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@ -187,7 +187,7 @@
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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">29 November 2019</h4>
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<h4 class="date">11 December 2019</h4>
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<div class="hidden name"><code>benchmarks.Rmd</code></div>
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@ -222,20 +222,20 @@
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<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
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<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 11 11 15 12 14 39 10</span></a>
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<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 36 38 49 48 60 65 10</span></a>
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<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 36 38 46 40 59 71 10</span></a>
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<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 11 11 21 11 37 37 10</span></a>
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<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 11 11 12 12 12 17 10</span></a>
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<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 26 29 36 32 48 53 10</span></a>
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<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 25 27 37 29 52 64 10</span></a>
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<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 33 34 39 36 45 53 10</span></a>
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<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 660 720 740 740 760 800 10</span></a>
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<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 350 360 410 380 400 660 10</span></a>
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<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 11 11 14 12 12 36 10</span></a>
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<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 21 23 27 26 28 47 10</span></a>
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<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 21 22 30 23 44 52 10</span></a>
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<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 20 20 24 21 21 52 10</span></a></code></pre></div>
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<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 11 11 15 11 14 33 10</span></a>
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<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 34 38 47 43 58 65 10</span></a>
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<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 34 37 45 39 59 65 10</span></a>
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<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 10 12 30 12 37 120 10</span></a>
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<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 11 11 20 12 34 45 10</span></a>
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<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 26 27 34 30 34 54 10</span></a>
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<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 26 27 44 28 28 160 10</span></a>
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<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 32 34 37 35 41 44 10</span></a>
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<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 640 690 710 700 720 810 10</span></a>
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<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 340 370 390 380 400 470 10</span></a>
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<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 11 11 14 12 12 35 10</span></a>
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<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 22 23 33 26 46 51 10</span></a>
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<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 20 22 25 24 26 43 10</span></a>
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<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 20 25 37 36 49 55 10</span></a></code></pre></div>
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<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="562.5"></p>
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<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
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<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
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@ -247,19 +247,19 @@
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<a class="sourceLine" id="cb3-6" data-line-number="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
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<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq max</span></a>
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<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1501.0 1506.00 1665.0 1569.00 1788.00 2141.00</span></a>
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<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1586.0 1610.00 1727.0 1675.00 1793.00 2002.00</span></a>
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<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 2266.0 2335.00 2587.0 2418.00 2524.00 3676.00</span></a>
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<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 2143.0 2252.00 2334.0 2331.00 2396.00 2540.00</span></a>
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<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 34.8 35.74 46.3 39.64 62.28 65.83</span></a>
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<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq max</span></a>
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<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1455.00 1534.00 1589.00 1546.00 1642.0 1856.0</span></a>
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<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1504.00 1560.00 1570.00 1568.00 1581.0 1668.0</span></a>
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<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 2262.00 2295.00 2338.00 2321.00 2361.0 2536.0</span></a>
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<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 2243.00 2261.00 2304.00 2302.00 2334.0 2397.0</span></a>
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<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 33.36 35.01 43.82 39.71 47.8 68.4</span></a>
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<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># neval</span></a>
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<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 10</span></a>
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<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 10</span></a>
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<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 10</span></a>
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<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 10</span></a>
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<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 10</span></a></code></pre></div>
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<p>That takes 15.6 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. Full names (like <em>Methanosarcina semesiae</em>) are almost fast - these are the most probable input from most data sets.</p>
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<p>That takes 14.9 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>Methanosarcina semesiae</em>) are almost fast - these are the most probable input from most data sets.</p>
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<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
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<p><img src="benchmarks_files/figure-html/unnamed-chunk-9-1.png" width="562.5"></p>
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<p>In reality, the <code><a href="../reference/as.mo.html">as.mo()</a></code> functions <strong>learns from its own output to speed up determinations for next times</strong>. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use <code><a href="../reference/as.mo.html">as.mo()</a></code> yourself:</p>
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@ -296,8 +296,8 @@
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<a class="sourceLine" id="cb4-24" data-line-number="24"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
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<a class="sourceLine" id="cb4-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 655 668 715 717 751 797 10</span></a></code></pre></div>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.72 seconds (717 ms). You only lose time on your unique input values.</p>
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<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 647 669 689 685 701 770 10</span></a></code></pre></div>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.69 seconds (685 ms). You only lose time on your unique input values.</p>
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</div>
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<div id="precalculated-results" class="section level3">
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<h3 class="hasAnchor">
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@ -309,11 +309,11 @@
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<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
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<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.70 6.710 9.690 7.18 7.850 31.90 10</span></a>
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<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 26.20 27.100 32.400 28.80 32.100 58.80 10</span></a>
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<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.78 0.837 0.924 0.88 0.965 1.24 10</span></a></code></pre></div>
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<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0009 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>
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<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.440 6.560 11.00 7.210 8.75 44.10 10</span></a>
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<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 25.400 25.700 31.40 27.900 34.90 53.80 10</span></a>
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<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.816 0.878 1.05 0.991 1.24 1.37 10</span></a></code></pre></div>
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<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.001 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>
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<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">run_it <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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>
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<a class="sourceLine" id="cb6-2" data-line-number="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>
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<a class="sourceLine" id="cb6-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
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@ -326,14 +326,14 @@
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<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
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<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.444 0.449 0.473 0.460 0.466 0.630 10</span></a>
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<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.483 0.496 0.511 0.505 0.535 0.539 10</span></a>
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<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.709 0.839 0.850 0.846 0.886 0.921 10</span></a>
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<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.463 0.483 0.521 0.499 0.548 0.694 10</span></a>
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<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.433 0.451 0.493 0.484 0.513 0.611 10</span></a>
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<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.434 0.450 0.481 0.458 0.484 0.582 10</span></a>
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<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.434 0.443 0.471 0.455 0.489 0.577 10</span></a>
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<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.434 0.436 0.471 0.451 0.480 0.614 10</span></a></code></pre></div>
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<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.461 0.485 0.613 0.608 0.739 0.775 10</span></a>
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||||
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.505 0.521 0.641 0.552 0.594 1.120 10</span></a>
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||||
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.759 0.846 1.040 0.870 1.270 1.680 10</span></a>
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<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.495 0.502 0.536 0.505 0.532 0.667 10</span></a>
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||||
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.459 0.470 0.549 0.478 0.510 0.830 10</span></a>
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||||
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.457 0.460 0.545 0.469 0.615 0.788 10</span></a>
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||||
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.455 0.474 0.572 0.516 0.694 0.830 10</span></a>
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<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.457 0.466 0.551 0.472 0.545 1.030 10</span></a></code></pre></div>
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<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>
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</div>
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<div id="results-in-other-languages" class="section level3">
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@ -360,13 +360,13 @@
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<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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>
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<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
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||||
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 22.05 22.65 29.93 25.35 27.03 53.36 10</span></a>
|
||||
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 22.86 23.16 30.45 27.22 28.33 62.68 10</span></a>
|
||||
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 28.99 29.69 34.37 30.32 31.78 65.15 10</span></a>
|
||||
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 22.45 23.17 30.84 23.73 28.02 64.67 10</span></a>
|
||||
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 22.76 24.59 30.36 26.23 29.97 66.70 10</span></a>
|
||||
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 23.00 24.20 30.70 27.00 29.22 51.23 10</span></a>
|
||||
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 23.31 24.41 26.92 27.31 28.39 31.00 10</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 20.61 21.92 22.93 22.53 24.17 26.26 10</span></a>
|
||||
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 22.19 22.61 28.83 23.28 28.22 51.89 10</span></a>
|
||||
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 27.45 28.26 29.07 29.34 29.78 30.03 10</span></a>
|
||||
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 22.05 23.69 30.82 28.10 30.51 51.22 10</span></a>
|
||||
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 23.00 24.39 31.27 27.07 33.34 49.78 10</span></a>
|
||||
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 22.13 23.03 26.94 23.83 25.55 52.39 10</span></a>
|
||||
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 22.43 24.94 33.02 28.38 45.69 49.11 10</span></a></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user