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@ -20,7 +20,7 @@
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<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script><meta property="og:title" content="Benchmarks">
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<meta property="og:description" content="AMR">
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@ -39,7 +39,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9030</span>
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</span>
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@ -157,8 +157,8 @@
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</ul>
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<ul class="nav navbar-nav navbar-right">
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<li>
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<a href="https://gitlab.com/msberends/AMR">
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<a href="https://github.com/msberends/AMR">
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Source Code
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@ -180,15 +180,15 @@
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</header><div class="row">
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</header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Benchmarks</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">28 May 2020</h4>
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<h4 class="date">09 July 2020</h4>
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<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
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<div class="hidden name"><code>benchmarks.Rmd</code></div>
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</div>
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@ -221,36 +221,21 @@
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<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
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<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">2</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max</span>
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<span class="co"># as.mo("sau") 8.5 11.0 17.0 12.0 12.0 43.0</span>
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<span class="co"># as.mo("stau") 120.0 130.0 150.0 140.0 160.0 180.0</span>
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<span class="co"># as.mo("STAU") 130.0 140.0 150.0 150.0 160.0 170.0</span>
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<span class="co"># as.mo("staaur") 7.7 9.1 13.0 11.0 12.0 38.0</span>
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<span class="co"># as.mo("STAAUR") 8.3 9.3 15.0 10.0 11.0 37.0</span>
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<span class="co"># as.mo("S. aureus") 11.0 12.0 18.0 13.0 14.0 41.0</span>
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<span class="co"># as.mo("S aureus") 8.8 11.0 17.0 12.0 13.0 41.0</span>
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<span class="co"># as.mo("Staphylococcus aureus") 6.4 6.6 7.4 7.6 7.8 9.1</span>
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<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 810.0 870.0 890.0 890.0 900.0 1000.0</span>
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<span class="co"># as.mo("Sthafilokkockus aaureuz") 320.0 340.0 370.0 350.0 400.0 490.0</span>
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<span class="co"># as.mo("MRSA") 9.2 10.0 13.0 11.0 12.0 37.0</span>
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<span class="co"># as.mo("VISA") 12.0 12.0 22.0 13.0 43.0 44.0</span>
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<span class="co"># as.mo("VRSA") 11.0 13.0 21.0 14.0 38.0 41.0</span>
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<span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 170.0 200.0</span>
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<span class="co"># neval</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span></pre></body></html></div>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># as.mo("sau") 9.9 14 22 15 36 48 10</span>
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<span class="co"># as.mo("stau") 160.0 160 180 170 210 210 10</span>
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<span class="co"># as.mo("STAU") 160.0 160 180 170 200 210 10</span>
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<span class="co"># as.mo("staaur") 9.5 13 14 14 16 17 10</span>
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<span class="co"># as.mo("STAAUR") 9.7 11 13 13 15 19 10</span>
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<span class="co"># as.mo("S. aureus") 12.0 13 17 15 18 35 10</span>
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<span class="co"># as.mo("S aureus") 11.0 16 26 19 42 43 10</span>
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<span class="co"># as.mo("Staphylococcus aureus") 8.7 11 19 13 14 55 10</span>
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<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 890.0 910 930 920 950 1000 10</span>
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<span class="co"># as.mo("Sthafilokkockus aaureuz") 420.0 430 450 440 470 510 10</span>
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<span class="co"># as.mo("MRSA") 9.8 10 13 12 14 19 10</span>
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<span class="co"># as.mo("VISA") 12.0 14 33 18 43 120 10</span>
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<span class="co"># as.mo("VRSA") 12.0 15 24 17 37 48 10</span>
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<span class="co"># as.mo(22242419) 140.0 150 150 150 150 180 10</span></pre></body></html></div>
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<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.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.</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 of this 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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@ -262,12 +247,12 @@
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<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
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<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max</span>
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<span class="co"># as.mo("metsem") 143.400 146.300 156.10 155.400 164.900 176.40</span>
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<span class="co"># as.mo("METSEM") 141.600 146.900 167.00 170.700 185.000 188.00</span>
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<span class="co"># as.mo("M. semesiae") 9.665 9.879 16.50 10.090 11.960 44.29</span>
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<span class="co"># as.mo("M. semesiae") 10.000 10.080 14.46 11.660 13.140 42.01</span>
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<span class="co"># as.mo("Methanosarcina semesiae") 7.161 7.389 10.40 7.542 9.294 33.00</span>
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<span class="co"># expr min lq mean median uq max</span>
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<span class="co"># as.mo("metsem") 169.600 189.900 199.30 199.70 211.00 223.90</span>
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<span class="co"># as.mo("METSEM") 170.000 186.900 197.40 191.80 210.70 232.30</span>
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<span class="co"># as.mo("M. semesiae") 11.330 11.620 12.37 12.21 13.20 13.78</span>
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<span class="co"># as.mo("M. semesiae") 11.410 12.090 15.74 12.48 13.55 43.19</span>
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<span class="co"># as.mo("Methanosarcina semesiae") 8.592 8.906 12.89 9.31 11.54 41.08</span>
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<span class="co"># neval</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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@ -287,11 +272,11 @@
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<span class="co"># keep only the unique ones</span>
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<span class="fu"><a href="https://rdrr.io/r/base/unique.html">unique</a></span>() <span class="kw">%>%</span>
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<span class="co"># pick 50 of them at random</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="fl">50</span>) <span class="kw">%>%</span>
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<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="fl">50</span>) <span class="kw">%>%</span>
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<span class="co"># paste that 10,000 times</span>
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<span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="fl">10000</span>) <span class="kw">%>%</span>
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<span class="co"># scramble it</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>()
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<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>()
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<span class="co"># got indeed 50 times 10,000 = half a million?</span>
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<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span>(<span class="no">x</span>)
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@ -307,8 +292,8 @@
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<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># mo_name(x) 1650 1730 1790 1790 1840 1900 10</span></pre></body></html></div>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.79 seconds. You only lose time on your unique input values.</p>
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<span class="co"># mo_name(x) 1610 1650 1680 1670 1710 1780 10</span></pre></body></html></div>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.67 seconds. 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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@ -320,11 +305,11 @@
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<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
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<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># A 5.680 5.820 9.61 6.36 6.850 39.500 10</span>
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<span class="co"># B 9.790 10.000 10.60 10.40 10.900 11.900 10</span>
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<span class="co"># C 0.229 0.259 0.27 0.27 0.286 0.311 10</span></pre></body></html></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 0.0003 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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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># A 8.15 8.69 9.63 9.05 10.40 12.40 10</span>
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<span class="co"># B 11.30 12.70 17.50 13.40 14.80 54.30 10</span>
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<span class="co"># C 1.04 1.17 1.28 1.28 1.38 1.59 10</span></pre></body></html></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 0.0013 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"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
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<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
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<span class="kw">C</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),
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@ -336,15 +321,15 @@
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<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
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<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># A 0.209 0.221 0.236 0.225 0.244 0.311 10</span>
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<span class="co"># B 0.197 0.201 0.215 0.212 0.222 0.266 10</span>
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<span class="co"># C 0.205 0.224 0.243 0.229 0.242 0.383 10</span>
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<span class="co"># D 0.199 0.207 0.216 0.211 0.214 0.270 10</span>
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<span class="co"># E 0.196 0.206 0.218 0.215 0.221 0.270 10</span>
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<span class="co"># F 0.188 0.197 0.212 0.210 0.216 0.269 10</span>
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<span class="co"># G 0.195 0.198 0.213 0.203 0.215 0.299 10</span>
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<span class="co"># H 0.184 0.193 0.205 0.201 0.207 0.252 10</span></pre></body></html></div>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># A 0.852 0.977 1.040 0.990 1.040 1.29 10</span>
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<span class="co"># B 0.802 0.933 1.070 0.994 1.160 1.65 10</span>
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<span class="co"># C 0.804 0.983 1.060 1.000 1.210 1.32 10</span>
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<span class="co"># D 0.783 0.855 0.996 0.989 1.030 1.36 10</span>
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<span class="co"># E 0.820 0.962 1.020 0.982 1.070 1.27 10</span>
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<span class="co"># F 0.770 0.785 0.937 0.953 0.996 1.30 10</span>
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<span class="co"># G 0.963 0.981 1.140 1.160 1.250 1.38 10</span>
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<span class="co"># H 0.778 0.842 0.985 0.977 0.995 1.30 10</span></pre></body></html></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> anyway, 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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@ -370,14 +355,14 @@
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<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
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<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># en 9.303 11.59 14.90 12.40 13.63 45.92 100</span>
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<span class="co"># de 10.080 12.39 15.77 13.11 14.45 46.27 100</span>
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<span class="co"># nl 13.200 16.26 20.88 17.80 19.52 49.93 100</span>
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<span class="co"># es 9.957 12.23 15.57 13.12 14.59 51.99 100</span>
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<span class="co"># it 10.210 12.44 19.02 13.34 14.74 52.96 100</span>
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<span class="co"># fr 10.040 12.40 18.90 13.26 15.07 54.40 100</span>
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<span class="co"># pt 10.450 12.67 16.91 13.46 14.68 51.47 100</span></pre></body></html></div>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># en 12.84 13.10 18.11 14.63 15.54 58.10 100</span>
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<span class="co"># de 13.58 14.02 18.05 14.61 16.58 69.21 100</span>
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<span class="co"># nl 17.07 17.89 22.36 18.97 20.85 68.70 100</span>
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<span class="co"># es 13.63 14.20 20.75 15.82 16.79 73.94 100</span>
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<span class="co"># it 13.64 13.95 16.95 15.40 16.57 50.96 100</span>
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<span class="co"># fr 13.74 14.12 19.84 15.81 16.62 61.13 100</span>
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<span class="co"># pt 13.58 14.02 19.00 14.90 16.49 53.41 100</span></pre></body></html></div>
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<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
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</div>
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</div>
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