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(v0.7.1.9005) new rsi calculations, atc class removal
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@ -40,7 +40,7 @@
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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">0.7.1.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
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</span>
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</div>
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@ -192,7 +192,7 @@
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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">23 June 2019</h4>
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<h4 class="date">01 July 2019</h4>
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<div class="hidden name"><code>benchmarks.Rmd</code></div>
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@ -217,14 +217,14 @@
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<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
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<a class="sourceLine" id="cb2-10" title="10"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 17.0 18.0 22.0 18.0 18.0 61.0 10</span></a>
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<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 66.0 66.0 75.0 66.0 68.0 110.0 10</span></a>
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<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 17.0 18.0 18.0 18.0 18.0 18.0 10</span></a>
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<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18.0 18.0 32.0 18.0 54.0 80.0 10</span></a>
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<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 52.0 53.0 57.0 53.0 53.0 96.0 10</span></a>
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<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 52.0 53.0 78.0 53.0 110.0 150.0 10</span></a>
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<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8.1 8.1 8.2 8.2 8.2 8.3 10</span></a></code></pre></div>
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<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18.0 18.0 22 18.0 18.0 61 10</span></a>
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<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 65.0 65.0 70 66.0 66.0 110 10</span></a>
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<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 18.0 18.0 33 18.0 62.0 81 10</span></a>
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<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18.0 18.0 18 18.0 18.0 19 10</span></a>
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<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 52.0 52.0 61 52.0 53.0 97 10</span></a>
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<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 52.0 52.0 71 53.0 97.0 150 10</span></a>
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<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8.1 8.1 14 8.1 8.2 63 10</span></a></code></pre></div>
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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>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
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<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
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@ -237,10 +237,10 @@
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<a class="sourceLine" id="cb3-8" title="8"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb3-9" title="9"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 390 390 420 440 440 440 10</span></a>
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<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 390 390 420 440 440 450 10</span></a>
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<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 210 250 250 250 260 270 10</span></a>
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<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 210 210 240 220 250 410 10</span></a>
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<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 72 72 82 72 73 120 10</span></a></code></pre></div>
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<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 390 390 410 400 440 440 10</span></a>
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<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 210 210 230 220 250 270 10</span></a>
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<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 210 210 240 260 260 280 10</span></a>
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<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 72 72 92 73 120 130 10</span></a></code></pre></div>
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<p>That takes 6.8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
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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>Thermus islandicus</em> (which is very uncommon):</p>
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<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
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@ -287,8 +287,8 @@
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<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
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<a class="sourceLine" id="cb5-25" title="25"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb5-26" title="26"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1120 1140 1190 1180 1210 1260 10</span></a></code></pre></div>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.18 seconds (1182 ms). You only lose time on your unique input values.</p>
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<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1050 1050 1100 1090 1120 1230 10</span></a></code></pre></div>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.09 seconds (1092 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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@ -300,11 +300,11 @@
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<a class="sourceLine" id="cb6-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
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<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
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<a class="sourceLine" id="cb6-6" title="6"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 12.90 13.1 18.50 13.60 13.90 63.60 10</span></a>
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<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 49.90 50.1 52.20 51.10 52.20 62.60 10</span></a>
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<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.49 1.7 1.76 1.73 1.96 1.98 10</span></a></code></pre></div>
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<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0017 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="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 13.00 13.20 13.60 13.60 14.00 14.40 10</span></a>
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<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 49.40 50.00 57.50 51.90 52.40 103.00 10</span></a>
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<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.52 1.72 1.81 1.78 1.98 1.99 10</span></a></code></pre></div>
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<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0018 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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
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<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
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<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
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@ -317,14 +317,14 @@
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<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
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<a class="sourceLine" id="cb7-11" title="11"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb7-12" title="12"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.518 0.544 0.630 0.620 0.683 0.752 10</span></a>
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<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.548 0.650 0.695 0.703 0.728 0.855 10</span></a>
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<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.530 1.600 1.750 1.780 1.880 1.950 10</span></a>
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<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.541 0.640 0.690 0.665 0.728 0.857 10</span></a>
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<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.496 0.545 0.610 0.612 0.680 0.754 10</span></a>
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<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.523 0.547 0.613 0.580 0.701 0.756 10</span></a>
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<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.528 0.547 0.586 0.568 0.600 0.743 10</span></a>
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<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.547 0.553 0.634 0.609 0.670 0.864 10</span></a></code></pre></div>
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<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.612 0.623 0.685 0.653 0.789 0.814 10</span></a>
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<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.556 0.575 0.680 0.671 0.689 0.958 10</span></a>
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<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.520 1.710 1.800 1.820 1.950 1.970 10</span></a>
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<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.547 0.665 0.723 0.688 0.811 0.997 10</span></a>
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<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.490 0.541 0.633 0.629 0.748 0.756 10</span></a>
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<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.482 0.569 0.612 0.590 0.663 0.756 10</span></a>
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<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.551 0.558 0.601 0.586 0.632 0.735 10</span></a>
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<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.494 0.564 0.595 0.575 0.608 0.757 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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@ -351,13 +351,13 @@
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<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
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<a class="sourceLine" id="cb8-19" title="19"><span class="co"># Unit: milliseconds</span></a>
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<a class="sourceLine" id="cb8-20" title="20"><span class="co"># expr min lq mean median uq max neval</span></a>
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<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 43.34 43.72 43.76 43.82 43.93 43.98 10</span></a>
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<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 45.77 45.82 46.40 45.90 46.21 50.16 10</span></a>
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<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 59.12 59.39 60.61 59.81 60.97 65.36 10</span></a>
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<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 45.35 45.70 55.58 46.30 50.91 90.30 10</span></a>
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<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 45.54 45.72 47.36 46.02 46.23 57.97 10</span></a>
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<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 45.44 45.68 55.49 45.91 46.30 97.86 10</span></a>
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<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 45.60 45.68 52.57 45.79 46.17 110.10 10</span></a></code></pre></div>
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<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 43.00 43.12 45.51 44.82 44.89 56.61 10</span></a>
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<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 46.47 46.99 52.11 47.57 48.11 93.77 10</span></a>
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<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 60.86 62.72 67.57 63.69 63.99 108.20 10</span></a>
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<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 45.74 46.05 52.37 46.42 47.98 103.00 10</span></a>
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<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 45.84 45.89 51.90 47.66 47.73 94.83 10</span></a>
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<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 45.97 46.92 47.44 47.76 47.86 48.49 10</span></a>
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<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 45.93 46.77 47.36 47.77 47.93 48.12 10</span></a></code></pre></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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