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@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9005</span>
</span>
</div>
@ -185,7 +185,7 @@
</header><div class="row">
</header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Benchmarks</h1>
@ -202,7 +202,7 @@
<p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/joshuaulrich/microbenchmark/" class="external-link">microbenchmark</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></code></pre></div>
<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>
<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>, its taxonomic kingdom).</p>
@ -222,23 +222,23 @@
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 10.0 12.0 20.0 12.0 15.0 53 25</span>
<span class="co"># as.mo("stau") 49.0 54.0 72.0 58.0 91.0 97 25</span>
<span class="co"># as.mo("STAU") 50.0 54.0 71.0 57.0 90.0 110 25</span>
<span class="co"># as.mo("staaur") 10.0 12.0 17.0 12.0 14.0 51 25</span>
<span class="co"># as.mo("STAAUR") 10.0 12.0 17.0 12.0 14.0 54 25</span>
<span class="co"># as.mo("S. aureus") 26.0 27.0 40.0 31.0 56.0 74 25</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 39.0 29.0 58.0 68 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.5 3.9 6.6 4.1 4.8 38 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 230.0 240.0 250.0 240.0 250.0 280 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0 190.0 200.0 290 25</span>
<span class="co"># as.mo("MRSA") 11.0 12.0 19.0 13.0 14.0 50 25</span>
<span class="co"># as.mo("VISA") 21.0 22.0 32.0 25.0 50.0 60 25</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 20.0 20.0 25.0 20.0 21 57 25</span>
<span class="co"># as.mo("stau") 94.0 94.0 110.0 95.0 130 130 25</span>
<span class="co"># as.mo("STAU") 94.0 95.0 110.0 130.0 130 130 25</span>
<span class="co"># as.mo("staaur") 20.0 20.0 28.0 20.0 21 58 25</span>
<span class="co"># as.mo("STAAUR") 20.0 20.0 25.0 20.0 21 57 25</span>
<span class="co"># as.mo("S. aureus") 56.0 56.0 72.0 57.0 92 97 25</span>
<span class="co"># as.mo("S aureus") 55.0 56.0 66.0 56.0 75 93 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 5.7 5.8 7.3 5.9 6 41 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 370.0 370.0 390.0 380.0 410 410 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 260.0 290.0 300.0 290.0 300 330 25</span>
<span class="co"># as.mo("MRSA") 20.0 20.0 23.0 20.0 20 56 25</span>
<span class="co"># as.mo("VISA") 34.0 35.0 48.0 35.0 35 220 25</span></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></p>
<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 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 47 times slower to determine.</p>
<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 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 65 times slower to determine.</p>
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div class="section level3">
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
@ -258,8 +258,8 @@
<span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># Class &lt;mo&gt;</span>
<span class="co"># [1] B_STPHY_AURS B_STRPT_EQNS B_KLBSL_PNMN B_STPHY_EPDR B_STPHY_AURS</span>
<span class="co"># [6] B_CRYNB_STRT</span>
<span class="co"># [1] B_PROTS_MRBL B_STPHY_CONS B_ESCHR_COLI B_PSDMN_AERG B_ENTRC_FCLS</span>
<span class="co"># [6] B_STPHY_AURS</span>
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -272,11 +272,11 @@
<span class="co"># now let's see:</span>
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</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) 196 209 274 223 364 388 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.223 seconds. That is 112 nanoseconds on average. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 265 269 357 298 471 516 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.298 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
</div>
<div class="section level3">
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
@ -287,13 +287,13 @@
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 8.00 9.16 9.19 9.28 9.46 9.73 10</span>
<span class="co"># B 23.40 27.20 32.60 27.90 28.10 80.20 10</span>
<span class="co"># C 1.85 2.25 2.40 2.47 2.62 2.90 10</span></code></pre></div>
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0025 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>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 12.30 12.30 12.60 12.50 12.60 14.2 10</span>
<span class="co"># B 61.70 61.90 62.70 62.40 62.50 66.2 10</span>
<span class="co"># C 3.04 3.05 6.92 3.12 3.21 40.9 10</span></code></pre></div>
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0031 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="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -304,17 +304,17 @@
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.76 1.80 2.07 1.95 2.26 2.90 10</span>
<span class="co"># B 1.69 1.73 1.90 1.81 2.03 2.48 10</span>
<span class="co"># C 1.71 1.77 1.92 1.91 2.05 2.17 10</span>
<span class="co"># D 1.68 1.71 1.76 1.76 1.82 1.88 10</span>
<span class="co"># E 1.68 1.70 1.89 1.89 2.04 2.26 10</span>
<span class="co"># F 1.67 1.75 1.93 1.89 2.11 2.35 10</span>
<span class="co"># G 1.70 1.76 1.97 1.88 2.12 2.43 10</span>
<span class="co"># H 1.67 1.71 1.83 1.75 1.98 2.14 10</span></code></pre></div>
<span class="co"># A 3.02 3.09 3.22 3.10 3.46 3.55 10</span>
<span class="co"># B 3.03 3.04 3.21 3.12 3.42 3.48 10</span>
<span class="co"># C 3.03 3.05 3.08 3.06 3.12 3.16 10</span>
<span class="co"># D 2.98 3.01 3.17 3.09 3.40 3.47 10</span>
<span class="co"># E 3.01 3.06 3.19 3.12 3.43 3.43 10</span>
<span class="co"># F 2.95 2.99 3.11 3.05 3.16 3.46 10</span>
<span class="co"># G 2.94 3.06 3.19 3.13 3.41 3.54 10</span>
<span class="co"># H 2.93 3.01 3.12 3.08 3.19 3.42 10</span></code></pre></div>
<p>Of course, when running <code>mo_phylum("Firmicutes")</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 contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
</div>
<div class="section level3">
@ -347,19 +347,19 @@
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># da 1.9470 2.0220 2.190 2.0720 2.358 3.234 100</span>
<span class="co"># de 1.9560 2.0330 3.649 2.1610 2.401 50.670 100</span>
<span class="co"># en 0.8937 0.9124 1.022 0.9776 1.120 1.748 100</span>
<span class="co"># es 1.9710 2.0290 2.216 2.1000 2.391 3.109 100</span>
<span class="co"># fr 1.8280 1.8960 3.214 1.9420 2.237 71.550 100</span>
<span class="co"># it 1.9370 1.9970 2.163 2.0610 2.339 3.210 100</span>
<span class="co"># nl 1.9710 2.0280 2.698 2.1110 2.421 49.340 100</span>
<span class="co"># pt 1.8920 1.9600 2.119 2.0200 2.261 3.265 100</span>
<span class="co"># ru 1.8630 1.9420 2.779 2.0270 2.335 66.660 100</span>
<span class="co"># sv 1.8680 1.9190 4.062 1.9890 2.263 78.870 100</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># da 3.579 3.689 3.811 3.737 3.894 4.626 100</span>
<span class="co"># de 3.600 3.694 4.205 3.750 3.869 43.820 100</span>
<span class="co"># en 1.686 1.720 1.828 1.766 1.822 2.244 100</span>
<span class="co"># es 3.618 3.688 4.633 3.772 4.083 43.890 100</span>
<span class="co"># fr 3.493 3.602 4.104 3.658 3.785 41.860 100</span>
<span class="co"># it 3.543 3.628 4.152 3.702 3.810 44.040 100</span>
<span class="co"># nl 3.625 3.716 5.024 3.763 3.924 44.220 100</span>
<span class="co"># pt 3.510 3.610 3.742 3.684 3.861 4.096 100</span>
<span class="co"># ru 3.568 3.680 4.534 3.742 3.871 41.170 100</span>
<span class="co"># sv 3.585 3.664 3.833 3.748 4.046 4.987 100</span></code></pre></div>
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
</div>
</div>
@ -379,7 +379,7 @@
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