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as.mo improvements

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dr. M.S. (Matthijs) Berends
2019-02-25 15:52:32 +01:00
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@ -210,56 +210,47 @@
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">S.aureus &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">"sau"</span>),</a>
<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>
<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>
<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>
<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>
<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>
<a class="sourceLine" id="cb2-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),</a>
<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>
<a class="sourceLine" id="cb2-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<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>
<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") 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>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 12.1 12.2 12.3 12.2 12.3 12.6 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 81.3 81.9 97.3 82.7 120.0 155.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 12.2 12.3 12.7 12.6 13.2 13.5 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 12.2 12.3 16.5 12.6 13.4 50.7 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 20.1 20.1 25.2 20.1 20.2 69.9 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 20.1 20.2 20.7 20.3 21.6 22.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 11.2 11.3 11.5 11.3 11.5 12.4 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>
<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>
<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>
<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>
<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>
<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>
<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</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>
<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>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &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">"theisl"</span>),</a>
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb3-6" title="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<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">3</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; as.mo("theisl") 446.0 452.0 478.0 486.0 488.0 506 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 446.0 446.0 471.0 467.0 489.0 528 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 76.5 77.1 87.4 77.2 85.4 127 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 76.9 76.9 81.4 77.1 79.1 116 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 67.6 67.7 80.0 67.9 106.0 112 10</span></a></code></pre></div>
<p>That takes 8.5 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>
<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>
<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="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></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">"M. leonicaptivi"</span>),</a>
<a class="sourceLine" id="cb4-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Mycoplasma leonicaptivi"</span>),</a>
<a class="sourceLine" id="cb4-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
<a class="sourceLine" id="cb4-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Prevotella brevis"</span>),</a>
<a class="sourceLine" id="cb4-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
<a class="sourceLine" id="cb4-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Escherichia coli"</span>),</a>
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></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">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb4-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Prevotella brevis"</span>),</a>
<a class="sourceLine" id="cb4-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Escherichia coli"</span>),</a>
<a class="sourceLine" id="cb4-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb4-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
<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>
<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">50</span>),</a>
<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>
<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>
@ -271,27 +262,33 @@
<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="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/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># take 500,000 random MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb5-3" title="3">x =<span class="st"> </span>septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-4" title="4"><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">%&gt;%</span></a>
<a class="sourceLine" id="cb5-5" title="5"><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="cb5-6" title="6"> </a>
<a class="sourceLine" id="cb5-7" title="7"><span class="co"># got the right length?</span></a>
<a class="sourceLine" id="cb5-8" title="8"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb5-9" title="9"><span class="co">#&gt; [1] 500000</span></a>
<a class="sourceLine" id="cb5-10" title="10"></a>
<a class="sourceLine" id="cb5-11" title="11"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb5-12" title="12"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb5-13" title="13"><span class="co">#&gt; [1] 95</span></a>
<a class="sourceLine" id="cb5-14" title="14"></a>
<a class="sourceLine" id="cb5-15" title="15"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb5-16" title="16">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="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
<a class="sourceLine" id="cb5-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<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) 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>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># take all MO codes from the septic_patients data set</span></a>
<a class="sourceLine" id="cb5-3" title="3">x &lt;-<span class="st"> </span>septic_patients<span class="op">$</span>mo <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-4" title="4"><span class="st"> </span><span class="co"># keep only the unique ones</span></a>
<a class="sourceLine" id="cb5-5" title="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/unique">unique</a></span>() <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-6" title="6"><span class="st"> </span><span class="co"># pick 50 of them at random</span></a>
<a class="sourceLine" id="cb5-7" title="7"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="dv">50</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-8" title="8"><span class="st"> </span><span class="co"># paste that 10,000 times</span></a>
<a class="sourceLine" id="cb5-9" title="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="dv">10000</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-10" title="10"><span class="st"> </span><span class="co"># scramble it</span></a>
<a class="sourceLine" id="cb5-11" title="11"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()</a>
<a class="sourceLine" id="cb5-12" title="12"> </a>
<a class="sourceLine" id="cb5-13" title="13"><span class="co"># got indeed 50 times 10,000 = half a million?</span></a>
<a class="sourceLine" id="cb5-14" title="14"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/length">length</a></span>(x)</a>
<a class="sourceLine" id="cb5-15" title="15"><span class="co">#&gt; [1] 500000</span></a>
<a class="sourceLine" id="cb5-16" title="16"></a>
<a class="sourceLine" id="cb5-17" title="17"><span class="co"># and how many unique values do we have?</span></a>
<a class="sourceLine" id="cb5-18" title="18"><span class="kw"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(x)</a>
<a class="sourceLine" id="cb5-19" title="19"><span class="co">#&gt; [1] 50</span></a>
<a class="sourceLine" id="cb5-20" title="20"></a>
<a class="sourceLine" id="cb5-21" title="21"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb5-22" title="22">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="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
<a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<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>
<a class="sourceLine" id="cb5-25" title="25"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#&gt; mo_fullname(x) 679 731 768 762 779 886 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.76 seconds (762 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -303,11 +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">#&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 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>
<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 10.200 10.400 10.800 10.700 10.900 12.00 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 20.700 20.800 21.000 20.900 21.100 22.30 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.305 0.313 0.454 0.441 0.568 0.72 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>
<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>
@ -320,14 +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">#&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 0.704 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>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.366 0.446 0.563 0.523 0.681 0.785 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.365 0.453 0.598 0.661 0.682 0.859 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.369 0.477 0.633 0.646 0.674 1.150 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.283 0.337 0.455 0.464 0.609 0.611 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.309 0.333 0.422 0.393 0.527 0.606 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.280 0.316 0.457 0.466 0.557 0.676 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.283 0.328 0.422 0.359 0.535 0.638 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.295 0.339 0.402 0.368 0.460 0.562 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">
@ -354,13 +351,13 @@
<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 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>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 13.28 13.65 27.39 31.90 36.32 47.03 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 21.46 22.08 32.62 22.15 45.37 80.16 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 21.54 22.09 29.93 22.23 44.86 55.15 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 21.53 22.09 28.80 22.10 22.16 57.05 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 22.00 22.16 23.19 22.28 23.35 27.89 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 22.15 22.17 26.42 22.34 23.48 45.54 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 22.05 22.09 28.13 22.31 23.76 55.38 10</span></a></code></pre></div>
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