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as.mo improvement

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dr. M.S. (Matthijs) Berends
2019-02-25 10:42:57 +01:00
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@ -192,7 +192,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">23 February 2019</h4>
<h4 class="date">25 February 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -217,14 +217,14 @@
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<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">3</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 15.0 15.0 21.8 15.2 15.5 80.5 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 90.4 90.6 106.0 91.0 92.7 180.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 15.0 15.1 19.2 15.2 15.7 54.5 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("S. aureus") 26.5 26.6 34.7 26.9 28.1 65.9 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 26.6 26.7 31.8 26.8 26.9 76.8 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("STAAUR") 15.0 15.1 19.2 15.2 15.5 54.2 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 13.4 13.5 17.7 13.6 14.7 52.1 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 16.4 16.5 28.4 16.8 54.9 55.8 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 86.0 86.5 97.3 88.9 100.0 132.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 16.3 16.6 23.0 16.8 21.0 56.8 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("S. aureus") 25.3 25.9 39.4 27.2 64.0 74.5 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 25.2 25.3 29.7 25.6 27.0 64.3 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("STAAUR") 16.3 16.7 21.1 17.0 18.0 56.8 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 13.5 13.9 20.5 14.4 17.5 51.2 10</span></a></code></pre></div>
<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 second input is the only one that has to be looked up thoroughly. All the others are known codes (the first is a WHONET code) or common laboratory codes, or common full organism names like the last one.</p>
<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>Mycoplasma leonicaptivi</em> (<code>B_MYCPL_LEO</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">M.leonicaptivi &lt;-<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>
@ -236,14 +236,21 @@
<a class="sourceLine" id="cb3-7" title="7"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><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>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("myle") 136 137 141 137 138 176 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("mycleo") 447 464 484 487 490 551 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("M. leonicaptivi") 206 208 225 210 248 252 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 207 208 230 229 251 255 10</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("MYCLEO") 444 446 462 446 486 487 10</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 147 148 170 173 187 192 10</span></a></code></pre></div>
<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.</p>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("myle") 135.0 135.0 147.0 135.0 174.0 176.0</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("mycleo") 211.0 213.0 233.0 232.0 251.0 262.0</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("M. leonicaptivi") 59.2 59.2 63.6 59.4 59.6 98.7</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 59.0 59.1 59.3 59.3 59.3 59.7</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("MYCLEO") 211.0 211.0 220.0 211.0 222.0 250.0</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 22.5 22.5 26.5 22.6 22.7 61.0</span></a>
<a class="sourceLine" id="cb3-17" title="17"><span class="co">#&gt; neval</span></a>
<a class="sourceLine" id="cb3-18" title="18"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-19" title="19"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-20" title="20"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-21" title="21"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-22" title="22"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-23" title="23"><span class="co">#&gt; 10</span></a></code></pre></div>
<p>That takes 3.4 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>
<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>Mycoplasma leonicaptivi</em> (which is very uncommon):</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>
@ -283,8 +290,8 @@
<a class="sourceLine" id="cb5-18" 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">3</span>)</a>
<a class="sourceLine" id="cb5-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-21" title="21"><span class="co">#&gt; mo_fullname(x) 615 647 698 649 801 851 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.65 seconds (649 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-21" title="21"><span class="co">#&gt; mo_fullname(x) 610 641 644 644 657 665 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.64 seconds (644 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -297,10 +304,10 @@
<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">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 6.420 6.570 6.670 6.730 6.760 6.780 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 27.100 27.200 28.000 27.600 27.800 32.900 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.255 0.383 0.394 0.412 0.431 0.527 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>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 7.500 7.540 7.720 7.610 7.710 8.750 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 25.800 26.200 27.100 27.800 27.800 27.900 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.604 0.628 0.704 0.729 0.755 0.791 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 0.0007 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 &lt;-<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>
@ -313,14 +320,14 @@
<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">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.311 0.355 0.435 0.437 0.492 0.566 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.283 0.299 0.340 0.337 0.362 0.411 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.393 0.447 0.503 0.496 0.566 0.662 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.253 0.288 0.324 0.305 0.325 0.523 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.243 0.249 0.315 0.288 0.342 0.506 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.239 0.295 0.349 0.327 0.411 0.482 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.249 0.323 0.364 0.347 0.410 0.493 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.226 0.303 0.368 0.339 0.478 0.523 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.704 0.806 0.897 0.867 1.040 1.130 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.671 0.722 0.841 0.807 0.903 1.110 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.702 0.768 0.856 0.816 0.967 1.160 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.641 0.695 0.746 0.746 0.755 0.976 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.627 0.702 0.781 0.762 0.789 1.100 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.651 0.694 0.779 0.733 0.761 1.220 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.552 0.745 0.801 0.764 0.815 1.090 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.637 0.661 0.722 0.724 0.766 0.803 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">
@ -347,13 +354,13 @@
<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">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 17.14 17.39 20.87 17.54 17.93 50.49 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 25.94 26.02 32.71 26.11 26.24 59.33 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 25.41 25.86 29.47 26.04 27.08 59.40 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 25.55 25.97 32.75 26.11 26.77 59.62 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 25.65 25.90 26.07 26.09 26.11 26.75 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 25.47 25.79 26.10 26.09 26.20 27.23 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 25.72 25.85 29.33 26.07 26.09 59.41 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 18.95 18.99 19.59 19.04 19.49 23.47 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 27.13 27.26 27.69 27.63 27.88 29.05 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 26.95 27.62 34.90 27.99 32.35 61.05 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 27.42 27.55 38.05 27.75 60.86 61.40 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 26.99 27.30 34.13 27.48 27.70 61.28 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 27.35 27.52 30.95 27.58 27.72 61.11 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 27.26 27.33 27.67 27.53 27.91 28.44 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>