our custom function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> to create more appealing plots:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_pita)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_TZP)</a></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"></a>
|
||||
<a class="sourceLine" id="cb7-2" title="2"><span class="co"># choose for error bars instead of a ribbon</span></a>
|
||||
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_pita, <span class="dt">ribbon =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
|
||||
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(predict_TZP, <span class="dt">ribbon =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-5-2.png" width="720"></p>
|
||||
<div id="choosing-the-right-model" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@@ -303,7 +303,7 @@
|
||||
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram positives, the spread (i.e. standard error) is enormous:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"vanc"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb8-4" title="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
|
||||
<a class="sourceLine" id="cb8-5" title="5"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
|
||||
@@ -348,13 +348,13 @@
|
||||
<p>For the vancomycin resistance in Gram positive bacteria, a linear model might be more appropriate since no (left half of a) binomial distribution is to be expected based on the observed years:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb9-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb9-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"vanc"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>, <span class="dt">model =</span> <span class="st">"linear"</span>) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb9-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>, <span class="dt">model =</span> <span class="st">"linear"</span>) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb9-4" title="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
|
||||
<a class="sourceLine" id="cb9-5" title="5"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
<p>This seems more likely, doesn’t it?</p>
|
||||
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">model <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/attributes">attributes</a></span>(predict_pita)<span class="op">$</span>model</a>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">model <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/attributes">attributes</a></span>(predict_TZP)<span class="op">$</span>model</a>
|
||||
<a class="sourceLine" id="cb10-2" title="2"></a>
|
||||
<a class="sourceLine" id="cb10-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(model)<span class="op">$</span>family</a>
|
||||
<a class="sourceLine" id="cb10-4" title="4"><span class="co">#> </span></a>
|
||||
@@ -363,8 +363,8 @@
|
||||
<a class="sourceLine" id="cb10-7" title="7"></a>
|
||||
<a class="sourceLine" id="cb10-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(model)<span class="op">$</span>coefficients</a>
|
||||
<a class="sourceLine" id="cb10-9" title="9"><span class="co">#> Estimate Std. Error z value Pr(>|z|)</span></a>
|
||||
<a class="sourceLine" id="cb10-10" title="10"><span class="co">#> (Intercept) -222.9285736 45.93922388 -4.852685 1.218012e-06</span></a>
|
||||
<a class="sourceLine" id="cb10-11" title="11"><span class="co">#> year 0.1099391 0.02283501 4.814500 1.475690e-06</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb10-10" title="10"><span class="co">#> (Intercept) -222.5105288 45.94675125 -4.842791 1.280277e-06</span></a>
|
||||
<a class="sourceLine" id="cb10-11" title="11"><span class="co">#> year 0.1097306 0.02283874 4.804581 1.550761e-06</span></a></code></pre></div>
|
||||
</div>
|
||||
</div>
|
||||
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|
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@@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -143,7 +143,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/atc_property.html">
|
||||
<a href="reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
|
||||
@@ -24,6 +24,10 @@
|
||||
// Add updated Font Awesome 5.6.3 library
|
||||
$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">');
|
||||
|
||||
// Email template for new GitLab issues
|
||||
//https://stackoverflow.com/a/33190494/4575331
|
||||
//incoming+msberends-amr-9011429-5miwzuo1xo70wbz9r6fwv4dmg-issue@incoming.gitlab.com
|
||||
|
||||
// Edit footer
|
||||
$( document ).ready(function() {
|
||||
|
||||
|
||||
@@ -42,7 +42,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -107,7 +107,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/atc_property.html">
|
||||
<a href="reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -197,7 +197,7 @@
|
||||
<p><em>(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
|
||||
<hr>
|
||||
<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any data format, including WHONET/EARS-Net data.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~65,000 microorganisms</strong></a> and <a href="./reference/antibiotics.html"><strong>~500 antibiotics</strong></a> by name and code, and knows all about valid RSI and MIC values.</p>
|
||||
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~65,000 microorganisms</strong></a> and <a href="./reference/antibiotics.html"><strong>~450 antibiotics</strong></a> by name and code, and knows all about valid RSI and MIC values.</p>
|
||||
<p><strong>Used to SPSS?</strong> Read our <a href="./articles/SPSS.html">tutorial on how to import data from SPSS, SAS or Stata</a> and learn in which ways R outclasses any of these statistical packages.</p>
|
||||
<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and is free software; you can freely use and distribute it for both personal and commercial (but <strong>not</strong> patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full license <a href="./LICENSE-text.html">here</a>.</p>
|
||||
<p>This package can be used for:</p>
|
||||
@@ -295,7 +295,7 @@
|
||||
<div>
|
||||
<img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p>
|
||||
</div>
|
||||
<p>This package contains <strong>all ~500 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
|
||||
<p>This package contains <strong>all ~450 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
|
||||
<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
|
||||
</div>
|
||||
<div id="whonet--ears-net" class="section level4">
|
||||
@@ -313,10 +313,10 @@
|
||||
<li>
|
||||
<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
|
||||
<ul>
|
||||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||||
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
|
||||
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
|
||||
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.</li>
|
||||
<li>Use <code><a href="reference/as.atc.html">as.atc()</a></code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.</li>
|
||||
<li>Use <code><a href="reference/as.ab.html">as.ab()</a></code> to get a antibiotic ID, which are abbreviations used by EARS-Net whenever available. Use <code><a href="reference/as.atc.html">as.atc()</a></code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
@@ -330,7 +330,7 @@
|
||||
</li>
|
||||
<li>Use <code><a href="reference/mdro.html">mdro()</a></code> (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.</li>
|
||||
<li>The <a href="./reference/microorganisms.html">data set <code>microorganisms</code></a> contains the complete taxonomic tree of ~65,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. As they use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> contains almost 500 antimicrobial drugs with their ATC code, EARS-Net code, common LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains hundreds of trade names. Use functions like <code><a href="reference/atc_property.html">atc_name()</a></code> and <code><a href="reference/atc_property.html">atc_tradenames()</a></code> to look up values. The <code>atc_*</code> functions use <code><a href="reference/as.atc.html">as.atc()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code><a href="reference/atc_property.html">atc_name("Fluclox")</a></code>, <code><a href="reference/atc_property.html">atc_name("Floxapen")</a></code> and <code><a href="reference/atc_property.html">atc_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
|
||||
<li>The <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code>, <code><a href="reference/ab_property.html">ab_group()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
|
||||
@@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -143,7 +143,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -237,24 +237,48 @@
|
||||
<a href="#amr-0619001" class="anchor"></a>AMR 0.6.1.9001<small> Unreleased </small>
|
||||
</h1>
|
||||
<p><strong>Note: latest development version</strong></p>
|
||||
<div id="new" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#changed" class="anchor"></a>Changed</h4>
|
||||
<ul>
|
||||
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>
|
||||
<li>Completely reworked the <code>antibiotics</code> data set:
|
||||
<ul>
|
||||
<li>All entries now have 3 different identifiers: a human readable EARS-Net code (<code>ab</code>, used by ECDC and WHONET), an ATC code (<code>atc</code>, used by WHO), and a CID code (<code>cid</code>, Compound ID, used by PubChem)</li>
|
||||
<li>Based on the Compound ID, more than a thousand official brand names have been added from many different countries</li>
|
||||
<li>All references to antibiotics in our package now use EARS-Net codes, like <code>AMX</code> for amoxicillin</li>
|
||||
<li>Functions <code>atc_certe</code>, <code>ab_umcg</code> and <code>atc_trivial_nl</code> have been removed</li>
|
||||
<li>All <code>atc_*</code> functions are superceded by <code>ab_*</code> functions</li>
|
||||
<li>
|
||||
<p>All output will be translated by using an included, local translation file that can be found after install with:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.file">system.file</a></span>(<span class="st">"translations.tsv"</span>, <span class="dt">package =</span> <span class="st">"AMR"</span>)</a></code></pre></div>
|
||||
Please create an issue in one of our repositories if you want additions in this file.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Improved intelligence of looking up antibiotic tables in data set using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
|
||||
</li>
|
||||
<li>Added ~5,000 more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><a href="../reference/as.mo.html">as.mo()</a></code> function</li>
|
||||
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code>rsi()</code>
|
||||
</li>
|
||||
<li>Frequency tables of microbial IDs speed improvement</li>
|
||||
<li>Removed all hardcoded EUCAST rules and replaced them with a new reference file: <code>./inst/eucast/eucast.tsv</code>.</li>
|
||||
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
|
||||
</li>
|
||||
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+.</li>
|
||||
<li>Fix for <code><a href="../reference/freq.html">freq()</a></code> for when all values are <code>NA</code>.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Support for R 3.6.0</li>
|
||||
<li>Prevented <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a> in R 3.6.0 and later by adding <code>StagedInstall: false</code> to the DESCRIPTION file</li>
|
||||
</ul>
|
||||
</div>
|
||||
@@ -283,9 +307,9 @@
|
||||
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
|
||||
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
|
||||
</ul>
|
||||
<div id="new" class="section level4">
|
||||
<div id="new-1" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h4>
|
||||
<a href="#new-1" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
|
||||
@@ -312,32 +336,32 @@ This data is updated annually - check the included version with the new function
|
||||
</li>
|
||||
<li>
|
||||
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb2-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb3-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">ab_property -><span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_property</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-2" title="2">ab_name -><span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_name</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-3" title="3">ab_official -><span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_official</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-4" title="4">ab_trivial_nl -><span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_trivial_nl</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-5" title="5">ab_certe -><span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_certe</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-6" title="6">ab_umcg -><span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_umcg</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-7" title="7">ab_tradenames -><span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_tradenames</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">ab_property -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-2" title="2">ab_name -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-3" title="3">ab_official -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-4" title="4">ab_trivial_nl -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-5" title="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||
<a class="sourceLine" id="cb4-6" title="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||
<a class="sourceLine" id="cb4-7" title="7">ab_tradenames -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
|
||||
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
|
||||
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
|
||||
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
|
||||
@@ -349,20 +373,20 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
|
||||
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
|
||||
<li>
|
||||
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||
<a class="sourceLine" id="cb4-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||
<a class="sourceLine" id="cb5-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb5-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
||||
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># or</span></a>
|
||||
<a class="sourceLine" id="cb5-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
||||
<a class="sourceLine" id="cb6-2" title="2"><span class="co"># or</span></a>
|
||||
<a class="sourceLine" id="cb6-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
||||
<p>is equal to:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb6-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb6-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb6-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
||||
</li>
|
||||
<li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
|
||||
</li>
|
||||
@@ -384,40 +408,40 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
|
||||
<li>Removed data sets <code>microorganisms.oldDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganismsDT</code> since they were no longer needed and only contained info already available in the <code>microorganisms</code> data set</li>
|
||||
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
|
||||
<li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
|
||||
<li>Functions <code><a href="../reference/AMR-deprecated.html">atc_ddd()</a></code> and <code><a href="../reference/AMR-deprecated.html">atc_groups()</a></code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
|
||||
<li>Functions <code>atc_ddd()</code> and <code>atc_groups()</code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
|
||||
<li>Function <code>guess_mo()</code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
|
||||
<li>Function <code>guess_atc()</code> is now deprecated in favour of <code><a href="../reference/as.atc.html">as.atc()</a></code> and will be removed in future versions</li>
|
||||
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
|
||||
<ul>
|
||||
<li>
|
||||
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
||||
<a class="sourceLine" id="cb7-2" title="2"></a>
|
||||
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
||||
<a class="sourceLine" id="cb7-4" title="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
||||
<a class="sourceLine" id="cb7-5" title="5"></a>
|
||||
<a class="sourceLine" id="cb7-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
||||
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
||||
<a class="sourceLine" id="cb8-2" title="2"></a>
|
||||
<a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
||||
<a class="sourceLine" id="cb8-4" title="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
||||
<a class="sourceLine" id="cb8-5" title="5"></a>
|
||||
<a class="sourceLine" id="cb8-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
||||
<a class="sourceLine" id="cb8-7" title="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># equal:</span></a>
|
||||
<a class="sourceLine" id="cb8-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
||||
<a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
||||
<a class="sourceLine" id="cb8-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb8-5" title="5"><span class="co"># also equal:</span></a>
|
||||
<a class="sourceLine" id="cb8-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
||||
<a class="sourceLine" id="cb8-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># equal:</span></a>
|
||||
<a class="sourceLine" id="cb9-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
||||
<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
||||
<a class="sourceLine" id="cb9-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb9-5" title="5"><span class="co"># also equal:</span></a>
|
||||
<a class="sourceLine" id="cb9-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
||||
<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
||||
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
|
||||
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
|
||||
</li>
|
||||
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
|
||||
<li>
|
||||
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
||||
<a class="sourceLine" id="cb9-2" title="2"><span class="co"># Warning: </span></a>
|
||||
<a class="sourceLine" id="cb9-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
||||
<a class="sourceLine" id="cb9-4" title="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
||||
<a class="sourceLine" id="cb10-2" title="2"><span class="co"># Warning: </span></a>
|
||||
<a class="sourceLine" id="cb10-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
||||
<a class="sourceLine" id="cb10-4" title="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Fix for vector containing only empty values</li>
|
||||
<li>Finds better results when input is in other languages</li>
|
||||
@@ -463,19 +487,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
||||
<a class="sourceLine" id="cb10-2" title="2"><span class="co"># OLD WAY</span></a>
|
||||
<a class="sourceLine" id="cb10-3" title="3">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb10-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb10-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb10-6" title="6"><span class="co"># NEW WAY</span></a>
|
||||
<a class="sourceLine" id="cb10-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb10-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb10-9" title="9"></a>
|
||||
<a class="sourceLine" id="cb10-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||
<a class="sourceLine" id="cb10-11" title="11">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb10-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb10-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
||||
<a class="sourceLine" id="cb11-2" title="2"><span class="co"># OLD WAY</span></a>
|
||||
<a class="sourceLine" id="cb11-3" title="3">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb11-6" title="6"><span class="co"># NEW WAY</span></a>
|
||||
<a class="sourceLine" id="cb11-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb11-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb11-9" title="9"></a>
|
||||
<a class="sourceLine" id="cb11-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||
<a class="sourceLine" id="cb11-11" title="11">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb11-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
</li>
|
||||
<li>Header info is now available as a list, with the <code>header</code> function</li>
|
||||
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
|
||||
@@ -510,9 +534,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
|
||||
</h1>
|
||||
<div id="new-1" class="section level4">
|
||||
<div id="new-2" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-1" class="anchor"></a>New</h4>
|
||||
<a href="#new-2" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Repository moved to GitLab: <a href="https://gitlab.com/msberends/AMR" class="uri">https://gitlab.com/msberends/AMR</a>
|
||||
</li>
|
||||
@@ -550,10 +574,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
|
||||
<li>
|
||||
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
||||
<a class="sourceLine" id="cb11-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
||||
<a class="sourceLine" id="cb11-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
||||
<a class="sourceLine" id="cb11-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
||||
<a class="sourceLine" id="cb12-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
||||
<a class="sourceLine" id="cb12-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
||||
<a class="sourceLine" id="cb12-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
|
||||
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
|
||||
@@ -566,15 +590,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb12-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb12-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
|
||||
</li>
|
||||
@@ -637,9 +661,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
|
||||
</h1>
|
||||
<div id="new-2" class="section level4">
|
||||
<div id="new-3" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-2" class="anchor"></a>New</h4>
|
||||
<a href="#new-3" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
|
||||
<li>New functions based on the existing function <code>mo_property</code>:
|
||||
@@ -654,18 +678,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
</ul>
|
||||
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb14-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
|
||||
<a class="sourceLine" id="cb14-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
||||
<a class="sourceLine" id="cb14-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
||||
<a class="sourceLine" id="cb14-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
||||
<a class="sourceLine" id="cb14-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
|
||||
<a class="sourceLine" id="cb14-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
||||
<a class="sourceLine" id="cb14-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb15-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
|
||||
<a class="sourceLine" id="cb15-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
||||
<a class="sourceLine" id="cb15-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
||||
<a class="sourceLine" id="cb15-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
||||
<a class="sourceLine" id="cb15-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
|
||||
<a class="sourceLine" id="cb15-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
||||
<a class="sourceLine" id="cb15-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
||||
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
||||
<a class="sourceLine" id="cb15-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
||||
<a class="sourceLine" id="cb15-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
||||
<a class="sourceLine" id="cb16-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
|
||||
<ul>
|
||||
@@ -676,18 +700,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb16-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
||||
<a class="sourceLine" id="cb16-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb17-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
||||
<a class="sourceLine" id="cb17-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb17-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-3" title="3"><span class="co"># Unit: seconds</span></a>
|
||||
<a class="sourceLine" id="cb17-4" title="4"><span class="co"># min median max neval</span></a>
|
||||
<a class="sourceLine" id="cb17-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb18-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<a class="sourceLine" id="cb18-3" title="3"><span class="co"># Unit: seconds</span></a>
|
||||
<a class="sourceLine" id="cb18-4" title="4"><span class="co"># min median max neval</span></a>
|
||||
<a class="sourceLine" id="cb18-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
|
||||
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
|
||||
@@ -715,12 +739,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
|
||||
<li>
|
||||
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
|
||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
|
||||
<a class="sourceLine" id="cb18-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||
<a class="sourceLine" id="cb18-3" title="3"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb18-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||
<a class="sourceLine" id="cb18-5" title="5"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb18-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
|
||||
<a class="sourceLine" id="cb19-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||
<a class="sourceLine" id="cb19-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb19-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||
<a class="sourceLine" id="cb19-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb19-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
|
||||
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
|
||||
@@ -731,13 +755,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
||||
<a class="sourceLine" id="cb19-2" title="2"><span class="co"># which is the same as:</span></a>
|
||||
<a class="sourceLine" id="cb19-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
||||
<a class="sourceLine" id="cb19-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb19-5" title="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
|
||||
<a class="sourceLine" id="cb19-6" title="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
|
||||
<a class="sourceLine" id="cb19-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
||||
<a class="sourceLine" id="cb20-2" title="2"><span class="co"># which is the same as:</span></a>
|
||||
<a class="sourceLine" id="cb20-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
||||
<a class="sourceLine" id="cb20-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb20-5" title="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
|
||||
<a class="sourceLine" id="cb20-6" title="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
|
||||
<a class="sourceLine" id="cb20-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
||||
</li>
|
||||
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
|
||||
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
|
||||
@@ -751,12 +775,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb20-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb21-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb21-2" title="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb21-3" title="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb22-2" title="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb22-3" title="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@@ -772,9 +796,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
|
||||
</h1>
|
||||
<div id="new-3" class="section level4">
|
||||
<div id="new-4" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-3" class="anchor"></a>New</h4>
|
||||
<a href="#new-4" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>
|
||||
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
|
||||
@@ -877,7 +901,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>Now possible to coerce MIC values with a space between operator and value, i.e. <code><a href="../reference/as.mic.html">as.mic("<= 0.002")</a></code> now works</li>
|
||||
<li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li>
|
||||
<li>Added <code>"groups"</code> option for <code><a href="../reference/atc_property.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <a href="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
|
||||
<li>Added <code>"groups"</code> option for <code><a href="../reference/AMR-deprecated.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <a href="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
|
||||
<li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li>
|
||||
<li>Improved <code>first_isolate</code> algorithm to exclude isolates where bacteria ID or genus is unavailable</li>
|
||||
<li>Fix for warning <em>hybrid evaluation forced for row_number</em> (<a href="https://github.com/tidyverse/dplyr/commit/924b62"><code>924b62</code></a>) from the <code>dplyr</code> package v0.7.5 and above</li>
|
||||
@@ -909,9 +933,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
|
||||
</h1>
|
||||
<div id="new-4" class="section level4">
|
||||
<div id="new-5" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#new-4" class="anchor"></a>New</h4>
|
||||
<a href="#new-5" class="anchor"></a>New</h4>
|
||||
<ul>
|
||||
<li>Full support for Windows, Linux and macOS</li>
|
||||
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
|
||||
|
||||
@@ -7,7 +7,7 @@ articles:
|
||||
G_test: G_test.html
|
||||
SPSS: SPSS.html
|
||||
WHONET: WHONET.html
|
||||
atc_property: atc_property.html
|
||||
ab_property: ab_property.html
|
||||
benchmarks: benchmarks.html
|
||||
freq: freq.html
|
||||
mo_property: mo_property.html
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -243,25 +243,19 @@
|
||||
|
||||
<pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)
|
||||
|
||||
<span class='fu'>ab_property</span>(<span class='no'>...</span>)
|
||||
<span class='fu'>abname</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_atc</span>(<span class='no'>...</span>)
|
||||
<span class='fu'>atc_property</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>atc_official</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_official</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_name</span>(<span class='no'>...</span>)
|
||||
<span class='fu'>atc_name</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_trivial_nl</span>(<span class='no'>...</span>)
|
||||
<span class='fu'>atc_trivial_nl</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_certe</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_umcg</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_tradenames</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>atc_ddd</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>atc_groups</span>(<span class='no'>...</span>)</pre>
|
||||
<span class='fu'>atc_tradenames</span>(<span class='no'>...</span>)</pre>
|
||||
|
||||
<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>
|
||||
|
||||
|
||||
@@ -47,7 +47,7 @@
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Property of an antibiotic — ab_property" />
|
||||
|
||||
<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set, based on their ATC code. Get such a code with as.atc." />
|
||||
<meta property="og:description" content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab." />
|
||||
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -110,12 +110,26 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/Predict.html">
|
||||
<a href="../articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET data
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/SPSS.html">
|
||||
<span class="fa fa-file-upload"></span>
|
||||
|
||||
Import data from SPSS/SAS/Stata
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
||||
@@ -124,14 +138,14 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/mo_property.html">
|
||||
<a href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get properties of a microorganism
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/ab_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -223,52 +237,89 @@
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>Use these functions to return a specific property of an antibiotic from the <code><a href='antibiotics.html'>antibiotics</a></code> data set, based on their ATC code. Get such a code with <code><a href='as.atc.html'>as.atc</a></code>.</p>
|
||||
<p>Use these functions to return a specific property of an antibiotic from the <code><a href='antibiotics.html'>antibiotics</a></code> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab</a></code>.</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"official"</span>)
|
||||
<pre class="usage"><span class='fu'>ab_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_atc</span>(<span class='no'>x</span>)
|
||||
<span class='fu'>ab_atc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_official</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
|
||||
<span class='fu'>ab_cid</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
|
||||
<span class='fu'>ab_synonyms</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_trivial_nl</span>(<span class='no'>x</span>)
|
||||
<span class='fu'>ab_tradenames</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_certe</span>(<span class='no'>x</span>)
|
||||
<span class='fu'>ab_group</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_umcg</span>(<span class='no'>x</span>)
|
||||
<span class='fu'>ab_atc_group1</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_tradenames</span>(<span class='no'>x</span>)</pre>
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_ddd</span>(<span class='no'>x</span>, <span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
|
||||
|
||||
<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>x</th>
|
||||
<td><p>a (vector of a) valid <code><a href='as.atc.html'>atc</a></code> code or any text that can be coerced to a valid atc with <code><a href='as.atc.html'>as.atc</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
<td><p>one of the column names of one of the <code><a href='antibiotics.html'>antibiotics</a></code> data set, like <code>"atc"</code> and <code>"official"</code></p></td>
|
||||
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.ab.html'>as.ab</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>language</th>
|
||||
<td><p>language of the returned text, defaults to English (<code>"en"</code>) and can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Either one of <code>"en"</code> (English) or <code>"nl"</code> (Dutch).</p></td>
|
||||
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>tolower</th>
|
||||
<td><p>logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>other parameters passed on to <code><a href='as.ab.html'>as.ab</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>administration</th>
|
||||
<td><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>units</th>
|
||||
<td><p>a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
<td><p>one of the column names of one of the <code><a href='antibiotics.html'>antibiotics</a></code> data set</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>A vector of values. In case of <code>ab_tradenames</code>, if <code>x</code> is of length one, a vector will be returned. Otherwise a <code><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></code>, with <code>x</code> as names.</p>
|
||||
|
||||
<ul>
|
||||
<li><p>An <code>integer</code> in case of <code>ab_cid</code></p></li>
|
||||
<li><p>A named <code>list</code> in case of multiple <code>ab_synonyms</code></p></li>
|
||||
<li><p>A <code>double</code> in case of <code>ab_ddd</code></p></li>
|
||||
<li><p>A <code>character</code> in all other cases</p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></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/logo.png' height=40px style=margin-bottom:5px /> <br />
|
||||
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
@@ -277,12 +328,33 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"amcl"</span>) <span class='co'># J01CR02</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"amcl"</span>) <span class='co'># Amoxicillin and beta-lactamase inhibitor</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"amcl"</span>, <span class='st'>"nl"</span>) <span class='co'># Amoxicilline met enzymremmer</span>
|
||||
<span class='fu'>ab_trivial_nl</span>(<span class='st'>"amcl"</span>) <span class='co'># Amoxicilline/clavulaanzuur</span>
|
||||
<span class='fu'>ab_certe</span>(<span class='st'>"amcl"</span>) <span class='co'># amcl</span>
|
||||
<span class='fu'>ab_umcg</span>(<span class='st'>"amcl"</span>) <span class='co'># AMCL</span>
|
||||
<span class='co'># all properties:</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"AMX"</span>) <span class='co'># "Amoxicillin"</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"AMX"</span>) <span class='co'># J01CA04 (ATC code from the WHO)</span>
|
||||
<span class='fu'>ab_cid</span>(<span class='st'>"AMX"</span>) <span class='co'># 33613 (Compound ID from PubChem)</span>
|
||||
|
||||
<span class='fu'>ab_synonyms</span>(<span class='st'>"AMX"</span>) <span class='co'># a list with brand names of amoxicillin</span>
|
||||
<span class='fu'>ab_tradenames</span>(<span class='st'>"AMX"</span>) <span class='co'># same</span>
|
||||
|
||||
<span class='fu'>ab_group</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactams/penicillins"</span>
|
||||
<span class='fu'>ab_atc_group1</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactam antibacterials, penicillins"</span>
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='st'>"AMX"</span>) <span class='co'># "Penicillins with extended spectrum"</span>
|
||||
|
||||
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>)) <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>),
|
||||
<span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
|
||||
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>) <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>) <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
|
||||
|
||||
<span class='co'># all ab_* functions use as.ab() internally:</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"Fluclox"</span>) <span class='co'># "Flucloxacillin"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"fluklox"</span>) <span class='co'># "Flucloxacillin"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"floxapen"</span>) <span class='co'># "Flucloxacillin"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='fl'>21319</span>) <span class='co'># "Flucloxacillin" (using CID)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"J01CF05"</span>) <span class='co'># "Flucloxacillin" (using ATC)</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
@@ -292,6 +364,10 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
|
||||
|
||||
<li><a href="#value">Value</a></li>
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#source">Source</a></li>
|
||||
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -252,7 +252,7 @@
|
||||
</tr>
|
||||
<tr>
|
||||
<th>split_at</th>
|
||||
<td><p>values to split <code>x</code> at, defaults to age groups 0-11, 12-24, 26-54, 55-74 and 75+. See Details.</p></td>
|
||||
<td><p>values to split <code>x</code> at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See Details.</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
@@ -264,7 +264,7 @@
|
||||
|
||||
<p>To split ages, the input can be:</p><ul>
|
||||
<li><p>A numeric vector. A vector of e.g. <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(10, 20)</a></code> will split on 0-9, 10-19 and 20+. A value of only <code>50</code> will split on 0-49 and 50+.
|
||||
The default is to split on young children (0-11), youth (12-24), young adults (26-54), middle-aged adults (55-74) and elderly (75+).</p></li>
|
||||
The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).</p></li>
|
||||
<li><p>A character:</p><ul>
|
||||
<li><p><code>"children"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(0, 1, 2, 4, 6, 13, 18)</a></code>. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.</p></li>
|
||||
<li><p><code>"elderly"</code> or <code>"seniors"</code>, equivalent of: <code><a href='https://www.rdocumentation.org/packages/base/topics/c'>c(65, 75, 85)</a></code>. This will split on 0-64, 65-74, 75-84, 85+.</p></li>
|
||||
@@ -314,7 +314,7 @@
|
||||
<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
|
||||
<span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
|
||||
@@ -6,7 +6,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Data set with ~500 antibiotics — antibiotics • AMR (for R)</title>
|
||||
<title>Data set with ~450 antibiotics — antibiotics • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
@@ -45,9 +45,9 @@
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Data set with ~500 antibiotics — antibiotics" />
|
||||
<meta property="og:title" content="Data set with ~450 antibiotics — antibiotics" />
|
||||
|
||||
<meta property="og:description" content="A data set containing all antibiotics with a J0 code and some other antimicrobial agents, with their DDDs. Except for trade names and abbreviations, all properties were downloaded from the WHO, see Source." />
|
||||
<meta property="og:description" content="A data set containing all antibiotics. Use as.ab or one of the ab_property functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes." />
|
||||
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -230,14 +230,14 @@
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Data set with ~500 antibiotics</h1>
|
||||
<h1>Data set with ~450 antibiotics</h1>
|
||||
|
||||
<div class="hidden name"><code>antibiotics.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>A data set containing all antibiotics with a J0 code and some other antimicrobial agents, with their DDDs. Except for trade names and abbreviations, all properties were downloaded from the WHO, see Source.</p>
|
||||
<p>A data set containing all antibiotics. Use <code><a href='as.ab.html'>as.ab</a></code> or one of the <code><a href='ab_property.html'>ab_property</a></code> functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes.</p>
|
||||
|
||||
</div>
|
||||
|
||||
@@ -245,33 +245,33 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 488 observations and 17 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical), like <code>J01CR02</code></p></dd>
|
||||
<dt><code>ears_net</code></dt><dd><p>EARS-Net code (European Antimicrobial Resistance Surveillance Network), like <code>AMC</code></p></dd>
|
||||
<dt><code>certe</code></dt><dd><p>Certe code, like <code>amcl</code></p></dd>
|
||||
<dt><code>umcg</code></dt><dd><p>UMCG code, like <code>AMCL</code></p></dd>
|
||||
<dt><code>abbr</code></dt><dd><p>Abbreviation as used by many countries, used internally by <code><a href='as.atc.html'>as.atc</a></code></p></dd>
|
||||
<dt><code>official</code></dt><dd><p>Official name by the WHO, like <code>"Amoxicillin and beta-lactamase inhibitor"</code></p></dd>
|
||||
<dt><code>official_nl</code></dt><dd><p>Official name in the Netherlands, like <code>"Amoxicilline met enzymremmer"</code></p></dd>
|
||||
<dt><code>trivial_nl</code></dt><dd><p>Trivial name in Dutch, like <code>"Amoxicilline/clavulaanzuur"</code></p></dd>
|
||||
<dt><code>trade_name</code></dt><dd><p>Trade name as used by many countries (a total of 294), used internally by <code><a href='as.atc.html'>as.atc</a></code></p></dd>
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 455 observations and 13 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>ab</code></dt><dd><p>Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></dd>
|
||||
<dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></dd>
|
||||
<dt><code>cid</code></dt><dd><p>Compound ID as found in PubChem</p></dd>
|
||||
<dt><code>name</code></dt><dd><p>Official name as used by WHONET/EARS-Net or the WHO</p></dd>
|
||||
<dt><code>group</code></dt><dd><p>A short and concise group name, based on WHONET and WHOCC definitions</p></dd>
|
||||
<dt><code>atc_group1</code></dt><dd><p>Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></dd>
|
||||
<dt><code>atc_group2</code></dt><dd><p>Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></dd>
|
||||
<dt><code>abbr</code></dt><dd><p>List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></dd>
|
||||
<dt><code>synonyms</code></dt><dd><p>Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></dd>
|
||||
<dt><code>oral_ddd</code></dt><dd><p>Defined Daily Dose (DDD), oral treatment</p></dd>
|
||||
<dt><code>oral_units</code></dt><dd><p>Units of <code>ddd_units</code></p></dd>
|
||||
<dt><code>iv_ddd</code></dt><dd><p>Defined Daily Dose (DDD), parenteral treatment</p></dd>
|
||||
<dt><code>iv_units</code></dt><dd><p>Units of <code>iv_ddd</code></p></dd>
|
||||
<dt><code>atc_group1</code></dt><dd><p>ATC group, like <code>"Macrolides, lincosamides and streptogramins"</code></p></dd>
|
||||
<dt><code>atc_group2</code></dt><dd><p>Subgroup of <code>atc_group1</code>, like <code>"Macrolides"</code></p></dd>
|
||||
<dt><code>useful_gramnegative</code></dt><dd><p><code>FALSE</code> if not useful according to EUCAST, <code>NA</code> otherwise (see Source)</p></dd>
|
||||
<dt><code>useful_grampositive</code></dt><dd><p><code>FALSE</code> if not useful according to EUCAST, <code>NA</code> otherwise (see Source)</p></dd>
|
||||
</dl>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>Table antibiotic coding EARSS (from WHONET 5.3): <a href='http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf'>http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf</a></p>
|
||||
<p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016: <a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p>
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code></p>
|
||||
<p>Synonyms (i.e. trade names) are derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
||||
|
||||
|
||||
@@ -299,6 +299,8 @@ This package contains <strong>all ~500 antimicrobial drugs</strong> and their An
|
||||
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<h1>Transform to antibiotic ID</h1>
|
||||
|
||||
<div class="hidden name"><code>as.ab.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <code><a href='antibiotics.html'>antibiotics</a></code> will be searched for abbreviations, official names and synonyms (brand names).</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.ab</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
<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>x</th>
|
||||
<td><p>character vector to determine to antibiotic ID</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>Character (vector) with class <code>"act"</code>. Unknown values will return <code>NA</code>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Use the <code><a href='ab_property.html'>ab_property</a></code> functions to get properties based on the returned ATC code, see Examples.</p>
|
||||
<p>In the ATC classification system, the active substances are classified in a hierarchy with five different levels. The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups. The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
|
||||
Source: <a href='https://www.whocc.no/atc/structure_and_principles/'>https://www.whocc.no/atc/structure_and_principles/</a></p>
|
||||
|
||||
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
||||
|
||||
|
||||
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
|
||||
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
|
||||
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
|
||||
|
||||
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
||||
|
||||
|
||||
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
||||
This package contains <strong>all ~500 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
||||
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
||||
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</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>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='antibiotics.html'>antibiotics</a></code> for the dataframe that is being used to determine ATCs.</p></div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># These examples all return "ERY", the ID of Erythromycin:</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"eryt"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>" eryt 123"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"ERYT"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"ERY"</span>)
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"erytromicine"</span>) <span class='co'># spelled wrong</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span>
|
||||
<span class='fu'>as.ab</span>(<span class='st'>"Romycin"</span>) <span class='co'># trade name</span>
|
||||
|
||||
<span class='co'># Use ab_* functions to get a specific properties (see ?ab_property);</span>
|
||||
<span class='co'># they use as.ab() internally:</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
|
||||
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
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<h2>Contents</h2>
|
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#arguments">Arguments</a></li>
|
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<li><a href="#value">Value</a></li>
|
||||
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||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#source">Source</a></li>
|
||||
|
||||
<li><a href="#whocc">WHOCC</a></li>
|
||||
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||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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||||
<li><a href="#see-also">See also</a></li>
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<li><a href="#examples">Examples</a></li>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
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||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
@@ -6,7 +6,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Transform to ATC code — as.atc • AMR (for R)</title>
|
||||
<title>Transform to ATC code — is.ab • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
@@ -45,7 +45,7 @@
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Transform to ATC code — as.atc" />
|
||||
<meta property="og:title" content="Transform to ATC code — is.ab" />
|
||||
|
||||
<meta property="og:description" content="Use this function to determine the ATC code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and trade names." />
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -241,7 +241,9 @@
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.atc</span>(<span class='no'>x</span>)
|
||||
<pre class="usage"><span class='fu'>is.ab</span>(<span class='no'>x</span>)
|
||||
|
||||
<span class='fu'>as.atc</span>(<span class='no'>x</span>)
|
||||
|
||||
<span class='fu'>is.atc</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
@@ -260,7 +262,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Use the <code><a href='AMR-deprecated.html'>ab_property</a></code> functions to get properties based on the returned ATC code, see Examples.</p>
|
||||
<p>Use the <code><a href='ab_property.html'>ab_property</a></code> functions to get properties based on the returned ATC code, see Examples.</p>
|
||||
<p>In the ATC classification system, the active substances are classified in a hierarchy with five different levels. The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups. The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
|
||||
Source: <a href='https://www.whocc.no/atc/structure_and_principles/'>https://www.whocc.no/atc/structure_and_principles/</a></p>
|
||||
|
||||
@@ -291,14 +293,6 @@ This package contains <strong>all ~500 antimicrobial drugs</strong> and their An
|
||||
<span class='fu'>as.atc</span>(<span class='st'>" eryt 123"</span>)
|
||||
<span class='fu'>as.atc</span>(<span class='st'>"ERYT"</span>)
|
||||
<span class='fu'>as.atc</span>(<span class='st'>"ERY"</span>)
|
||||
<span class='fu'>as.atc</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># Trade name</span>
|
||||
<span class='fu'>as.atc</span>(<span class='st'>"Eryzole"</span>) <span class='co'># Trade name</span>
|
||||
<span class='fu'>as.atc</span>(<span class='st'>"Pediamycin"</span>) <span class='co'># Trade name</span>
|
||||
|
||||
<span class='co'># Use ab_* functions to get a specific property based on an ATC code</span>
|
||||
<span class='no'>Cipro</span> <span class='kw'><-</span> <span class='fu'>as.atc</span>(<span class='st'>"cipro"</span>) <span class='co'># returns `J01MA02`</span>
|
||||
<span class='fu'><a href='atc_property.html'>atc_official</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "Ciprofloxacin"</span>
|
||||
<span class='fu'><a href='atc_property.html'>atc_umcg</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "CIPR", the code used in the UMCG</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
|
||||
343
docs/reference/as.disk.html
Normal file
343
docs/reference/as.disk.html
Normal file
@@ -0,0 +1,343 @@
|
||||
<!-- Generated by pkgdown: do not edit by hand -->
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
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<meta charset="utf-8">
|
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Class 'disk' — as.disk • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
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<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<!-- jquery -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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|
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<!-- Font Awesome icons -->
|
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
|
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|
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<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
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|
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<!-- sticky kit -->
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
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<link href="../docsearch.css" rel="stylesheet">
|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
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|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Class 'disk' — as.disk" />
|
||||
|
||||
<meta property="og:description" content="This transforms a vector to a new class disk, which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 99." />
|
||||
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
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<meta name="twitter:card" content="summary" />
|
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|
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|
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|
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<!-- mathjax -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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|
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<!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
<![endif]-->
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
<div class="container">
|
||||
<div class="navbar-header">
|
||||
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
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||||
<span class="sr-only">Toggle navigation</span>
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<span class="icon-bar"></span>
|
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
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|
||||
<div id="navbar" class="navbar-collapse collapse">
|
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<ul class="nav navbar-nav">
|
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<li>
|
||||
<a href="../index.html">
|
||||
<span class="fa fa-home"></span>
|
||||
|
||||
Home
|
||||
</a>
|
||||
</li>
|
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<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="../articles/AMR.html">
|
||||
<span class="fa fa-directions"></span>
|
||||
|
||||
Conduct AMR analysis
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/resistance_predict.html">
|
||||
<span class="fa fa-dice"></span>
|
||||
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/WHONET.html">
|
||||
<span class="fa fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET data
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/SPSS.html">
|
||||
<span class="fa fa-file-upload"></span>
|
||||
|
||||
Import data from SPSS/SAS/Stata
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/EUCAST.html">
|
||||
<span class="fa fa-exchange-alt"></span>
|
||||
|
||||
Apply EUCAST rules
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/mo_property.html">
|
||||
<span class="fa fa-bug"></span>
|
||||
|
||||
Get properties of a microorganism
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/freq.html">
|
||||
<span class="fa fa-sort-amount-down"></span>
|
||||
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/G_test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
Other: benchmarks
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/">
|
||||
<span class="fa fa-book-open"></span>
|
||||
|
||||
Manual
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../authors.html">
|
||||
<span class="fa fa-users"></span>
|
||||
|
||||
Authors
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../news/">
|
||||
<span class="far fa far fa-newspaper"></span>
|
||||
|
||||
Changelog
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://gitlab.com/msberends/AMR">
|
||||
<span class="fab fa fab fa-gitlab"></span>
|
||||
|
||||
Source Code
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../LICENSE-text.html">
|
||||
<span class="fa fa-book"></span>
|
||||
|
||||
Licence
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<form class="navbar-form navbar-right" role="search">
|
||||
<div class="form-group">
|
||||
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
||||
</div>
|
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</form>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Class 'disk'</h1>
|
||||
|
||||
<div class="hidden name"><code>as.disk.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>This transforms a vector to a new class <code>disk</code>, which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 99.</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.disk</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>is.disk</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
<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>x</th>
|
||||
<td><p>vector</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>na.rm</th>
|
||||
<td><p>a logical indicating whether missing values should be removed</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
<p>Ordered integer factor with new class <code>disk</code></p>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Interpret disk values as RSI values with <code><a href='as.rsi.html'>as.rsi</a></code>. It supports guidelines from EUCAST and CLSI.</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>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='as.rsi.html'>as.rsi</a></code></p></div>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># interpret disk values</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>12</span>,
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>12</span>,
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CLSI"</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
|
||||
<li><a href="#value">Value</a></li>
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
|
||||
<li><a href="#examples">Examples</a></li>
|
||||
</ul>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
|
||||
</div>
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
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hit.url = updateHitURL(hit);
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return hit;
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</script>
|
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||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -262,6 +262,10 @@
|
||||
|
||||
<p>Ordered factor with new class <code>mic</code></p>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Interpret MIC values as RSI values with <code><a href='as.rsi.html'>as.rsi</a></code>. It supports guidelines from EUCAST and CLSI.</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>
|
||||
|
||||
|
||||
@@ -280,6 +284,16 @@
|
||||
<span class='co'># this can also coerce combined MIC/RSI values:</span>
|
||||
<span class='fu'>as.mic</span>(<span class='st'>"<=0.002; S"</span>) <span class='co'># will return <=0.002</span>
|
||||
|
||||
<span class='co'># interpret MIC values</span>
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.mic</span>(<span class='fl'>2</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>as.mic</span>(<span class='fl'>4</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>mic_data</span>)
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>mic_data</span>)
|
||||
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>mic_data</span>)
|
||||
@@ -292,6 +306,8 @@
|
||||
|
||||
<li><a href="#value">Value</a></li>
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
|
||||
<li><a href="#see-also">See also</a></li>
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -351,7 +351,7 @@ The intelligent rules takes into account microbial prevalence of pathogens in hu
|
||||
|
||||
|
||||
<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
|
||||
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong>. 2019. Clin Microbiol Infect. 2019 Mar 11. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
|
||||
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
|
||||
<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
|
||||
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
|
||||
|
||||
|
||||
@@ -47,7 +47,7 @@
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Class 'rsi' — as.rsi" />
|
||||
|
||||
<meta property="og:description" content="This transforms a vector to a new class rsi, which is an ordered factor with levels S &lt; I &lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
|
||||
<meta property="og:description" content="Interpret MIC values according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &lt; I &lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
|
||||
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -237,11 +237,21 @@
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>This transforms a vector to a new class <code>rsi</code>, which is an ordered factor with levels <code>S < I < R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
|
||||
<p>Interpret MIC values according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S < I < R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>)
|
||||
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='co'># S3 method for mic</span>
|
||||
<span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>mo</span>, <span class='no'>ab</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='co'># S3 method for disk</span>
|
||||
<span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>mo</span>, <span class='no'>ab</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='co'># S3 method for data.frame</span>
|
||||
<span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
|
||||
<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
|
||||
|
||||
@@ -252,7 +262,27 @@
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>vector</p></td>
|
||||
<td><p>vector of values (for class <code>mic</code>: an MIC value in mg/L, for class <code>disk</code>: a disk diffusion radius in millimeters)</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>parameters passed on to methods</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>mo</th>
|
||||
<td><p>a microorganism code, generated with <code><a href='as.mo.html'>as.mo</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>ab</th>
|
||||
<td><p>an antibiotic code, generated with <code><a href='as.ab.html'>as.ab</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>guideline</th>
|
||||
<td><p>defaults to the latest included EUCAST guideline, run <code><a href='https://www.rdocumentation.org/packages/base/topics/unique'>unique(AMR::rsi_translation$guideline)</a></code> for all options</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>col_mo</th>
|
||||
<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>threshold</th>
|
||||
@@ -266,8 +296,9 @@
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p><strong>NOTE:</strong> This function does not translate MIC values to RSI values. If more than 50% of the input resembles MIC values, it will warn about this.<br /> You can use <code><a href='eucast_rules.html'>eucast_rules</a></code> to (1) apply inferred susceptibility and resistance based on results of other antibiotics and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
|
||||
<p>The function <code>is.rsi.eligible</code> returns <code>TRUE</code> when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and <code>FALSE</code> otherwise.</p>
|
||||
<p>Run <code><a href='https://www.rdocumentation.org/packages/base/topics/unique'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines.</p>
|
||||
<p>After using <code>as.rsi</code>, you can use <code><a href='eucast_rules.html'>eucast_rules</a></code> to (1) apply inferred susceptibility and resistance based on results of other antibiotics and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
|
||||
<p>The function <code>is.rsi.eligible</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</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>
|
||||
|
||||
@@ -288,6 +319,16 @@
|
||||
<span class='co'># this can also coerce combined MIC/RSI values:</span>
|
||||
<span class='fu'>as.rsi</span>(<span class='st'>"<= 0.002; S"</span>) <span class='co'># will return S</span>
|
||||
|
||||
<span class='co'># interpret MIC values</span>
|
||||
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>2</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
<span class='fu'>as.rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span>(<span class='fl'>4</span>),
|
||||
<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"S. pneumoniae"</span>),
|
||||
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>)
|
||||
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span>
|
||||
<span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span>
|
||||
@@ -295,7 +336,7 @@
|
||||
<span class='co'># using dplyr's mutate</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>PEN</span>:<span class='no'>RIF</span>), <span class='no'>as.rsi</span>)
|
||||
|
||||
|
||||
<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
|
||||
@@ -305,7 +346,7 @@
|
||||
|
||||
<span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
|
||||
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>) <span class='co'># fails, >80% is invalid</span>
|
||||
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.9</span>) <span class='co'># succeeds</span>
|
||||
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.99</span>) <span class='co'># succeeds</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
|
||||
@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -146,7 +146,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -257,8 +257,8 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
||||
|
||||
<span class='fu'>n_rsi</span>(<span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"get_antibiotic_names"</span>,
|
||||
<span class='st'>"official"</span>), <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
<span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -277,7 +277,11 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
||||
</tr>
|
||||
<tr>
|
||||
<th>translate_ab</th>
|
||||
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='abname.html'>abname</a></code>. This can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("get_antibiotic_names")</code>.</p></td>
|
||||
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>language</th>
|
||||
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>combine_IR</th>
|
||||
@@ -315,55 +319,55 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
||||
?<span class='no'>septic_patients</span>
|
||||
|
||||
<span class='co'># Count resistant isolates</span>
|
||||
<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
|
||||
<span class='co'># Or susceptible isolates</span>
|
||||
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
|
||||
<span class='co'># Count all available isolates</span>
|
||||
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
|
||||
<span class='co'># Since n_rsi counts available isolates, you can</span>
|
||||
<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
|
||||
<span class='co'># This results in the same:</span>
|
||||
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>CIP</span>),
|
||||
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>CIP</span>),
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>CIP</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
|
||||
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
|
||||
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
|
||||
<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
|
||||
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1342 (71.4%)</span>
|
||||
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1879</span>
|
||||
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># S = 1342 (71.4%)</span>
|
||||
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
|
||||
|
||||
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># S = 1372 (74.0%)</span>
|
||||
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># n = 1855</span>
|
||||
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># S = 1372 (74.0%)</span>
|
||||
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
|
||||
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
|
||||
<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1660 (92.3%)</span>
|
||||
<span class='fu'>count_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>)) <span class='co'># S = 1660 (92.3%)</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1798</span>
|
||||
<span class='fu'>n_rsi</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>))
|
||||
<span class='fu'>n_rsi</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>))
|
||||
|
||||
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -242,38 +242,7 @@
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>,
|
||||
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>azlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>mezl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>oxac</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pris</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='no'>...</span>)
|
||||
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>eucast_rules_file</span>()</pre>
|
||||
|
||||
@@ -282,7 +251,7 @@
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>data with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td>
|
||||
<td><p>data with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>col_mo</th>
|
||||
@@ -300,13 +269,9 @@
|
||||
<th>verbose</th>
|
||||
<td><p>a logical to indicate whether extensive info should be returned as a <code>data.frame</code> with info about which rows and columns are effected. It runs all EUCAST rules, but will not be applied to an output - only an informative <code>data.frame</code> with changes will be returned as output.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>parameters that are passed on to <code>eucast_rules</code></p></td>
|
||||
<td><p>column name of an antibiotic, see section Antibiotics</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
@@ -321,7 +286,7 @@
|
||||
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
|
||||
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
|
||||
</ul>
|
||||
<p>For editing the reference file (which is available with <code>eucast_rules_file</code>), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: <code>"amcl, fluoroquinolones"</code>. The mo_property can be any column name from the <code><a href='microorganisms.html'>microorganisms</a></code> data set, or <code>genus_species</code> or <code>gramstain</code>. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).</p>
|
||||
<p>For editing the reference file (which is available with <code>eucast_rules_file</code>), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like AMC. They can be separated by comma: <code>"AMC, fluoroquinolones"</code>. The mo_property can be any column name from the <code><a href='microorganisms.html'>microorganisms</a></code> data set, or <code>genus_species</code> or <code>gramstain</code>. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).</p>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
@@ -329,79 +294,81 @@
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p><strong>NOTE:</strong> This function does not translate MIC values to RSI values. It only applies (1) inferred susceptibility and resistance based on results of other antibiotics and (2) intrinsic resistance based on taxonomic properties of a microorganism.</p>
|
||||
<p>The file used for applying all EUCAST rules can be retrieved with <code>eucast_rules_file()</code>. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: <br />
|
||||
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi</a></code> for that. <br />
|
||||
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
|
||||
<p>The file used for applying all EUCAST rules can be retrieved with <code>eucast_rules_file()</code>. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by <code>eucast_rules()</code> can be found by running this command: <br />
|
||||
<code>AMR::EUCAST_RULES_FILE_LOCATION</code> (without brackets).</p>
|
||||
<p>In the source code it is located under <a href='https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv'><code>./inst/eucast/eucast_rules.tsv</code></a>.</p>
|
||||
<p><strong>Note:</strong> When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
|
||||
<p>In the source code the file containing all rules is located <a href='https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv'>here</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
|
||||
|
||||
|
||||
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
|
||||
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
|
||||
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
|
||||
<strong>amik</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
|
||||
<strong>amox</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
|
||||
<strong>ampi</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
|
||||
<strong>azit</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
|
||||
<strong>azlo</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
|
||||
<strong>aztr</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
|
||||
<strong>cefa</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
|
||||
<strong>cfep</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
|
||||
<strong>cfot</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
|
||||
<strong>cfox</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
|
||||
<strong>cfra</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
|
||||
<strong>cfta</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
|
||||
<strong>cftr</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
|
||||
<strong>cfur</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
|
||||
<strong>chlo</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
|
||||
<strong>cipr</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
|
||||
<strong>clar</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
|
||||
<strong>clin</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
|
||||
<strong>clox</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
|
||||
<strong>coli</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
|
||||
<strong>czol</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
|
||||
<strong>dapt</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
|
||||
<strong>doxy</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
|
||||
<strong>erta</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
|
||||
<strong>eryt</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
|
||||
<strong>fosf</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
|
||||
<strong>fusi</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
|
||||
<strong>gent</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
|
||||
<strong>imip</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
|
||||
<strong>kana</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
|
||||
<strong>levo</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
|
||||
<strong>linc</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
|
||||
<strong>line</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
|
||||
<strong>mero</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
|
||||
<strong>mezl</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
|
||||
<strong>mino</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
|
||||
<strong>moxi</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
|
||||
<strong>nali</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
|
||||
<strong>neom</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
|
||||
<strong>neti</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
|
||||
<strong>nitr</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
|
||||
<strong>norf</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
|
||||
<strong>novo</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
|
||||
<strong>oflo</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
|
||||
<strong>peni</strong>: (benzyl)penicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
|
||||
<strong>pipe</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
|
||||
<strong>pita</strong>: piperacillin+tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
|
||||
<strong>poly</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
|
||||
<strong>pris</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
|
||||
<strong>qida</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
|
||||
<strong>rifa</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
|
||||
<strong>roxi</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
|
||||
<strong>siso</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
|
||||
<strong>teic</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
|
||||
<strong>tetr</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
|
||||
<strong>tica</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
|
||||
<strong>tige</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
|
||||
<strong>tobr</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
|
||||
<strong>trim</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
|
||||
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
|
||||
<strong>vanc</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
|
||||
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
|
||||
<p>Available abbrevations of the column containing antibiotics in the form '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)':</p>
|
||||
<p><strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
|
||||
<strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
|
||||
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
|
||||
<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
|
||||
<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
|
||||
<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
|
||||
<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
|
||||
<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
|
||||
<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
|
||||
<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
|
||||
<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
|
||||
<strong>CED</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
|
||||
<strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
|
||||
<strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
|
||||
<strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
|
||||
<strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
|
||||
<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
|
||||
<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
|
||||
<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
|
||||
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
|
||||
<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
|
||||
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
|
||||
<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
|
||||
<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
|
||||
<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
|
||||
<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
|
||||
<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
|
||||
<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
|
||||
<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
|
||||
<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
|
||||
<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
|
||||
<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
|
||||
<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
|
||||
<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
|
||||
<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
|
||||
<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
|
||||
<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
|
||||
<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
|
||||
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01XD01</a>),
|
||||
<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
|
||||
<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
|
||||
<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
|
||||
<strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
|
||||
<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
|
||||
<strong>NOV</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
|
||||
<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
|
||||
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01CF04</a>),
|
||||
<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
|
||||
<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
|
||||
<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
|
||||
<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
|
||||
<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
|
||||
<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
|
||||
<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
|
||||
<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
|
||||
<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
|
||||
<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
|
||||
<strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
|
||||
<strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
|
||||
<strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
|
||||
<strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
|
||||
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
|
||||
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
|
||||
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</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>
|
||||
|
||||
@@ -418,17 +385,17 @@
|
||||
<span class='st'>"Escherichia coli"</span>,
|
||||
<span class='st'>"Klebsiella pneumoniae"</span>,
|
||||
<span class='st'>"Pseudomonas aeruginosa"</span>),
|
||||
<span class='kw'>vanc</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
|
||||
<span class='kw'>amox</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
|
||||
<span class='kw'>coli</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
|
||||
<span class='kw'>cfta</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
|
||||
<span class='kw'>cfur</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
|
||||
<span class='kw'>peni</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
|
||||
<span class='kw'>cfox</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
|
||||
<span class='kw'>VAN</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
|
||||
<span class='kw'>AMX</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
|
||||
<span class='kw'>COL</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
|
||||
<span class='kw'>CAZ</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
|
||||
<span class='kw'>CXM</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
|
||||
<span class='kw'>PEN</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Penicillin G</span>
|
||||
<span class='kw'>FOX</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
|
||||
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='no'>a</span>
|
||||
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
|
||||
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
|
||||
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
|
||||
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
|
||||
<span class='co'># 3 Escherichia coli - - - - - S S</span>
|
||||
@@ -440,7 +407,7 @@
|
||||
<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>)
|
||||
|
||||
<span class='no'>b</span>
|
||||
<span class='co'># mo vanc amox coli cfta cfur peni cfox</span>
|
||||
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
|
||||
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
|
||||
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
|
||||
<span class='co'># 3 Escherichia coli R - - - - R S</span>
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -302,9 +302,9 @@
|
||||
<span class='co'># filter on isolates that have any result for any aminoglycoside</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>filter_aminoglycosides</span>()
|
||||
|
||||
<span class='co'># this is essentially the same as:</span>
|
||||
<span class='co'># this is essentially the same as (but without determination of column names):</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></span>(<span class='kw'>.vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"gent"</span>, <span class='st'>"tobr"</span>, <span class='st'>"amik"</span>, <span class='st'>"kana"</span>)),
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></span>(<span class='kw'>.vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"GEN"</span>, <span class='st'>"TOB"</span>, <span class='st'>"AMK"</span>, <span class='st'>"KAN"</span>)),
|
||||
<span class='kw'>.vars_predicate</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/all_vars.html'>any_vars</a></span>(<span class='no'>.</span> <span class='kw'>%in%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>)))
|
||||
|
||||
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -397,14 +397,14 @@ To conduct an analysis of antimicrobial resistance, you should only include the
|
||||
<span class='co'># Now let's see if first isolates matter:</span>
|
||||
<span class='no'>A</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
|
||||
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
|
||||
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
|
||||
|
||||
<span class='no'>B</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%>%</span> <span class='co'># the 1st isolate filter</span>
|
||||
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%>%</span> <span class='co'># the 1st isolate filter</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
|
||||
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
|
||||
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
|
||||
|
||||
<span class='co'># Have a look at A and B.</span>
|
||||
<span class='co'># B is more reliable because every isolate is only counted once.</span>
|
||||
|
||||
@@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -146,7 +146,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -487,8 +487,8 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
|
||||
|
||||
|
||||
<span class='co'># check differences between frequency tables</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/diff'>diff</a></span>(<span class='fu'>freq</span>(<span class='no'>septic_patients</span>$<span class='no'>trim</span>),
|
||||
<span class='fu'>freq</span>(<span class='no'>septic_patients</span>$<span class='no'>trsu</span>))
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/diff'>diff</a></span>(<span class='fu'>freq</span>(<span class='no'>septic_patients</span>$<span class='no'>TMP</span>),
|
||||
<span class='fu'>freq</span>(<span class='no'>septic_patients</span>$<span class='no'>SXT</span>))
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -243,13 +243,13 @@
|
||||
|
||||
<pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
|
||||
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
|
||||
<span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"official"</span>, <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
|
||||
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>,
|
||||
<span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"grey15"</span>, <span class='no'>...</span>)
|
||||
<span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>datalabels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"grey15"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Antibiotic"</span>, <span class='st'>"Interpretation"</span>),
|
||||
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"official"</span>, <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
|
||||
<span class='no'>...</span>)
|
||||
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
|
||||
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Interpretation"</span>, <span class='st'>"Antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
|
||||
|
||||
@@ -295,7 +295,11 @@
|
||||
</tr>
|
||||
<tr>
|
||||
<th>translate_ab</th>
|
||||
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations into, using <code><a href='abname.html'>abname</a></code>. Default behaviour is to translate to official names according to the WHO. Use <code>translate_ab = FALSE</code> to disable translation.</p></td>
|
||||
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations into, using <code><a href='ab_property.html'>ab_name</a></code>. Default behaviour is to translate to official names according to the WHO. Use <code>translate_ab = FALSE</code> to disable translation.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>language</th>
|
||||
<td><p>the language used for translation of antibiotic names</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>fun</th>
|
||||
@@ -325,7 +329,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='abname.html'>abname</a></code>. This can be set with the option <code>get_antibiotic_names</code> (a logical value), so change it e.g. to <code>FALSE</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options(get_antibiotic_names = FALSE)</a></code>.</p>
|
||||
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name</a></code>. This can be set with the option <code>get_antibiotic_names</code> (a logical value), so change it e.g. to <code>FALSE</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options(get_antibiotic_names = FALSE)</a></code>.</p>
|
||||
<p><strong>The functions</strong><br />
|
||||
<code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
|
||||
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap'>facet_wrap</a></code>.</p>
|
||||
@@ -347,11 +351,11 @@
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>)
|
||||
|
||||
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>)) +
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
|
||||
<span class='fu'>geom_rsi</span>()
|
||||
|
||||
<span class='co'># prettify the plot using some additional functions:</span>
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>septic_patients</span>[, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"nitr"</span>, <span class='st'>"fosf"</span>, <span class='st'>"trim"</span>, <span class='st'>"cipr"</span>)]
|
||||
<span class='no'>df</span> <span class='kw'><-</span> <span class='no'>septic_patients</span>[, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMX"</span>, <span class='st'>"NIT"</span>, <span class='st'>"FOS"</span>, <span class='st'>"TMP"</span>, <span class='st'>"CIP"</span>)]
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>df</span>) +
|
||||
<span class='fu'>geom_rsi</span>() +
|
||||
<span class='fu'>scale_y_percent</span>() +
|
||||
@@ -361,17 +365,17 @@
|
||||
|
||||
<span class='co'># or better yet, simplify this using the wrapper function - a single command:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>()
|
||||
|
||||
<span class='co'># get only portions and no counts:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>portion_df</span>)
|
||||
|
||||
<span class='co'># add other ggplot2 parameters as you like:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
|
||||
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>,
|
||||
<span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>,
|
||||
@@ -386,18 +390,18 @@
|
||||
<span class='co'># `age_group` is also a function of this package:</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span>(<span class='no'>age</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
|
||||
<span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
|
||||
<span class='co'># }</span><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_viridis'>scale_fill_viridis_d</a></span>()
|
||||
|
||||
|
||||
<span class='co'># it also supports groups (don't forget to use the group var on `x` or `facet`):</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>nitr</span>, <span class='no'>fosf</span>, <span class='no'>trim</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>hospital_id</span>,
|
||||
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='no'>Antibiotic</span>,
|
||||
@@ -421,7 +425,7 @@
|
||||
<span class='co'># get short MO names (like "E. coli")</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%>%</span>
|
||||
<span class='co'># select this short name and some antiseptic drugs</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>cfur</span>, <span class='no'>gent</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='co'># group by MO</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>mo</span>) <span class='kw'>%>%</span>
|
||||
<span class='co'># plot the thing, putting MOs on the facet</span>
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -273,7 +273,7 @@
|
||||
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"amoxicillin"</span>)
|
||||
<span class='co'># [1] "amox"</span>
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of Tetracycline</span>
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of tetracycline</span>
|
||||
<span class='co'># [1] "tetr"</span>
|
||||
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01AA07"</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
|
||||
@@ -287,7 +287,7 @@
|
||||
<span class='co'># [1] "AMP_ND10"</span>
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='st'>"J01CR02"</span>)
|
||||
<span class='co'># [1] "AMC_ED20"</span>
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='fu'><a href='as.atc.html'>as.atc</a></span>(<span class='st'>"augmentin"</span>))
|
||||
<span class='fu'>guess_ab_col</span>(<span class='no'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"augmentin"</span>))
|
||||
<span class='co'># [1] "AMC_ED20"</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
|
||||
@@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -143,7 +143,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -281,11 +281,23 @@
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="as.atc.html">as.atc()</a></code> <code><a href="as.atc.html">is.atc()</a></code> </p>
|
||||
<p><code><a href="as.ab.html">as.ab()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Transform to antibiotic ID</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="as.atc.html">is.ab()</a></code> <code><a href="as.atc.html">as.atc()</a></code> <code><a href="as.atc.html">is.atc()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Transform to ATC code</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="as.disk.html">as.disk()</a></code> <code><a href="as.disk.html">is.disk()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Class 'disk'</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">is.mic()</a></code> </p>
|
||||
</td>
|
||||
@@ -316,6 +328,12 @@
|
||||
<td><p>EUCAST rules</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set for RSI interpretation</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="guess_ab_col.html">guess_ab_col()</a></code> </p>
|
||||
</td>
|
||||
@@ -361,23 +379,11 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="atc_property.html">atc_property()</a></code> <code><a href="atc_property.html">atc_official()</a></code> <code><a href="atc_property.html">atc_name()</a></code> <code><a href="atc_property.html">atc_trivial_nl()</a></code> <code><a href="atc_property.html">atc_certe()</a></code> <code><a href="atc_property.html">atc_umcg()</a></code> <code><a href="atc_property.html">atc_tradenames()</a></code> </p>
|
||||
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of an antibiotic</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="abname.html">abname()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Name of an antibiotic</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="age.html">age()</a></code> </p>
|
||||
</td>
|
||||
@@ -400,6 +406,12 @@
|
||||
<p><code><a href="join.html">inner_join_microorganisms()</a></code> <code><a href="join.html">left_join_microorganisms()</a></code> <code><a href="join.html">right_join_microorganisms()</a></code> <code><a href="join.html">full_join_microorganisms()</a></code> <code><a href="join.html">semi_join_microorganisms()</a></code> <code><a href="join.html">anti_join_microorganisms()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Join a table with <code>microorganisms</code></p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get ATC properties from WHOCC website</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
@@ -464,12 +476,6 @@
|
||||
<td><p>Predict antimicrobial resistance</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="rsi.html">rsi()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Calculate resistance of isolates</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="skewness.html">skewness()</a></code> </p>
|
||||
</td>
|
||||
@@ -487,7 +493,7 @@
|
||||
<td>
|
||||
<p><code><a href="antibiotics.html">antibiotics</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data set with ~500 antibiotics</p></td>
|
||||
<td><p>Data set with ~450 antibiotics</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@@ -529,9 +535,9 @@
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="get_locale.html">get_locale()</a></code> </p>
|
||||
<p><code><a href="translate.html">get_locale()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get language for AMR</p></td>
|
||||
<td><p>Translate strings from AMR package</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@@ -549,7 +555,7 @@
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> <code><a href="AMR-deprecated.html">atc_ddd()</a></code> <code><a href="AMR-deprecated.html">atc_groups()</a></code> </p>
|
||||
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">abname()</a></code> <code><a href="AMR-deprecated.html">atc_property()</a></code> <code><a href="AMR-deprecated.html">atc_official()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">atc_name()</a></code> <code><a href="AMR-deprecated.html">atc_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">atc_tradenames()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Deprecated functions</p></td>
|
||||
</tr>
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -242,19 +242,19 @@
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"amox"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"amcl"</span>),
|
||||
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfur"</span>),
|
||||
<span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"pita"</span>),
|
||||
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cipr"</span>),
|
||||
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"trsu"</span>),
|
||||
<span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"vanc"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"teic"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"tetr"</span>),
|
||||
<span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"eryt"</span>), <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"oxac"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"rifa"</span>),
|
||||
<span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"gent"</span>), <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"tobr"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"coli"</span>),
|
||||
<span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfot"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"cfta"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"mero"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||
<span class='st'>"AMX"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"AMC"</span>),
|
||||
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"CXM"</span>),
|
||||
<span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"TZP"</span>),
|
||||
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"CIP"</span>),
|
||||
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"SXT"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"VAN"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"TEC"</span>),
|
||||
<span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"TCY"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"ERY"</span>), <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"OXA"</span>),
|
||||
<span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"RIF"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"GEN"</span>), <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"TOB"</span>),
|
||||
<span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"COL"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
|
||||
<span class='st'>"CTX"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"CAZ"</span>),
|
||||
<span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"MEM"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
|
||||
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -241,50 +241,21 @@
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>metr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(),
|
||||
<span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>x</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>brmo</span>(<span class='no'>...</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
|
||||
|
||||
<span class='fu'>mrgn</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"de"</span>, <span class='no'>...</span>)
|
||||
<span class='fu'>mrgn</span>(<span class='no'>x</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"de"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
|
||||
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>x</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
|
||||
|
||||
<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>tbl</th>
|
||||
<td><p>table with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td>
|
||||
<th>x</th>
|
||||
<td><p>table with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>country</th>
|
||||
@@ -298,253 +269,13 @@
|
||||
<th>info</th>
|
||||
<td><p>print progress</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>amcl</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>amik</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>amox</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>ampi</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>azit</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>aztr</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cefa</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cfra</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cfep</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cfot</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cfox</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cfta</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cftr</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cfur</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>chlo</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>cipr</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>clar</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>clin</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>clox</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>coli</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>czol</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>dapt</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>doxy</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>erta</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>eryt</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>fosf</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>fusi</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>gent</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>imip</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>kana</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>levo</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>linc</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>line</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>mero</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>metr</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>mino</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>moxi</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>nali</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>neom</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>neti</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>nitr</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>novo</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>norf</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>oflo</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>peni</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>pipe</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>pita</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>poly</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>qida</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>rifa</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>roxi</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>siso</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>teic</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>tetr</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>tica</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>tige</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>tobr</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>trim</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>trsu</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>vanc</th>
|
||||
<td><p>column name of an antibiotic, see Antibiotics</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>verbose</th>
|
||||
<td><p>print additional info: missing antibiotic columns per parameter</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>parameters that are passed on to methods</p></td>
|
||||
<td><p>column name of an antibiotic, see section Antibiotics</p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
@@ -559,70 +290,72 @@
|
||||
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
|
||||
|
||||
|
||||
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive) or use <code>NULL</code> to skip a column (e.g. <code>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p>
|
||||
<p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p>
|
||||
<p><strong>amcl</strong>: amoxicillin+clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
|
||||
<strong>amik</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
|
||||
<strong>amox</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
|
||||
<strong>ampi</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
|
||||
<strong>azit</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
|
||||
<strong>azlo</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
|
||||
<strong>aztr</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
|
||||
<strong>cefa</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
|
||||
<strong>cfep</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
|
||||
<strong>cfot</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
|
||||
<strong>cfox</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
|
||||
<strong>cfra</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
|
||||
<strong>cfta</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
|
||||
<strong>cftr</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
|
||||
<strong>cfur</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
|
||||
<strong>chlo</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
|
||||
<strong>cipr</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
|
||||
<strong>clar</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
|
||||
<strong>clin</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
|
||||
<strong>clox</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
|
||||
<strong>coli</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
|
||||
<strong>czol</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
|
||||
<strong>dapt</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
|
||||
<strong>doxy</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
|
||||
<strong>erta</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
|
||||
<strong>eryt</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
|
||||
<strong>fosf</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
|
||||
<strong>fusi</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
|
||||
<strong>gent</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
|
||||
<strong>imip</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
|
||||
<strong>kana</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
|
||||
<strong>levo</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
|
||||
<strong>linc</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
|
||||
<strong>line</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
|
||||
<strong>mero</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
|
||||
<strong>mezl</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
|
||||
<strong>mino</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
|
||||
<strong>moxi</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
|
||||
<strong>nali</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
|
||||
<strong>neom</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
|
||||
<strong>neti</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
|
||||
<strong>nitr</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
|
||||
<strong>norf</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
|
||||
<strong>novo</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
|
||||
<strong>oflo</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
|
||||
<strong>peni</strong>: (benzyl)penicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
|
||||
<strong>pipe</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
|
||||
<strong>pita</strong>: piperacillin+tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
|
||||
<strong>poly</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
|
||||
<strong>pris</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
|
||||
<strong>qida</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
|
||||
<strong>rifa</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
|
||||
<strong>roxi</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
|
||||
<strong>siso</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
|
||||
<strong>teic</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
|
||||
<strong>tetr</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
|
||||
<strong>tica</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
|
||||
<strong>tige</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
|
||||
<strong>tobr</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
|
||||
<strong>trim</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
|
||||
<strong>trsu</strong>: sulfamethoxazole and trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
|
||||
<strong>vanc</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
|
||||
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
|
||||
<p>Available abbrevations of the column containing antibiotics in the form '<strong>antimicrobial ID</strong>: name (<em>ATC code</em>)':</p>
|
||||
<p><strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
|
||||
<strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
|
||||
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
|
||||
<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
|
||||
<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
|
||||
<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
|
||||
<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
|
||||
<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
|
||||
<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
|
||||
<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
|
||||
<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
|
||||
<strong>CED</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
|
||||
<strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
|
||||
<strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
|
||||
<strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
|
||||
<strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
|
||||
<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
|
||||
<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
|
||||
<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
|
||||
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
|
||||
<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
|
||||
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
|
||||
<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
|
||||
<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
|
||||
<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
|
||||
<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
|
||||
<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
|
||||
<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
|
||||
<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
|
||||
<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
|
||||
<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
|
||||
<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
|
||||
<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
|
||||
<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
|
||||
<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
|
||||
<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
|
||||
<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
|
||||
<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
|
||||
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01XD01</a>),
|
||||
<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
|
||||
<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
|
||||
<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
|
||||
<strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
|
||||
<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
|
||||
<strong>NOV</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
|
||||
<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
|
||||
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01CF04</a>),
|
||||
<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
|
||||
<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
|
||||
<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
|
||||
<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
|
||||
<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
|
||||
<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
|
||||
<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
|
||||
<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
|
||||
<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
|
||||
<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
|
||||
<strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
|
||||
<strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
|
||||
<strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
|
||||
<strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
|
||||
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
|
||||
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
|
||||
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</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>
|
||||
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -241,29 +241,29 @@
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<pre class="usage"><span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_shortname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_shortname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_subspecies</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_subspecies</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_species</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_species</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_genus</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_genus</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_family</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_family</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_order</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_order</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_class</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_class</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_phylum</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_phylum</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_kingdom</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_kingdom</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_type</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_type</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_ref</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
@@ -273,11 +273,11 @@
|
||||
|
||||
<span class='fu'>mo_rank</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"fullname"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
|
||||
<span class='fu'>mo_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"fullname"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -288,7 +288,7 @@
|
||||
</tr>
|
||||
<tr>
|
||||
<th>language</th>
|
||||
<td><p>language of the returned text, defaults to system language (see <code><a href='get_locale.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
|
||||
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
@@ -323,13 +323,9 @@
|
||||
<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
|
||||
</ul>
|
||||
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
|
||||
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
|
||||
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="supported-languages"><a class="anchor" href="#supported-languages"></a>Supported languages</h2>
|
||||
|
||||
|
||||
<p>Supported languages are <code>"en"</code> (English), <code>"de"</code> (German), <code>"nl"</code> (Dutch), <code>"es"</code> (Spanish), <code>"it"</code> (Italian), <code>"fr"</code> (French), and <code>"pt"</code> (Portuguese).</p>
|
||||
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
|
||||
|
||||
@@ -341,7 +337,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
|
||||
<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
|
||||
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong>. 2019. Clin Microbiol Infect. 2019 Mar 11. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
|
||||
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
|
||||
<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
|
||||
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
|
||||
|
||||
@@ -375,7 +371,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram negative"</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom)</span>
|
||||
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
|
||||
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the Catalogue of Life</span>
|
||||
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
|
||||
|
||||
<span class='co'>## scientific reference</span>
|
||||
<span class='fu'>mo_ref</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Castellani et al., 1919"</span>
|
||||
@@ -433,7 +429,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='co'># "Streptococcus groep A"</span>
|
||||
|
||||
|
||||
<span class='co'># get a list with the complete taxonomy (kingdom to subspecies)</span>
|
||||
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
@@ -446,8 +442,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#supported-languages">Supported languages</a></li>
|
||||
|
||||
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
|
||||
|
||||
<li><a href="#source">Source</a></li>
|
||||
|
||||
@@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -146,7 +146,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -258,8 +258,8 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
<span class='fu'>portion_S</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>portion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"get_antibiotic_names"</span>,
|
||||
<span class='st'>"official"</span>), <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
<span class='fu'>portion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
@@ -286,7 +286,11 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
</tr>
|
||||
<tr>
|
||||
<th>translate_ab</th>
|
||||
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='abname.html'>abname</a></code>. This can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("get_antibiotic_names")</code>.</p></td>
|
||||
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>language</th>
|
||||
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>combine_IR</th>
|
||||
@@ -307,8 +311,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
|
||||
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
|
||||
<p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. <em>Low counts can infuence the outcome - these <code>portion</code> functions may camouflage this, since they only return the portion albeit being dependent on the <code>minimum</code> parameter.</em></p>
|
||||
<p><code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
|
||||
<p>The old <code><a href='rsi.html'>rsi</a></code> function is still available for backwards compatibility but is deprecated.
|
||||
<p><code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.
|
||||
<br /><br />
|
||||
To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula:
|
||||
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
|
||||
@@ -338,63 +341,63 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
?<span class='no'>septic_patients</span>
|
||||
|
||||
<span class='co'># Calculate resistance</span>
|
||||
<span class='fu'>portion_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>portion_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>portion_R</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>portion_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
|
||||
<span class='co'># Or susceptibility</span>
|
||||
<span class='fu'>portion_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>portion_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
|
||||
<span class='fu'>portion_S</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
<span class='fu'>portion_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>AMX</span>)
|
||||
|
||||
<span class='co'># Do the above with pipes:</span>
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_R</span>(<span class='no'>amox</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_IR</span>(<span class='no'>amox</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_SI</span>(<span class='no'>amox</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_R</span>(<span class='no'>AMX</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_IR</span>(<span class='no'>AMX</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>AMX</span>)
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_SI</span>(<span class='no'>AMX</span>)
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>),
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>)) <span class='co'># n_rsi works like n_distinct in dplyr</span>
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>portion_R</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>portion_I</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
|
||||
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
|
||||
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
|
||||
|
||||
<span class='co'># Calculate co-resistance between amoxicillin/clav acid and gentamicin,</span>
|
||||
<span class='co'># so we can see that combination therapy does a lot more than mono therapy:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>) <span class='co'># S = 71.4%</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>) <span class='co'># n = 1879</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>AMC</span>) <span class='co'># S = 71.4%</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>) <span class='co'># n = 1879</span>
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>) <span class='co'># S = 74.0%</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>) <span class='co'># n = 1855</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>GEN</span>) <span class='co'># S = 74.0%</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>) <span class='co'># n = 1855</span>
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># S = 92.3%</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amcl</span>, <span class='no'>gent</span>) <span class='co'># n = 1798</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>portion_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># S = 92.3%</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># n = 1798</span>
|
||||
|
||||
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>),
|
||||
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>gent</span>),
|
||||
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>cipr</span>, <span class='no'>gent</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>cipr</span>, <span class='no'>gent</span>))
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>cipro_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>cipro_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>),
|
||||
<span class='kw'>genta_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>genta_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>GEN</span>),
|
||||
<span class='kw'>combination_p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
|
||||
<span class='kw'>combination_n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>CIP</span>, <span class='no'>GEN</span>))
|
||||
|
||||
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='co'># It also supports grouping variables</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>portion_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
@@ -404,8 +407,8 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
<span class='no'>my_table</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>,
|
||||
<span class='no'>genus</span> <span class='kw'>==</span> <span class='st'>"Helicobacter"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>amox</span>, <span class='no'>metr</span>), <span class='co'># amoxicillin with metronidazole</span>
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>amox</span>, <span class='no'>metr</span>))
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'>portion_S</span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>), <span class='co'># amoxicillin with metronidazole</span>
|
||||
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMX</span>, <span class='no'>MTR</span>))
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
|
||||
@@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9003</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
@@ -357,7 +357,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'>resistance_predict</span>(<span class='no'>septic_patients</span>, <span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"amox"</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>)
|
||||
<span class='no'>x</span> <span class='kw'><-</span> <span class='fu'>resistance_predict</span>(<span class='no'>septic_patients</span>, <span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>, <span class='kw'>year_min</span> <span class='kw'>=</span> <span class='fl'>2010</span>)
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
|
||||
<span class='fu'>ggplot_rsi_predict</span>(<span class='no'>x</span>)
|
||||
|
||||
@@ -366,7 +366,7 @@
|
||||
<span class='no'>x</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span>(<span class='st'>"peni"</span>)
|
||||
<span class='fu'>resistance_predict</span>(<span class='st'>"PEN"</span>)
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>)
|
||||
|
||||
|
||||
@@ -380,7 +380,7 @@
|
||||
|
||||
<span class='no'>data</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%>%</span>
|
||||
<span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"amox"</span>,
|
||||
<span class='fu'>resistance_predict</span>(<span class='kw'>col_ab</span> <span class='kw'>=</span> <span class='st'>"AMX"</span>,
|
||||
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
|
||||
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
||||
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>15</span>)
|
||||
|
||||
311
docs/reference/rsi_translation.html
Normal file
311
docs/reference/rsi_translation.html
Normal file
@@ -0,0 +1,311 @@
|
||||
<!-- Generated by pkgdown: do not edit by hand -->
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Data set for RSI interpretation — rsi_translation • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- sticky kit -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
<!-- docsearch -->
|
||||
<script src="../docsearch.js"></script>
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
||||
<link href="../docsearch.css" rel="stylesheet">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Data set for RSI interpretation — rsi_translation" />
|
||||
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<h1>Data set for RSI interpretation</h1>
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<div class="ref-description">
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||||
<p>Data set to interpret MIC and disk diffusion to RSI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use <code><a href='as.rsi.html'>as.rsi</a></code> to transform MICs or disks measurements to RSI values.</p>
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<pre class="usage"><span class='no'>rsi_translation</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
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<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 11,559 observations and 9 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>guideline</code></dt><dd><p>Name of the guideline</p></dd>
|
||||
<dt><code>mo</code></dt><dd><p>Microbial ID, see <code><a href='as.mo.html'>as.mo</a></code></p></dd>
|
||||
<dt><code>ab</code></dt><dd><p>Antibiotic ID, see <code><a href='as.ab.html'>as.ab</a></code></p></dd>
|
||||
<dt><code>ref_tbl</code></dt><dd><p>Info about where the guideline rule can be found</p></dd>
|
||||
<dt><code>S_mic</code></dt><dd><p>Lowest MIC value that leads to "S"</p></dd>
|
||||
<dt><code>R_mic</code></dt><dd><p>Highest MIC value that leads to "R"</p></dd>
|
||||
<dt><code>dose_disk</code></dt><dd><p>Dose of the used disk diffusion method</p></dd>
|
||||
<dt><code>S_disk</code></dt><dd><p>Lowest number of millimeters that leads to "S"</p></dd>
|
||||
<dt><code>R_disk</code></dt><dd><p>Highest number of millimeters that leads to "R"</p></dd>
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|
||||
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|
||||
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||||
|
||||
Create frequency tables
|
||||
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||||
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||||
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|
||||
<a href="../articles/G_test.html">
|
||||
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||||
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||||
Use the G-test
|
||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
Other: benchmarks
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||||
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||||
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|
||||
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|
||||
<h1>Translate strings from AMR package</h1>
|
||||
|
||||
<div class="hidden name"><code>translate.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>For language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_fullname</a></code> and <code><a href='mo_property.html'>mo_type</a></code>.</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>get_locale</span>()</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Strings will be translated to foreign languages if they are defined in a local translation file. This file comes with this package and can be found when running:</p>
|
||||
<p><code><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file("translations.tsv", package = "AMR")</a></code></p>
|
||||
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.). Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation suggestion'>by creating a new issue on our repository</a>.</p>
|
||||
<p>The system language will be used at default, if supported, using <code>get_locale</code>. The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</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>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># The 'language' parameter of below functions</span>
|
||||
<span class='co'># will be set automatically to your system language</span>
|
||||
<span class='co'># with get_locale()</span>
|
||||
|
||||
<span class='co'># English</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"en"</span>)
|
||||
<span class='co'>#> "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
|
||||
<span class='co'># German</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"de"</span>)
|
||||
<span class='co'>#> "Koagulase-negative Staphylococcus (KNS)"</span>
|
||||
|
||||
<span class='co'># Dutch</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
|
||||
<span class='co'>#> "Coagulase-negatieve Staphylococcus (CNS)"</span>
|
||||
|
||||
<span class='co'># Spanish</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"es"</span>)
|
||||
<span class='co'>#> "Staphylococcus coagulasa negativo (SCN)"</span>
|
||||
|
||||
<span class='co'># Italian</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"it"</span>)
|
||||
<span class='co'>#> "Staphylococcus negativo coagulasi (CoNS)"</span>
|
||||
|
||||
<span class='co'># Portuguese</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"CoNS"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='st'>"pt"</span>)
|
||||
<span class='co'>#> "Staphylococcus coagulase negativo (CoNS)"</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
||||
|
||||
<li><a href="#examples">Examples</a></li>
|
||||
</ul>
|
||||
|
||||
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|
||||
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||||
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|
||||
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|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
|
||||
</div>
|
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|
||||
<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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docsearch({
|
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|
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
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|
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|
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|
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||||
</html>
|
||||
|
||||
@@ -16,7 +16,7 @@
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/WHONET.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/abname.html</loc>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/ab_property.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/age.html</loc>
|
||||
@@ -27,9 +27,15 @@
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/antibiotics.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/as.ab.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/as.atc.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/as.disk.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/as.mic.html</loc>
|
||||
</url>
|
||||
@@ -42,9 +48,6 @@
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/atc_online.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/atc_property.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/availability.html</loc>
|
||||
</url>
|
||||
@@ -72,9 +75,6 @@
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/g.test.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/get_locale.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/ggplot_rsi.html</loc>
|
||||
</url>
|
||||
@@ -124,7 +124,7 @@
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/resistance_predict.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/rsi.html</loc>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/rsi_translation.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/septic_patients.html</loc>
|
||||
@@ -132,6 +132,9 @@
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/skewness.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/translate.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/articles/AMR.html</loc>
|
||||
</url>
|
||||
@@ -148,7 +151,7 @@
|
||||
<loc>https://msberends.gitlab.io/AMR/articles/WHONET.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/articles/atc_property.html</loc>
|
||||
<loc>https://msberends.gitlab.io/AMR/articles/ab_property.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/articles/benchmarks.html</loc>
|
||||
|
||||
Reference in New Issue
Block a user