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(v1.3.0) small MIC fix

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dr. M.S. (Matthijs) Berends
2020-07-30 12:37:01 +02:00
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commit 8ff46eefe9
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@ -39,7 +39,7 @@
</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="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">24 July 2020</h4>
<h4 class="date">30 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -222,20 +222,20 @@
<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>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 11 13 16 14 15 38 10</span>
<span class="co"># as.mo("stau") 170 170 180 180 190 200 10</span>
<span class="co"># as.mo("STAU") 160 170 190 190 200 210 10</span>
<span class="co"># as.mo("staaur") 12 13 15 14 15 20 10</span>
<span class="co"># as.mo("STAAUR") 13 14 17 15 15 38 10</span>
<span class="co"># as.mo("S. aureus") 13 14 23 17 36 42 10</span>
<span class="co"># as.mo("S aureus") 14 15 31 25 43 82 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 11 11 17 12 14 42 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 920 940 960 950 970 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 420 440 460 460 460 500 10</span>
<span class="co"># as.mo("MRSA") 13 14 20 14 16 43 10</span>
<span class="co"># as.mo("VISA") 15 15 28 27 40 42 10</span>
<span class="co"># as.mo("VRSA") 13 15 18 15 17 45 10</span>
<span class="co"># as.mo(22242419) 130 140 150 150 170 180 10</span></pre></body></html></div>
<span class="co"># as.mo("sau") 11 12 17 13 15 51 10</span>
<span class="co"># as.mo("stau") 150 160 170 170 190 200 10</span>
<span class="co"># as.mo("STAU") 160 160 180 190 190 210 10</span>
<span class="co"># as.mo("staaur") 12 13 23 15 20 68 10</span>
<span class="co"># as.mo("STAAUR") 11 12 20 16 18 44 10</span>
<span class="co"># as.mo("S. aureus") 11 13 29 17 44 84 10</span>
<span class="co"># as.mo("S aureus") 11 15 21 16 18 46 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 11 13 16 13 15 41 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870 890 920 900 950 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 400 410 430 440 450 490 10</span>
<span class="co"># as.mo("MRSA") 13 13 17 14 16 40 10</span>
<span class="co"># as.mo("VISA") 14 17 25 19 36 46 10</span>
<span class="co"># as.mo("VRSA") 13 15 21 17 21 50 10</span>
<span class="co"># as.mo(22242419) 130 140 150 150 150 180 10</span></pre></body></html></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></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 100 milliseconds, this is only 10 input values per second.</p>
<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>
@ -247,12 +247,12 @@
<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">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>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 180.20 190.40 199.00 199.10 204.40 218.80</span>
<span class="co"># as.mo("METSEM") 190.00 191.50 203.30 193.70 221.00 236.30</span>
<span class="co"># as.mo("M. semesiae") 11.60 12.58 15.84 13.42 14.40 37.45</span>
<span class="co"># as.mo("M. semesiae") 12.14 12.59 19.44 14.19 14.78 43.90</span>
<span class="co"># as.mo("Methanosarcina semesiae") 10.65 10.78 16.81 12.13 14.08 37.01</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 176.800 179.200 189.20 185.90 194.00 212.60</span>
<span class="co"># as.mo("METSEM") 164.400 170.800 193.00 188.20 211.10 243.00</span>
<span class="co"># as.mo("M. semesiae") 10.950 11.310 19.92 15.41 18.79 50.84</span>
<span class="co"># as.mo("M. semesiae") 11.560 11.860 17.66 14.15 16.96 50.76</span>
<span class="co"># as.mo("Methanosarcina semesiae") 9.408 9.669 18.03 14.12 15.24 42.57</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -292,8 +292,8 @@
<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) 1840 1850 1910 1900 1950 2020 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.9 seconds. You only lose time on your unique input values.</p>
<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">
@ -306,9 +306,9 @@
<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 8.08 8.52 8.94 8.57 9.49 10.50 10</span>
<span class="co"># B 10.40 10.70 14.60 11.00 11.70 45.70 10</span>
<span class="co"># C 1.04 1.10 1.19 1.15 1.29 1.46 10</span></pre></body></html></div>
<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">&lt;-</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>),
@ -321,15 +321,15 @@
<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 0.862 1.030 1.070 1.060 1.08 1.33 10</span>
<span class="co"># B 0.837 1.020 1.010 1.030 1.05 1.13 10</span>
<span class="co"># C 0.836 0.936 0.993 1.020 1.03 1.17 10</span>
<span class="co"># D 0.838 0.947 1.030 1.050 1.10 1.31 10</span>
<span class="co"># E 0.807 0.906 0.994 1.010 1.03 1.28 10</span>
<span class="co"># F 0.804 0.920 1.060 1.040 1.11 1.54 10</span>
<span class="co"># G 0.805 0.906 1.000 1.030 1.07 1.25 10</span>
<span class="co"># H 0.792 0.805 0.949 0.941 1.04 1.29 10</span></pre></body></html></div>
<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">
@ -355,14 +355,14 @@
<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 12.45 16.18 12.63 13.57 48.69 100</span>
<span class="co"># de 13.01 13.51 16.67 13.82 15.26 48.22 100</span>
<span class="co"># nl 16.88 17.25 19.13 17.54 18.36 51.99 100</span>
<span class="co"># es 13.13 13.42 18.26 13.69 14.59 53.66 100</span>
<span class="co"># it 13.01 13.35 17.33 13.71 15.16 50.65 100</span>
<span class="co"># fr 13.13 13.40 16.31 13.64 13.88 49.44 100</span>
<span class="co"># pt 13.17 13.38 15.10 13.54 13.94 49.61 100</span></pre></body></html></div>
<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>
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