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(v1.1.0.9021) 1st isolates update

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dr. M.S. (Matthijs) Berends
2020-05-28 10:51:56 +02:00
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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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9021</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">25 May 2020</h4>
<h4 class="date">28 May 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -221,21 +221,36 @@
<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">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") 9.7 11.0 15 11.0 12.0 49 10</span>
<span class="co"># as.mo("stau") 130.0 150.0 180 170.0 190.0 270 10</span>
<span class="co"># as.mo("STAU") 130.0 130.0 140 140.0 150.0 170 10</span>
<span class="co"># as.mo("staaur") 7.9 9.6 15 11.0 12.0 40 10</span>
<span class="co"># as.mo("STAAUR") 9.1 9.4 16 11.0 12.0 41 10</span>
<span class="co"># as.mo("S. aureus") 8.5 11.0 12 12.0 13.0 16 10</span>
<span class="co"># as.mo("S aureus") 8.4 11.0 17 12.0 14.0 47 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 6.4 8.6 12 8.8 9.8 40 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 830.0 860.0 910 900.0 930.0 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 370.0 390.0 410 400.0 430.0 440 10</span>
<span class="co"># as.mo("MRSA") 9.2 9.5 16 11.0 11.0 63 10</span>
<span class="co"># as.mo("VISA") 22.0 22.0 36 26.0 54.0 59 10</span>
<span class="co"># as.mo("VRSA") 21.0 23.0 48 27.0 55.0 180 10</span>
<span class="co"># as.mo(22242419) 150.0 160.0 160 160.0 170.0 190 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 8.2 9.7 22.0 14.0 38.0 43</span>
<span class="co"># as.mo("stau") 130.0 130.0 160.0 170.0 170.0 190</span>
<span class="co"># as.mo("STAU") 120.0 130.0 150.0 150.0 180.0 190</span>
<span class="co"># as.mo("staaur") 8.3 9.1 13.0 9.4 10.0 40</span>
<span class="co"># as.mo("STAAUR") 8.0 9.3 15.0 10.0 13.0 35</span>
<span class="co"># as.mo("S. aureus") 9.3 11.0 26.0 14.0 15.0 120</span>
<span class="co"># as.mo("S aureus") 10.0 12.0 22.0 13.0 38.0 49</span>
<span class="co"># as.mo("Staphylococcus aureus") 6.6 7.7 8.5 8.6 9.1 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 820.0 860.0 890.0 880.0 930.0 1000</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 350.0 350.0 370.0 370.0 370.0 380</span>
<span class="co"># as.mo("MRSA") 7.8 9.1 13.0 10.0 11.0 42</span>
<span class="co"># as.mo("VISA") 11.0 12.0 19.0 13.0 15.0 47</span>
<span class="co"># as.mo("VRSA") 11.0 12.0 21.0 14.0 39.0 42</span>
<span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 150.0 190</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
<span class="co"># 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 +262,12 @@
<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") 152.700 163.100 172.10 171.40 176.20 213.80</span>
<span class="co"># as.mo("METSEM") 148.300 167.900 181.50 185.30 196.70 204.60</span>
<span class="co"># as.mo("M. semesiae") 8.610 9.468 13.88 10.05 15.28 35.20</span>
<span class="co"># as.mo("M. semesiae") 9.164 9.530 21.29 11.58 42.98 50.57</span>
<span class="co"># as.mo("Methanosarcina semesiae") 6.625 7.229 14.25 7.98 11.32 42.18</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 135.600 143.500 157.800 153.400 175.70 191.40</span>
<span class="co"># as.mo("METSEM") 139.700 140.800 158.100 148.300 176.10 188.50</span>
<span class="co"># as.mo("M. semesiae") 9.010 9.317 13.280 9.802 12.51 40.46</span>
<span class="co"># as.mo("M. semesiae") 9.155 9.321 9.665 9.557 10.07 10.37</span>
<span class="co"># as.mo("Methanosarcina semesiae") 6.737 7.160 16.020 8.413 33.21 37.10</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -292,8 +307,8 @@
<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) 1700 1760 1780 1770 1800 1880 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.77 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 1670 1740 1800 1790 1880 1900 10</span></pre></body></html></div>
<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>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -305,10 +320,10 @@
<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 5.640 5.890 10.300 6.580 6.850 44.400 10</span>
<span class="co"># B 11.000 11.300 11.500 11.400 11.500 12.400 10</span>
<span class="co"># C 0.217 0.238 0.271 0.267 0.298 0.383 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 5.630 5.900 6.420 6.480 6.910 7.120 10</span>
<span class="co"># B 9.940 11.300 15.000 11.800 12.300 45.300 10</span>
<span class="co"># C 0.247 0.277 0.315 0.295 0.358 0.386 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 0.0003 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>
<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>),
@ -322,14 +337,14 @@
<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 0.205 0.208 0.230 0.219 0.240 0.307 10</span>
<span class="co"># B 0.201 0.216 0.227 0.223 0.229 0.293 10</span>
<span class="co"># C 0.209 0.210 0.224 0.218 0.241 0.255 10</span>
<span class="co"># D 0.200 0.211 0.222 0.217 0.224 0.279 10</span>
<span class="co"># E 0.199 0.209 0.220 0.211 0.219 0.280 10</span>
<span class="co"># F 0.201 0.205 0.228 0.212 0.217 0.346 10</span>
<span class="co"># G 0.193 0.208 0.218 0.217 0.220 0.272 10</span>
<span class="co"># H 0.190 0.195 0.206 0.200 0.203 0.263 10</span></pre></body></html></div>
<span class="co"># A 0.207 0.214 0.241 0.218 0.240 0.412 10</span>
<span class="co"># B 0.178 0.207 0.215 0.211 0.219 0.272 10</span>
<span class="co"># C 0.218 0.221 0.234 0.233 0.240 0.264 10</span>
<span class="co"># D 0.203 0.211 0.221 0.214 0.218 0.290 10</span>
<span class="co"># E 0.208 0.209 0.223 0.214 0.227 0.279 10</span>
<span class="co"># F 0.172 0.203 0.222 0.212 0.222 0.302 10</span>
<span class="co"># G 0.200 0.202 0.212 0.208 0.213 0.253 10</span>
<span class="co"># H 0.193 0.194 0.208 0.200 0.215 0.261 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">
@ -356,13 +371,13 @@
<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 20.45 21.03 25.78 21.63 27.29 71.19 100</span>
<span class="co"># de 21.48 22.06 28.50 22.81 28.56 73.54 100</span>
<span class="co"># nl 25.11 26.21 33.48 27.31 35.01 81.28 100</span>
<span class="co"># es 21.59 22.20 29.02 23.05 30.33 73.83 100</span>
<span class="co"># it 21.46 22.05 28.45 22.79 29.45 64.36 100</span>
<span class="co"># fr 21.47 22.12 31.87 22.83 31.24 174.10 100</span>
<span class="co"># pt 21.53 22.22 27.19 22.91 25.67 71.87 100</span></pre></body></html></div>
<span class="co"># en 11.24 11.97 16.09 13.31 13.71 48.40 100</span>
<span class="co"># de 12.18 12.84 19.63 14.33 15.00 55.14 100</span>
<span class="co"># nl 16.24 17.07 24.36 18.61 19.83 55.70 100</span>
<span class="co"># es 12.23 12.77 17.38 13.71 14.72 51.57 100</span>
<span class="co"># it 12.15 13.01 18.55 14.03 14.81 146.90 100</span>
<span class="co"># fr 12.23 13.08 16.81 14.30 14.86 49.30 100</span>
<span class="co"># pt 12.30 12.85 18.13 14.24 14.88 49.70 100</span></pre></body></html></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>