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(v1.3.0.9002) intrinsic_resistant data set

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dr. M.S. (Matthijs) Berends
2020-08-14 13:36:10 +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">1.3.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 August 2020</h4>
<h4 class="date">14 August 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>
@ -224,21 +224,21 @@
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <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") 11.0 14 21 15 16 51 10</span>
<span class="co"># as.mo("stau") 170.0 170 190 190 210 240 10</span>
<span class="co"># as.mo("STAU") 160.0 170 180 180 200 210 10</span>
<span class="co"># as.mo("staaur") 11.0 13 19 14 18 48 10</span>
<span class="co"># as.mo("STAAUR") 11.0 13 22 17 37 40 10</span>
<span class="co"># as.mo("S. aureus") 15.0 15 24 17 26 56 10</span>
<span class="co"># as.mo("S aureus") 12.0 13 21 16 23 49 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 9.8 13 21 14 15 65 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 960.0 960 1100 980 1100 1400 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 440.0 450 480 470 480 570 10</span>
<span class="co"># as.mo("MRSA") 12.0 14 22 15 17 86 10</span>
<span class="co"># as.mo("VISA") 15.0 18 25 19 40 42 10</span>
<span class="co"># as.mo("VRSA") 14.0 15 30 22 44 69 10</span>
<span class="co"># as.mo(22242419) 130.0 150 160 170 180 190 10</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 9.1 11.0 21 11 13 77 10</span>
<span class="co"># as.mo("stau") 180.0 180.0 190 180 190 210 10</span>
<span class="co"># as.mo("STAU") 170.0 170.0 190 180 210 210 10</span>
<span class="co"># as.mo("staaur") 8.7 12.0 18 12 14 47 10</span>
<span class="co"># as.mo("STAAUR") 9.9 10.0 12 12 12 13 10</span>
<span class="co"># as.mo("S. aureus") 13.0 15.0 29 28 43 47 10</span>
<span class="co"># as.mo("S aureus") 12.0 16.0 25 17 40 52 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 9.1 9.7 14 11 11 44 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 920.0 960.0 990 980 1000 1100 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 430.0 440.0 460 460 460 510 10</span>
<span class="co"># as.mo("MRSA") 9.1 11.0 16 12 12 37 10</span>
<span class="co"># as.mo("VISA") 15.0 17.0 23 18 20 47 10</span>
<span class="co"># as.mo("VRSA") 15.0 17.0 27 19 44 50 10</span>
<span class="co"># as.mo(22242419) 140.0 140.0 150 150 160 170 10</span>
</pre></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>
@ -252,12 +252,12 @@
times = <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">M.semesiae</span>, unit = <span class="st">"ms"</span>, signif = <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") 186.900 192.90 204.70 199.10 207.70 251.20</span>
<span class="co"># as.mo("METSEM") 175.500 199.70 215.20 218.20 232.00 240.40</span>
<span class="co"># as.mo("M. semesiae") 11.500 13.29 16.47 13.85 16.84 36.90</span>
<span class="co"># as.mo("M. semesiae") 11.690 11.94 16.81 14.40 15.75 42.76</span>
<span class="co"># as.mo("Methanosarcina semesiae") 9.688 10.28 14.55 11.99 13.72 39.41</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 193.600 200.200 209.30 202.800 218.00 238.20</span>
<span class="co"># as.mo("METSEM") 186.500 193.500 208.40 202.600 228.90 244.80</span>
<span class="co"># as.mo("M. semesiae") 12.280 13.090 18.86 14.430 15.48 59.40</span>
<span class="co"># as.mo("M. semesiae") 14.060 14.520 20.98 16.420 17.56 46.18</span>
<span class="co"># as.mo("Methanosarcina semesiae") 8.065 9.203 12.65 9.715 10.65 39.96</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -299,9 +299,9 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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 1870 1950 1940 1980 2140 10</span>
<span class="co"># mo_name(x) 1920 1940 2010 1990 2060 2120 10</span>
</pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.94 seconds. You only lose time on your unique input values.</p>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.99 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -315,11 +315,11 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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 8.17 8.49 9.32 9.32 9.90 10.90 10</span>
<span class="co"># B 10.90 11.80 16.30 13.20 14.70 45.60 10</span>
<span class="co"># C 1.06 1.22 1.32 1.28 1.44 1.57 10</span>
<span class="co"># A 5.90 6.16 6.93 7.24 7.43 7.89 10</span>
<span class="co"># B 11.40 12.00 16.20 13.20 14.20 45.20 10</span>
<span class="co"># C 1.05 1.07 1.18 1.13 1.28 1.40 10</span>
</pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0013 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>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0011 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"><pre class="downlit">
<span class="kw">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span>(A = <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
@ -333,14 +333,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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 1.020 1.030 1.11 1.060 1.22 1.33 10</span>
<span class="co"># B 0.982 1.010 1.10 1.040 1.21 1.38 10</span>
<span class="co"># C 0.992 1.020 1.13 1.040 1.24 1.58 10</span>
<span class="co"># D 0.987 1.000 1.07 1.030 1.08 1.29 10</span>
<span class="co"># E 0.978 0.982 1.02 0.999 1.03 1.15 10</span>
<span class="co"># F 0.975 0.992 1.05 1.000 1.03 1.26 10</span>
<span class="co"># G 0.976 0.983 1.02 0.994 1.03 1.22 10</span>
<span class="co"># H 0.977 1.010 1.11 1.090 1.21 1.28 10</span>
<span class="co"># A 0.976 0.993 1.13 1.07 1.29 1.34 10</span>
<span class="co"># B 1.000 1.060 1.13 1.07 1.15 1.40 10</span>
<span class="co"># C 0.927 1.030 1.08 1.06 1.11 1.35 10</span>
<span class="co"># D 0.896 0.983 1.11 1.08 1.27 1.41 10</span>
<span class="co"># E 0.866 1.020 1.10 1.07 1.23 1.37 10</span>
<span class="co"># F 0.967 0.993 1.16 1.05 1.32 1.61 10</span>
<span class="co"># G 0.855 1.020 1.07 1.07 1.17 1.31 10</span>
<span class="co"># H 0.966 1.010 1.12 1.06 1.19 1.36 10</span>
</pre></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>
@ -368,14 +368,14 @@
times = <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <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 12.40 14.34 17.88 14.89 15.48 55.22 100</span>
<span class="co"># de 13.17 14.30 17.90 15.84 16.66 56.60 100</span>
<span class="co"># nl 17.14 19.86 24.99 20.78 21.70 64.66 100</span>
<span class="co"># es 13.43 15.29 17.65 15.93 16.59 54.38 100</span>
<span class="co"># it 13.33 14.83 18.35 15.68 16.36 57.61 100</span>
<span class="co"># fr 13.40 15.43 18.66 16.01 16.59 54.35 100</span>
<span class="co"># pt 13.47 15.33 18.93 16.15 16.84 57.28 100</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 13.09 14.02 18.36 14.59 16.22 61.92 100</span>
<span class="co"># de 14.00 14.83 18.06 15.48 16.85 56.01 100</span>
<span class="co"># nl 17.71 18.99 24.79 20.09 22.22 58.50 100</span>
<span class="co"># es 13.99 15.02 20.94 15.88 16.70 141.90 100</span>
<span class="co"># it 13.68 14.97 19.02 15.52 16.72 50.26 100</span>
<span class="co"># fr 13.96 15.05 20.63 15.72 17.14 52.71 100</span>
<span class="co"># pt 14.13 14.86 19.81 15.69 17.46 53.89 100</span>
</pre></div>
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