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(v1.3.0.9006) website update
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@ -39,7 +39,7 @@
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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">1.3.0.9005</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
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</span>
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</div>
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@ -229,21 +229,21 @@
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times = <span class="fl">10</span>)
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<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>)
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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"># as.mo("sau") 8.8 10.0 24 12 38 57 10</span>
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<span class="co"># as.mo("stau") 170.0 170.0 180 170 190 210 10</span>
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<span class="co"># as.mo("STAU") 160.0 170.0 180 170 200 220 10</span>
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<span class="co"># as.mo("staaur") 9.6 10.0 13 11 12 36 10</span>
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<span class="co"># as.mo("STAAUR") 10.0 10.0 25 12 34 80 10</span>
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<span class="co"># as.mo("S. aureus") 14.0 15.0 21 15 18 47 10</span>
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<span class="co"># as.mo("S aureus") 12.0 15.0 21 16 18 45 10</span>
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<span class="co"># as.mo("Staphylococcus aureus") 8.9 9.4 15 11 12 37 10</span>
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<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 900.0 920.0 940 940 960 1000 10</span>
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<span class="co"># as.mo("Sthafilokkockus aaureuz") 410.0 420.0 450 450 470 520 10</span>
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<span class="co"># as.mo("MRSA") 8.8 10.0 16 11 12 38 10</span>
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<span class="co"># as.mo("VISA") 13.0 16.0 27 19 41 47 10</span>
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<span class="co"># as.mo("VRSA") 13.0 16.0 22 18 19 42 10</span>
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<span class="co"># as.mo(22242419) 140.0 140.0 150 140 160 170 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") 8.7 9.3 13 9.8 12 40 10</span>
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<span class="co"># as.mo("stau") 160.0 180.0 200 200.0 210 220 10</span>
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<span class="co"># as.mo("STAU") 160.0 180.0 190 190.0 200 210 10</span>
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<span class="co"># as.mo("staaur") 9.8 12.0 15 12.0 12 42 10</span>
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<span class="co"># as.mo("STAAUR") 8.4 8.7 13 10.0 12 37 10</span>
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<span class="co"># as.mo("S. aureus") 13.0 16.0 38 18.0 45 150 10</span>
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<span class="co"># as.mo("S aureus") 12.0 17.0 21 17.0 18 48 10</span>
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<span class="co"># as.mo("Staphylococcus aureus") 7.1 8.7 12 9.7 11 38 10</span>
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<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 880.0 920.0 930 930.0 960 980 10</span>
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<span class="co"># as.mo("Sthafilokkockus aaureuz") 400.0 430.0 450 440.0 460 500 10</span>
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<span class="co"># as.mo("MRSA") 8.6 12.0 20 12.0 37 42 10</span>
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<span class="co"># as.mo("VISA") 15.0 17.0 20 18.0 19 40 10</span>
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<span class="co"># as.mo("VRSA") 13.0 14.0 19 17.0 19 46 10</span>
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<span class="co"># as.mo(22242419) 140.0 140.0 160 150.0 170 210 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.</p>
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@ -278,9 +278,9 @@
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<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>)
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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) 1810 1850 1980 1940 2130 2230 10</span>
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<span class="co"># mo_name(x) 1750 1790 1830 1810 1850 1950 10</span>
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</pre></div>
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<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>
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<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.81 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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@ -293,12 +293,12 @@
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times = <span class="fl">10</span>)
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<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>)
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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 5.080 5.220 5.81 5.66 6.46 7.16 10</span>
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<span class="co"># B 10.000 10.200 14.40 10.60 11.30 49.00 10</span>
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<span class="co"># C 0.862 0.875 1.04 1.05 1.14 1.40 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 6.08 6.23 10.40 6.56 7.03 44.90 10</span>
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<span class="co"># B 11.70 12.00 12.70 12.70 13.60 13.90 10</span>
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<span class="co"># C 1.05 1.11 1.19 1.13 1.25 1.55 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 0.001 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 0.0011 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>
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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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@ -311,15 +311,15 @@
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times = <span class="fl">10</span>)
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<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>)
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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 0.869 0.889 0.951 0.904 1.010 1.19 10</span>
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<span class="co"># B 0.837 0.873 0.977 0.937 1.010 1.36 10</span>
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<span class="co"># C 0.869 0.874 1.020 0.921 1.130 1.40 10</span>
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<span class="co"># D 0.829 0.858 0.898 0.862 0.873 1.21 10</span>
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<span class="co"># E 0.862 0.870 0.983 0.918 1.050 1.36 10</span>
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<span class="co"># F 0.841 0.850 0.915 0.867 0.907 1.24 10</span>
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<span class="co"># G 0.842 0.851 0.940 0.898 1.000 1.16 10</span>
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<span class="co"># H 0.854 0.864 1.030 0.920 1.170 1.60 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 0.886 1.010 1.040 1.020 1.06 1.25 10</span>
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<span class="co"># B 1.010 1.030 1.150 1.040 1.27 1.64 10</span>
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<span class="co"># C 0.885 1.030 1.110 1.060 1.26 1.29 10</span>
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<span class="co"># D 0.812 0.822 1.000 1.000 1.05 1.43 10</span>
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<span class="co"># E 0.827 0.989 1.070 1.030 1.23 1.35 10</span>
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<span class="co"># F 0.887 0.994 1.070 1.040 1.08 1.35 10</span>
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<span class="co"># G 0.812 0.839 0.969 0.916 1.04 1.32 10</span>
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<span class="co"># H 0.815 1.020 1.090 1.050 1.30 1.37 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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@ -347,14 +347,14 @@
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times = <span class="fl">100</span>)
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<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>)
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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 10.72 11.54 15.34 12.76 13.82 44.53 100</span>
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<span class="co"># de 11.47 12.77 17.24 13.60 14.78 55.48 100</span>
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<span class="co"># nl 14.58 15.91 19.06 16.96 18.46 46.24 100</span>
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<span class="co"># es 11.24 11.96 16.86 13.17 14.70 50.05 100</span>
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<span class="co"># it 11.35 12.42 17.79 13.52 16.28 50.31 100</span>
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<span class="co"># fr 11.41 12.29 17.08 13.43 15.44 53.91 100</span>
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<span class="co"># pt 11.34 12.06 16.23 13.25 14.80 51.96 100</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 12.88 13.52 16.72 14.63 16.00 55.03 100</span>
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<span class="co"># de 13.79 14.51 18.36 15.11 16.67 136.90 100</span>
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<span class="co"># nl 17.72 18.59 22.30 20.15 21.87 54.69 100</span>
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<span class="co"># es 13.78 14.38 19.16 15.35 16.86 49.96 100</span>
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<span class="co"># it 13.83 14.40 18.57 15.24 16.32 58.12 100</span>
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<span class="co"># fr 13.72 14.47 19.67 15.21 17.46 52.22 100</span>
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<span class="co"># pt 13.73 14.43 17.76 15.10 16.85 51.69 100</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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