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as.mo improvement

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dr. M.S. (Matthijs) Berends
2019-02-23 16:02:31 +01:00
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@ -192,7 +192,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">22 February 2019</h4>
<h4 class="date">23 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") 42.9 43.2 43.9 44.0 44.2 45.1 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 86.8 87.0 88.9 87.3 88.2 101.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 42.6 43.6 51.5 43.8 44.5 82.8 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("S. aureus") 23.2 23.3 31.0 23.5 23.6 61.8 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 23.1 23.3 26.4 23.7 24.4 51.2 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("STAAUR") 42.8 43.4 44.5 44.3 44.5 47.8 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 14.3 14.5 20.4 14.8 16.0 64.6 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") 10.4 10.5 10.7 10.6 10.7 11.2 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 84.4 84.7 95.6 85.2 101.0 136.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 10.5 10.6 10.8 10.6 11.1 11.2 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("S. aureus") 21.3 21.4 31.4 21.9 41.6 60.3 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 21.3 21.4 21.8 21.4 21.5 24.9 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("STAAUR") 10.5 10.6 23.5 10.6 43.8 65.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 16.1 16.2 20.7 16.4 17.5 57.7 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 more an input value resembles a full name, the faster the result will be found.</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>
@ -237,13 +237,13 @@
<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") 141 142 162 142 142 299 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("mycleo") 479 481 520 525 530 634 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("M. leonicaptivi") 241 242 273 263 281 382 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 239 241 268 282 283 299 10</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("MYCLEO") 487 520 525 524 528 601 10</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 152 156 183 174 200 261 10</span></a></code></pre></div>
<p>That takes 7.3 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="cb3-11" title="11"><span class="co">#&gt; as.mo("myle") 131 132 132 132 133 133 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("mycleo") 439 445 471 481 488 505 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("M. leonicaptivi") 202 205 234 243 247 262 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 202 202 221 212 242 249 10</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("MYCLEO") 441 449 469 480 486 493 10</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 143 143 165 165 185 190 10</span></a></code></pre></div>
<p>That takes 9.2 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.</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 +283,8 @@
<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) 400 405 463 441 533 558 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.44 seconds (441 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) 618 653 729 695 813 846 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.69 seconds (694 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -296,10 +296,10 @@
<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">#&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 39.000 39.80 40.000 40.100 40.300 41.100 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 24.400 24.70 25.000 24.900 25.200 25.600 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.294 0.39 0.422 0.401 0.505 0.535 10</span></a></code></pre></div>
<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 6.460 6.560 6.660 6.650 6.720 6.950 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 22.300 22.400 22.700 22.700 22.900 23.000 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.254 0.263 0.378 0.396 0.413 0.563 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="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>
@ -313,14 +313,14 @@
<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 0.298 0.327 0.398 0.400 0.452 0.535 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.251 0.287 0.339 0.344 0.377 0.436 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.293 0.403 0.451 0.487 0.500 0.537 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.250 0.262 0.300 0.277 0.336 0.395 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.249 0.261 0.306 0.313 0.344 0.384 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.273 0.283 0.325 0.326 0.338 0.420 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.238 0.293 0.312 0.325 0.342 0.356 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.250 0.262 0.304 0.316 0.337 0.358 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.303 0.338 0.414 0.431 0.453 0.550 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.244 0.282 0.339 0.363 0.372 0.395 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.302 0.404 0.437 0.430 0.490 0.527 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.257 0.279 0.315 0.310 0.344 0.378 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.219 0.270 0.306 0.298 0.355 0.377 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.248 0.296 0.312 0.317 0.334 0.349 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.228 0.248 0.287 0.278 0.336 0.367 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.250 0.255 0.312 0.312 0.352 0.398 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 +347,13 @@
<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 10.78 11.11 11.15 11.14 11.30 11.41 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 19.60 19.65 23.24 19.76 20.61 52.47 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 19.14 19.71 19.75 19.72 19.87 20.22 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 19.64 19.73 28.36 20.60 25.91 64.67 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 19.33 19.49 23.13 19.68 19.97 52.72 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 19.43 19.54 20.08 19.72 20.60 21.46 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 19.34 19.66 23.15 19.80 20.48 52.40 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 12.45 12.60 15.94 12.66 12.69 45.75 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 20.73 20.87 24.50 21.13 21.29 54.54 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 21.02 21.14 24.63 21.22 21.44 54.44 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 20.56 21.15 21.46 21.21 22.02 22.39 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 20.54 20.80 21.08 20.93 21.19 22.15 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 20.86 21.11 24.55 21.21 21.45 54.12 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 20.74 20.93 28.96 21.17 21.60 66.52 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>