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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">30 July 2020</h4>
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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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<p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
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<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code>microbenchmark()</code> runs different input expressions independently of each other and measures their time-to-result.</p>
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<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">microbenchmark</span> <span class="kw"><-</span> <span class="kw pkg">microbenchmark</span><span class="kw ns">::</span><span class="no"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>
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<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">AMR</span>)
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<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">dplyr</span>)</pre></body></html></div>
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<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
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<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
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<p>But the calculation time differs a lot:</p>
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<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">S.aureus</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span>
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"stau"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAU"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"staaur"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"STAAUR"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S aureus"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>), <span class="co"># official taxonomic name</span>
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus (MRSA)"</span>), <span class="co"># additional text</span>
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Sthafilokkockus aaureuz"</span>), <span class="co"># incorrect spelling</span>
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>), <span class="co"># Methicillin Resistant S. aureus</span>
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VISA"</span>), <span class="co"># Vancomycin Intermediate S. aureus</span>
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"VRSA"</span>), <span class="co"># Vancomycin Resistant S. aureus</span>
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fl">22242419</span>), <span class="co"># Catalogue of Life ID</span>
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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 neval</span>
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<span class="co"># as.mo("sau") 11 12 17 13 15 51 10</span>
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<span class="co"># as.mo("stau") 150 160 170 170 190 200 10</span>
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<span class="co"># as.mo("STAU") 160 160 180 190 190 210 10</span>
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<span class="co"># as.mo("staaur") 12 13 23 15 20 68 10</span>
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<span class="co"># as.mo("STAAUR") 11 12 20 16 18 44 10</span>
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<span class="co"># as.mo("S. aureus") 11 13 29 17 44 84 10</span>
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<span class="co"># as.mo("S aureus") 11 15 21 16 18 46 10</span>
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<span class="co"># as.mo("Staphylococcus aureus") 11 13 16 13 15 41 10</span>
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<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870 890 920 900 950 1100 10</span>
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<span class="co"># as.mo("Sthafilokkockus aaureuz") 400 410 430 440 450 490 10</span>
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<span class="co"># as.mo("MRSA") 13 13 17 14 16 40 10</span>
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<span class="co"># as.mo("VISA") 14 17 25 19 36 46 10</span>
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<span class="co"># as.mo("VRSA") 13 15 21 17 21 50 10</span>
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<span class="co"># as.mo(22242419) 130 140 150 150 150 180 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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<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">M.semesiae</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),
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<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Methanosarcina semesiae"</span>),
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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") 176.800 179.200 189.20 185.90 194.00 212.60</span>
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<span class="co"># as.mo("METSEM") 164.400 170.800 193.00 188.20 211.10 243.00</span>
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<span class="co"># as.mo("M. semesiae") 10.950 11.310 19.92 15.41 18.79 50.84</span>
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<span class="co"># as.mo("M. semesiae") 11.560 11.860 17.66 14.15 16.96 50.76</span>
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<span class="co"># as.mo("Methanosarcina semesiae") 9.408 9.669 18.03 14.12 15.24 42.57</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></pre></body></html></div>
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<p>Looking up arbitrary codes of less prevalent microorganisms costs the most time. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they 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-6-1.png" width="900"></p>
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<p>Uncommon microorganisms take some more time than common microorganisms. To further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
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<div id="repetitive-results" class="section level3">
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<h3 class="hasAnchor">
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<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
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<p>Repetitive results are unique values that 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_name()</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>
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<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="co"># take all MO codes from the example_isolates data set</span>
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<span class="no">x</span> <span class="kw"><-</span> <span class="no">example_isolates</span>$<span class="no">mo</span> <span class="kw">%>%</span>
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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://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://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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<span class="co"># [1] 500000</span>
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<span class="co"># and how many unique values do we have?</span>
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html">n_distinct</a></span>(<span class="no">x</span>)
|
||
<span class="co"># [1] 50</span>
|
||
|
||
<span class="co"># now let's see:</span>
|
||
<span class="no">run_it</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="no">x</span>),
|
||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||
<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>)
|
||
<span class="co"># Unit: milliseconds</span>
|
||
<span class="co"># expr min lq mean median uq max neval</span>
|
||
<span class="co"># mo_name(x) 1720 1760 1820 1800 1830 1990 10</span></pre></body></html></div>
|
||
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.8 seconds. You only lose time on your unique input values.</p>
|
||
</div>
|
||
<div id="precalculated-results" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#precalculated-results" class="anchor"></a>Precalculated results</h3>
|
||
<p>What about precalculated results? If the input is an already precalculated result of a helper function like <code><a href="../reference/mo_property.html">mo_name()</a></code>, it almost doesn’t take any time at all (see ‘C’ below):</p>
|
||
<div class="sourceCode" id="cb5"><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_name</a></span>(<span class="st">"B_STPHY_AURS"</span>),
|
||
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"S. aureus"</span>),
|
||
<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>),
|
||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||
<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>)
|
||
<span class="co"># Unit: milliseconds</span>
|
||
<span class="co"># expr min lq mean median uq max neval</span>
|
||
<span class="co"># A 8.16 8.35 9.06 8.97 9.75 10.20 10</span>
|
||
<span class="co"># B 10.50 10.60 15.50 12.20 12.80 49.90 10</span>
|
||
<span class="co"># C 1.04 1.15 1.21 1.19 1.27 1.53 10</span></pre></body></html></div>
|
||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0012 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="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>),
|
||
<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>),
|
||
<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>),
|
||
<span class="kw">D</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),
|
||
<span class="kw">E</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),
|
||
<span class="kw">F</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),
|
||
<span class="kw">G</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),
|
||
<span class="kw">H</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),
|
||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
|
||
<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>)
|
||
<span class="co"># Unit: milliseconds</span>
|
||
<span class="co"># expr min lq mean median uq max neval</span>
|
||
<span class="co"># A 0.948 0.971 1.14 1.020 1.39 1.52 10</span>
|
||
<span class="co"># B 0.968 1.040 1.22 1.190 1.41 1.56 10</span>
|
||
<span class="co"># C 0.979 1.020 1.31 1.260 1.58 1.66 10</span>
|
||
<span class="co"># D 0.964 1.010 1.24 1.190 1.45 1.83 10</span>
|
||
<span class="co"># E 0.977 0.995 1.15 1.030 1.40 1.45 10</span>
|
||
<span class="co"># F 0.878 0.982 1.11 1.010 1.37 1.43 10</span>
|
||
<span class="co"># G 0.929 0.961 1.18 1.000 1.43 1.58 10</span>
|
||
<span class="co"># H 0.901 0.967 1.09 0.998 1.35 1.40 10</span></pre></body></html></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> 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>
|
||
</div>
|
||
<div id="results-in-other-languages" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#results-in-other-languages" class="anchor"></a>Results in other languages</h3>
|
||
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
|
||
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>) <span class="co"># or just mo_name("CoNS") on an English system</span>
|
||
<span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>) <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
|
||
<span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span>
|
||
|
||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>) <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
|
||
<span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span>
|
||
|
||
<span class="no">run_it</span> <span class="kw"><-</span> <span class="fu">microbenchmark</span>(<span class="kw">en</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"en"</span>),
|
||
<span class="kw">de</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"de"</span>),
|
||
<span class="kw">nl</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"nl"</span>),
|
||
<span class="kw">es</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"es"</span>),
|
||
<span class="kw">it</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"it"</span>),
|
||
<span class="kw">fr</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"fr"</span>),
|
||
<span class="kw">pt</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="kw">language</span> <span class="kw">=</span> <span class="st">"pt"</span>),
|
||
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
|
||
<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>)
|
||
<span class="co"># Unit: milliseconds</span>
|
||
<span class="co"># expr min lq mean median uq max neval</span>
|
||
<span class="co"># en 12.09 12.46 15.90 13.86 14.55 57.62 100</span>
|
||
<span class="co"># de 12.92 13.26 19.73 14.63 16.01 61.55 100</span>
|
||
<span class="co"># nl 16.53 17.00 20.26 17.64 19.93 57.54 100</span>
|
||
<span class="co"># es 12.98 13.28 18.27 14.76 15.64 179.30 100</span>
|
||
<span class="co"># it 12.92 13.15 19.20 14.08 16.08 64.07 100</span>
|
||
<span class="co"># fr 12.99 13.21 17.81 13.59 15.71 67.97 100</span>
|
||
<span class="co"># pt 13.00 13.23 17.30 14.35 15.65 69.85 100</span></pre></body></html></div>
|
||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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