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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">20 February 2019</h4>
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<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the Catalogue of Life (<a href="http://catalogueoflife.org" class="uri">http://catalogueoflife.org</a>). We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using AI (Artificial Intelligence) combined with the taxonomic tree of Catalogue of Life.</p>
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<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</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="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(microbenchmark)</a>
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<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR)</a></code></pre></div>
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<p>In the next test, we try to ‘coerce’ different input values for <em>Staphylococcus aureus</em>. The actual result is the same every time: it returns its MO code <code>B_STPHY_AUR</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
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<p>But the calculation time differs a lot. Here, the AI effect can be reviewed best:</p>
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<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">S.aureus <-<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">"sau"</span>),</a>
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<a class="sourceLine" id="cb2-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),</a>
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<a class="sourceLine" id="cb2-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),</a>
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<a class="sourceLine" id="cb2-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
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<a class="sourceLine" id="cb2-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
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<a class="sourceLine" id="cb2-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a>
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<a class="sourceLine" id="cb2-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
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<a class="sourceLine" id="cb2-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
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<a class="sourceLine" id="cb2-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb2-10" title="10"><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>)</a>
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<a class="sourceLine" id="cb2-11" title="11"><span class="co">#> Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb2-12" title="12"><span class="co">#> expr min lq mean median</span></a>
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<a class="sourceLine" id="cb2-13" title="13"><span class="co">#> as.mo("sau") 42.58139 42.645368 43.3006677 42.970095</span></a>
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<a class="sourceLine" id="cb2-14" title="14"><span class="co">#> as.mo("stau") 76.60094 77.168264 83.7686909 77.316642</span></a>
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<a class="sourceLine" id="cb2-15" title="15"><span class="co">#> as.mo("staaur") 42.86607 42.947083 43.5035571 43.497293</span></a>
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<a class="sourceLine" id="cb2-16" title="16"><span class="co">#> as.mo("S. aureus") 18.39354 18.432582 22.4304233 18.495928</span></a>
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<a class="sourceLine" id="cb2-17" title="17"><span class="co">#> as.mo("S. aureus") 18.46513 18.559903 18.6640991 18.579110</span></a>
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<a class="sourceLine" id="cb2-18" title="18"><span class="co">#> as.mo("STAAUR") 42.71975 42.788612 44.3280682 43.069864</span></a>
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<a class="sourceLine" id="cb2-19" title="19"><span class="co">#> as.mo("Staphylococcus aureus") 11.56285 11.591419 15.9457298 11.667161</span></a>
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<a class="sourceLine" id="cb2-20" title="20"><span class="co">#> as.mo("B_STPHY_AUR") 0.40487 0.450128 0.5036822 0.481417</span></a>
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<a class="sourceLine" id="cb2-21" title="21"><span class="co">#> uq max neval</span></a>
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<a class="sourceLine" id="cb2-22" title="22"><span class="co">#> 43.448543 45.058105 10</span></a>
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<a class="sourceLine" id="cb2-23" title="23"><span class="co">#> 78.335591 127.180349 10</span></a>
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<a class="sourceLine" id="cb2-24" title="24"><span class="co">#> 43.817095 44.999509 10</span></a>
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<a class="sourceLine" id="cb2-25" title="25"><span class="co">#> 19.007097 56.501460 10</span></a>
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<a class="sourceLine" id="cb2-26" title="26"><span class="co">#> 18.651814 19.373275 10</span></a>
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<a class="sourceLine" id="cb2-27" title="27"><span class="co">#> 43.741388 54.703256 10</span></a>
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<a class="sourceLine" id="cb2-28" title="28"><span class="co">#> 12.323077 50.121808 10</span></a>
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<a class="sourceLine" id="cb2-29" title="29"><span class="co">#> 0.519271 0.766578 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 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of <code><a href="../reference/as.mo.html">as.mo("B_STPHY_AUR")</a></code>, the input is already a valid MO code, so it only almost takes no time at all (404 millionths of seconds).</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 far less faster. See this example for the ID of <em>Mycoplasma leonicaptivi</em> (<code>B_MYCPL_LEO</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">M.leonicaptivi <-<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">"myle"</span>),</a>
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<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"mycleo"</span>),</a>
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||
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. leonicaptivi"</span>),</a>
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<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. leonicaptivi"</span>),</a>
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<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MYCLEO"</span>),</a>
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||
<a class="sourceLine" id="cb3-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Mycoplasma leonicaptivi"</span>),</a>
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<a class="sourceLine" id="cb3-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_MYCPL_LEO"</span>),</a>
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<a class="sourceLine" id="cb3-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(M.leonicaptivi, <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
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<a class="sourceLine" id="cb3-10" title="10"><span class="co">#> Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb3-11" title="11"><span class="co">#> expr min lq mean</span></a>
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<a class="sourceLine" id="cb3-12" title="12"><span class="co">#> as.mo("myle") 112.28656 112.372601 112.751678</span></a>
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<a class="sourceLine" id="cb3-13" title="13"><span class="co">#> as.mo("mycleo") 382.46812 382.757612 383.432440</span></a>
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<a class="sourceLine" id="cb3-14" title="14"><span class="co">#> as.mo("M. leonicaptivi") 202.68674 203.654949 210.461303</span></a>
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<a class="sourceLine" id="cb3-15" title="15"><span class="co">#> as.mo("M. leonicaptivi") 202.89759 203.440956 203.816387</span></a>
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<a class="sourceLine" id="cb3-16" title="16"><span class="co">#> as.mo("MYCLEO") 382.27864 383.090895 401.904482</span></a>
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<a class="sourceLine" id="cb3-17" title="17"><span class="co">#> as.mo("Mycoplasma leonicaptivi") 102.99676 103.191196 109.196394</span></a>
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<a class="sourceLine" id="cb3-18" title="18"><span class="co">#> as.mo("B_MYCPL_LEO") 0.32155 0.564807 4.320068</span></a>
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<a class="sourceLine" id="cb3-19" title="19"><span class="co">#> median uq max neval</span></a>
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<a class="sourceLine" id="cb3-20" title="20"><span class="co">#> 112.540884 112.76874 113.76321 10</span></a>
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<a class="sourceLine" id="cb3-21" title="21"><span class="co">#> 383.232219 384.05897 385.28587 10</span></a>
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<a class="sourceLine" id="cb3-22" title="22"><span class="co">#> 204.255445 205.80976 242.53035 10</span></a>
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<a class="sourceLine" id="cb3-23" title="23"><span class="co">#> 203.613673 203.82802 206.15038 10</span></a>
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<a class="sourceLine" id="cb3-24" title="24"><span class="co">#> 386.478757 421.87837 437.26978 10</span></a>
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<a class="sourceLine" id="cb3-25" title="25"><span class="co">#> 103.596136 104.65940 142.25748 10</span></a>
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<a class="sourceLine" id="cb3-26" title="26"><span class="co">#> 0.593652 0.62522 37.96384 10</span></a></code></pre></div>
|
||
<p>That takes 6 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:</p>
|
||
<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>
|
||
<a class="sourceLine" id="cb4-2" title="2"></a>
|
||
<a class="sourceLine" id="cb4-3" title="3"><span class="co"># highest value on y axis</span></a>
|
||
<a class="sourceLine" id="cb4-4" title="4">max_y_axis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Extremes">max</a></span>(S.aureus<span class="op">$</span>time, M.leonicaptivi<span class="op">$</span>time, <span class="dt">na.rm =</span> <span class="ot">TRUE</span>) <span class="op">/</span><span class="st"> </span><span class="fl">1e6</span></a>
|
||
<a class="sourceLine" id="cb4-5" title="5"></a>
|
||
<a class="sourceLine" id="cb4-6" title="6"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(S.aureus, <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">"ms"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>, <span class="dt">xlab =</span> <span class="st">""</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>, max_y_axis),</a>
|
||
<a class="sourceLine" id="cb4-7" title="7"> <span class="dt">main =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/expression">expression</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Benchmark of "</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/plotmath">italic</a></span>(<span class="st">"Staphylococcus aureus"</span>))))</a></code></pre></div>
|
||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
|
||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"></a>
|
||
<a class="sourceLine" id="cb5-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>(M.leonicaptivi, <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">"ms"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>, <span class="dt">xlab =</span> <span class="st">""</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>, max_y_axis),</a>
|
||
<a class="sourceLine" id="cb5-3" title="3"> <span class="dt">main =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/expression">expression</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(<span class="st">"Benchmark of "</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/grDevices/topics/plotmath">italic</a></span>(<span class="st">"Mycoplasma leonicaptivi"</span>))))</a></code></pre></div>
|
||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-2.png" width="720"></p>
|
||
<p>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>
|
||
<div id="repetitive-results" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
|
||
<p>Repetitive results mean that unique values are present more than once. Unique values will only be calculated once by <code><a href="../reference/as.mo.html">as.mo()</a></code>. We will use <code><a href="../reference/mo_property.html">mo_fullname()</a></code> for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses <code><a href="../reference/as.mo.html">as.mo()</a></code> internally.</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="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
|
||
<a class="sourceLine" id="cb6-2" title="2"><span class="co">#> </span></a>
|
||
<a class="sourceLine" id="cb6-3" title="3"><span class="co">#> Attaching package: 'dplyr'</span></a>
|
||
<a class="sourceLine" id="cb6-4" title="4"><span class="co">#> The following objects are masked from 'package:stats':</span></a>
|
||
<a class="sourceLine" id="cb6-5" title="5"><span class="co">#> </span></a>
|
||
<a class="sourceLine" id="cb6-6" title="6"><span class="co">#> filter, lag</span></a>
|
||
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#> The following objects are masked from 'package:base':</span></a>
|
||
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#> </span></a>
|
||
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#> intersect, setdiff, setequal, union</span></a>
|
||
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># take 500,000 random MO codes from the septic_patients data set</span></a>
|
||
<a class="sourceLine" id="cb6-11" title="11">x =<span class="st"> </span>septic_patients <span class="op">%>%</span></a>
|
||
<a class="sourceLine" id="cb6-12" title="12"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample_n</a></span>(<span class="dv">500000</span>, <span class="dt">replace =</span> <span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||
<a class="sourceLine" id="cb6-13" title="13"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(mo)</a>
|
||
<a class="sourceLine" id="cb6-14" title="14"> </a>
|
||
<a class="sourceLine" id="cb6-15" title="15"><span class="co"># got the right length?</span></a>
|
||
<a class="sourceLine" id="cb6-16" title="16"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
|
||
<a class="sourceLine" id="cb6-17" title="17"><span class="co">#> [1] 500000</span></a>
|
||
<a class="sourceLine" id="cb6-18" title="18"></a>
|
||
<a class="sourceLine" id="cb6-19" title="19"><span class="co"># and how many unique values do we have?</span></a>
|
||
<a class="sourceLine" id="cb6-20" title="20"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
|
||
<a class="sourceLine" id="cb6-21" title="21"><span class="co">#> [1] 95</span></a>
|
||
<a class="sourceLine" id="cb6-22" title="22"></a>
|
||
<a class="sourceLine" id="cb6-23" title="23"><span class="co"># now let's see:</span></a>
|
||
<a class="sourceLine" id="cb6-24" title="24">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">X =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
|
||
<a class="sourceLine" id="cb6-25" title="25"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||
<a class="sourceLine" id="cb6-26" title="26"><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>)</a>
|
||
<a class="sourceLine" id="cb6-27" title="27"><span class="co">#> Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb6-28" title="28"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb6-29" title="29"><span class="co">#> X 435.7086 442.1682 465.5949 468.8453 477.1915 505.961 10</span></a></code></pre></div>
|
||
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.47 seconds (468 ms). You only lose time on your unique input values.</p>
|
||
</div>
|
||
<div id="precalculated-results" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
|
||
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_fullname()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</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_fullname</a></span>(<span class="st">"B_STPHY_AUR"</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_fullname</a></span>(<span class="st">"S. aureus"</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>
|
||
<a class="sourceLine" id="cb7-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
|
||
<a class="sourceLine" id="cb7-5" 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>)</a>
|
||
<a class="sourceLine" id="cb7-6" title="6"><span class="co">#> Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb7-8" title="8"><span class="co">#> A 38.887977 38.920313 39.3674024 39.076862 39.258415 42.166327 10</span></a>
|
||
<a class="sourceLine" id="cb7-9" title="9"><span class="co">#> B 19.589084 19.631059 19.8682396 19.781567 19.955611 20.751941 10</span></a>
|
||
<a class="sourceLine" id="cb7-10" title="10"><span class="co">#> C 0.255829 0.382732 0.4199913 0.400156 0.499156 0.564807 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 0.0004 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="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><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="cb8-2" 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="cb8-3" 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>
|
||
<a class="sourceLine" id="cb8-4" title="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
|
||
<a class="sourceLine" id="cb8-5" title="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
|
||
<a class="sourceLine" id="cb8-6" title="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
|
||
<a class="sourceLine" id="cb8-7" title="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
|
||
<a class="sourceLine" id="cb8-8" title="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
|
||
<a class="sourceLine" id="cb8-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
|
||
<a class="sourceLine" id="cb8-10" title="10"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb8-11" title="11"><span class="co">#> Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb8-12" title="12"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb8-13" title="13"><span class="co">#> A 0.250242 0.292496 0.3891774 0.4266960 0.456902 0.520388 10</span></a>
|
||
<a class="sourceLine" id="cb8-14" title="14"><span class="co">#> B 0.259461 0.311702 0.3428727 0.3412800 0.374141 0.443912 10</span></a>
|
||
<a class="sourceLine" id="cb8-15" title="15"><span class="co">#> C 0.290960 0.313169 0.4334429 0.4097595 0.520389 0.725373 10</span></a>
|
||
<a class="sourceLine" id="cb8-16" title="16"><span class="co">#> D 0.271823 0.282789 0.3187217 0.3192800 0.352909 0.375398 10</span></a>
|
||
<a class="sourceLine" id="cb8-17" title="17"><span class="co">#> E 0.245353 0.270985 0.3081197 0.2960235 0.330839 0.429036 10</span></a>
|
||
<a class="sourceLine" id="cb8-18" title="18"><span class="co">#> F 0.246122 0.266585 0.2991101 0.3089435 0.332794 0.351582 10</span></a>
|
||
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#> G 0.271893 0.272452 0.3085039 0.2850580 0.368204 0.385525 10</span></a>
|
||
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#> H 0.252686 0.259251 0.3161791 0.2985025 0.334820 0.422680 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">
|
||
<h3 class="hasAnchor">
|
||
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
|
||
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions take a little while longer:</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_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_fullname("CoNS") on an English system</span></a>
|
||
<a class="sourceLine" id="cb9-2" title="2"><span class="co">#> [1] "Coagulase Negative Staphylococcus (CoNS)"</span></a>
|
||
<a class="sourceLine" id="cb9-3" title="3"></a>
|
||
<a class="sourceLine" id="cb9-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>) <span class="co"># or just mo_fullname("CoNS") on a French system</span></a>
|
||
<a class="sourceLine" id="cb9-5" title="5"><span class="co">#> [1] "Staphylococcus à coagulase négative (CoNS)"</span></a>
|
||
<a class="sourceLine" id="cb9-6" title="6"></a>
|
||
<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
|
||
<a class="sourceLine" id="cb9-8" title="8"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
|
||
<a class="sourceLine" id="cb9-9" title="9"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
|
||
<a class="sourceLine" id="cb9-10" title="10"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
|
||
<a class="sourceLine" id="cb9-11" title="11"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
|
||
<a class="sourceLine" id="cb9-12" title="12"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
|
||
<a class="sourceLine" id="cb9-13" title="13"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
|
||
<a class="sourceLine" id="cb9-14" title="14"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
|
||
<a class="sourceLine" id="cb9-15" title="15"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
|
||
<a class="sourceLine" id="cb9-16" title="16"><span class="co">#> Unit: milliseconds</span></a>
|
||
<a class="sourceLine" id="cb9-17" title="17"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||
<a class="sourceLine" id="cb9-18" title="18"><span class="co">#> en 10.67105 11.03136 11.06332 11.07271 11.15310 11.45006 10</span></a>
|
||
<a class="sourceLine" id="cb9-19" title="19"><span class="co">#> de 19.13393 19.50080 26.13799 19.61419 20.23400 52.66501 10</span></a>
|
||
<a class="sourceLine" id="cb9-20" title="20"><span class="co">#> nl 19.05410 19.53789 22.94707 19.59205 20.12616 52.47399 10</span></a>
|
||
<a class="sourceLine" id="cb9-21" title="21"><span class="co">#> es 19.31635 19.55221 26.22342 19.58633 20.01875 52.97636 10</span></a>
|
||
<a class="sourceLine" id="cb9-22" title="22"><span class="co">#> it 19.21725 19.47105 19.63980 19.58053 19.68162 20.58914 10</span></a>
|
||
<a class="sourceLine" id="cb9-23" title="23"><span class="co">#> fr 19.07854 19.45450 19.67303 19.56153 19.64517 20.45651 10</span></a>
|
||
<a class="sourceLine" id="cb9-24" title="24"><span class="co">#> pt 19.00668 19.28388 19.53493 19.57857 19.66423 20.55317 10</span></a></code></pre></div>
|
||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||
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|
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<footer><div class="copyright">
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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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