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(v1.4.0) matching score update
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@ -187,7 +187,7 @@
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</header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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</header><script src="benchmarks_files/header-attrs-2.3/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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<div class="col-md-9 contents">
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Benchmarks</h1>
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@ -288,34 +288,20 @@
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<span class="co"># Result of one value was guessed with uncertainty. Use mo_uncertainties() to review it.</span>
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<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">S.aureus</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">2</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max</span>
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<span class="co"># as.mo("sau") 13.0 14.0 15.0 14.0 16.0 17.0</span>
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<span class="co"># as.mo("stau") 220.0 230.0 250.0 260.0 280.0 280.0</span>
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<span class="co"># as.mo("STAU") 220.0 240.0 270.0 250.0 290.0 330.0</span>
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<span class="co"># as.mo("staaur") 13.0 14.0 28.0 15.0 44.0 62.0</span>
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<span class="co"># as.mo("STAAUR") 11.0 14.0 17.0 14.0 15.0 48.0</span>
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<span class="co"># as.mo("S. aureus") 30.0 56.0 56.0 61.0 63.0 66.0</span>
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<span class="co"># as.mo("S aureus") 28.0 33.0 48.0 38.0 66.0 77.0</span>
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<span class="co"># as.mo("Staphylococcus aureus") 1.7 1.9 2.4 2.5 2.6 3.1</span>
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<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 860.0 890.0 920.0 910.0 930.0 1000.0</span>
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<span class="co"># as.mo("Sthafilokkockus aaureuz") 350.0 370.0 380.0 390.0 390.0 410.0</span>
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<span class="co"># as.mo("MRSA") 13.0 15.0 28.0 18.0 42.0 61.0</span>
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<span class="co"># as.mo("VISA") 21.0 22.0 31.0 22.0 43.0 52.0</span>
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<span class="co"># as.mo("VRSA") 23.0 24.0 39.0 45.0 49.0 55.0</span>
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<span class="co"># neval</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># 10</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># as.mo("sau") 11.0 12.0 25.0 13.0 14.0 130 10</span>
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<span class="co"># as.mo("stau") 210.0 230.0 240.0 250.0 250.0 260 10</span>
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<span class="co"># as.mo("STAU") 210.0 210.0 240.0 240.0 260.0 270 10</span>
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<span class="co"># as.mo("staaur") 12.0 14.0 22.0 14.0 41.0 43 10</span>
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<span class="co"># as.mo("STAAUR") 12.0 12.0 19.0 13.0 14.0 47 10</span>
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<span class="co"># as.mo("S. aureus") 26.0 28.0 38.0 30.0 58.0 62 10</span>
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<span class="co"># as.mo("S aureus") 28.0 29.0 45.0 52.0 56.0 60 10</span>
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<span class="co"># as.mo("Staphylococcus aureus") 2.1 2.2 7.9 2.4 2.6 32 10</span>
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<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 840.0 880.0 890.0 890.0 890.0 930 10</span>
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<span class="co"># as.mo("Sthafilokkockus aaureuz") 340.0 370.0 390.0 390.0 410.0 490 10</span>
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<span class="co"># as.mo("MRSA") 11.0 12.0 16.0 13.0 14.0 44 10</span>
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<span class="co"># as.mo("VISA") 19.0 20.0 32.0 22.0 50.0 51 10</span>
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<span class="co"># as.mo("VRSA") 18.0 22.0 24.0 22.0 23.0 46 10</span>
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</pre></div>
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<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
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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. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
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@ -345,10 +331,10 @@
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times = <span class="fl">10</span>)
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<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># mo_name(x) 99.2 127 145 143 145 243 10</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># mo_name(x) 131 161 200 168 187 341 10</span>
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</pre></div>
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<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.143 seconds. You only lose time on your unique input values.</p>
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<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.168 seconds. 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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@ -372,11 +358,11 @@
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<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># A 7.53 8.50 8.77 8.83 9.14 9.89 10</span>
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<span class="co"># B 23.00 24.20 32.40 26.30 28.80 60.10 10</span>
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<span class="co"># C 1.91 1.98 2.33 2.30 2.66 2.83 10</span>
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<span class="co"># A 6.85 7.05 7.57 7.51 8.05 8.52 10</span>
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<span class="co"># B 21.50 21.70 27.40 23.80 25.00 64.70 10</span>
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<span class="co"># C 1.75 1.86 1.99 1.93 2.08 2.27 10</span>
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</pre></div>
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<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0023 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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<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 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="cb5"><pre class="downlit">
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<span class="kw">run_it</span> <span class="op"><-</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>),
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B = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
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@ -389,15 +375,15 @@
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times = <span class="fl">10</span>)
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<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">3</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># A 1.55 1.74 1.91 1.98 2.06 2.16 10</span>
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<span class="co"># B 1.52 1.70 1.95 1.88 2.03 2.62 10</span>
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<span class="co"># C 1.61 1.68 6.25 2.04 2.18 44.80 10</span>
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<span class="co"># D 1.65 1.71 1.92 1.95 2.02 2.22 10</span>
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<span class="co"># E 1.56 1.79 1.92 1.99 2.01 2.14 10</span>
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<span class="co"># F 1.62 1.67 1.82 1.78 1.94 2.09 10</span>
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<span class="co"># G 1.61 1.70 1.92 1.97 2.01 2.31 10</span>
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<span class="co"># H 1.62 1.69 1.83 1.87 1.95 2.01 10</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># A 1.38 1.57 1.60 1.61 1.67 1.71 10</span>
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<span class="co"># B 1.55 1.60 1.73 1.63 1.92 2.05 10</span>
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<span class="co"># C 1.39 1.50 1.70 1.62 1.84 2.39 10</span>
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<span class="co"># D 1.32 1.51 1.59 1.57 1.61 2.04 10</span>
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<span class="co"># E 1.34 1.40 1.52 1.53 1.65 1.66 10</span>
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<span class="co"># F 1.28 1.53 1.56 1.60 1.66 1.72 10</span>
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<span class="co"># G 1.30 1.33 1.59 1.61 1.74 1.98 10</span>
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<span class="co"># H 1.31 1.45 1.62 1.55 1.70 2.46 10</span>
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</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> 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>
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</div>
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@ -425,14 +411,14 @@
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times = <span class="fl">100</span>)
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<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span>(<span class="kw">run_it</span>, unit = <span class="st">"ms"</span>, signif = <span class="fl">4</span>)
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<span class="co"># Unit: milliseconds</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># en 13.92 14.62 19.73 15.07 17.06 71.77 100</span>
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<span class="co"># de 16.83 17.63 22.19 18.10 20.41 58.61 100</span>
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<span class="co"># nl 28.71 30.05 35.19 31.64 34.09 69.34 100</span>
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<span class="co"># es 16.78 17.61 22.57 18.56 20.21 57.98 100</span>
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<span class="co"># it 16.61 17.39 21.59 18.32 20.74 56.86 100</span>
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<span class="co"># fr 16.48 17.31 21.96 17.84 20.26 55.84 100</span>
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<span class="co"># pt 16.66 17.45 24.03 18.26 20.85 67.60 100</span>
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<span class="co"># expr min lq mean median uq max neval</span>
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<span class="co"># en 14.00 14.36 18.52 14.64 15.18 57.58 100</span>
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<span class="co"># de 17.04 17.33 20.94 17.63 18.49 56.23 100</span>
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<span class="co"># nl 28.21 29.20 32.15 30.06 31.02 72.91 100</span>
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<span class="co"># es 16.85 17.26 19.83 17.44 17.95 152.20 100</span>
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<span class="co"># it 16.58 17.10 19.03 17.43 18.24 54.28 100</span>
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<span class="co"># fr 16.71 17.20 21.24 17.52 19.02 63.25 100</span>
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<span class="co"># pt 16.76 17.29 23.27 17.62 19.14 65.28 100</span>
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</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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