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(v1.5.0.9025) big plot and ggplot generics update

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dr. M.S. (Matthijs) Berends
2021-02-25 10:33:08 +01:00
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commit a673407904
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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">1.5.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
</span>
</div>
@ -226,19 +226,19 @@
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</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") 9.3 10 11.0 10 11.0 13.0 25</span>
<span class="co"># as.mo("stau") 52.0 55 73.0 58 92.0 100.0 25</span>
<span class="co"># as.mo("STAU") 50.0 54 73.0 58 96.0 110.0 25</span>
<span class="co"># as.mo("staaur") 9.7 10 14.0 11 12.0 57.0 25</span>
<span class="co"># as.mo("STAAUR") 8.9 10 14.0 10 11.0 52.0 25</span>
<span class="co"># as.mo("S. aureus") 26.0 28 41.0 29 67.0 76.0 25</span>
<span class="co"># as.mo("S aureus") 27.0 28 41.0 30 65.0 76.0 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 2.6 3 3.2 3 3.3 4.6 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 260 270.0 260 270.0 380.0 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 190 200.0 200 200.0 300.0 25</span>
<span class="co"># as.mo("MRSA") 9.3 10 15.0 10 12.0 49.0 25</span>
<span class="co"># as.mo("VISA") 18.0 19 31.0 21 54.0 67.0 25</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 10 11.0 15 11.0 13.0 47 25</span>
<span class="co"># as.mo("stau") 56 57.0 75 62.0 95.0 100 25</span>
<span class="co"># as.mo("STAU") 54 56.0 67 58.0 66.0 110 25</span>
<span class="co"># as.mo("staaur") 10 11.0 12 11.0 12.0 13 25</span>
<span class="co"># as.mo("STAAUR") 10 11.0 16 11.0 12.0 50 25</span>
<span class="co"># as.mo("S. aureus") 28 31.0 46 33.0 65.0 71 25</span>
<span class="co"># as.mo("S aureus") 29 30.0 42 33.0 64.0 67 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3 3.2 5 3.3 3.7 40 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240 260.0 270 270.0 280.0 290 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 170 200.0 210 200.0 210.0 280 25</span>
<span class="co"># as.mo("MRSA") 10 11.0 17 11.0 13.0 51 25</span>
<span class="co"># as.mo("VISA") 19 20.0 36 21.0 50.0 150 25</span></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="750"></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 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 200 times slower to determine.</p>
<p>To improve performance, we implemented two important algorithms to save unnecessary calculations: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -260,8 +260,8 @@
<span class="co"># what do these values look like? They are of class &lt;mo&gt;:</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
<span class="co"># Class &lt;mo&gt;</span>
<span class="co"># [1] B_STPHY_AURS B_STRPT_GRPC B_STPHY_CONS B_STPHY_EPDR B_STRPT_PNMN</span>
<span class="co"># [6] B_PROTS_VLGR</span>
<span class="co"># [1] B_ESCHR_COLI B_PROTS_MRBL B_PROTS_MRBL B_PROTS_MRBL B_STPHY_CONS</span>
<span class="co"># [6] B_ENTRC</span>
<span class="co"># as the example_isolates data set has 2,000 rows, we should have 2 million items</span>
<span class="fu"><a href="https://rdrr.io/r/base/length.html">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -277,8 +277,8 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</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) 157 187 222 206 224 372 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.206 seconds. That is 2.471 milliseconds per unique item on average. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 160 189 224 201 228 356 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.201 seconds. That is 101 nanoseconds on average. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -291,10 +291,10 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 6.97 7.10 7.55 7.21 8.18 8.32 10</span>
<span class="co"># B 23.70 24.20 36.30 26.30 29.00 89.70 10</span>
<span class="co"># C 1.53 1.65 1.80 1.76 2.00 2.19 10</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 6.80 7.17 7.46 7.54 7.81 8.0 10</span>
<span class="co"># B 24.30 25.80 31.60 26.20 28.80 75.6 10</span>
<span class="co"># C 1.59 1.70 1.89 1.84 2.02 2.5 10</span></code></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 0.0018 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="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
@ -309,14 +309,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.44 1.72 1.69 1.74 1.75 1.78 10</span>
<span class="co"># B 1.47 1.55 1.67 1.73 1.74 1.89 10</span>
<span class="co"># C 1.52 1.59 1.73 1.74 1.89 1.91 10</span>
<span class="co"># D 1.46 1.51 1.64 1.64 1.75 1.89 10</span>
<span class="co"># E 1.42 1.47 1.60 1.52 1.71 1.97 10</span>
<span class="co"># F 1.44 1.71 1.69 1.72 1.75 1.88 10</span>
<span class="co"># G 1.42 1.50 1.68 1.61 1.73 2.36 10</span>
<span class="co"># H 1.52 1.54 1.66 1.71 1.73 1.87 10</span></code></pre></div>
<span class="co"># A 1.25 1.28 1.39 1.39 1.50 1.56 10</span>
<span class="co"># B 1.17 1.19 1.41 1.43 1.48 1.92 10</span>
<span class="co"># C 1.20 1.33 1.43 1.46 1.50 1.61 10</span>
<span class="co"># D 1.43 1.45 1.50 1.49 1.53 1.61 10</span>
<span class="co"># E 1.26 1.40 1.45 1.43 1.49 1.81 10</span>
<span class="co"># F 1.15 1.17 1.32 1.26 1.44 1.69 10</span>
<span class="co"># G 1.19 1.25 1.37 1.35 1.47 1.58 10</span>
<span class="co"># H 1.20 1.25 1.46 1.31 1.53 2.33 10</span></code></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 contains all phyla of all known bacteria, it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -343,14 +343,14 @@
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 17.12 17.40 22.65 17.54 18.39 78.39 100</span>
<span class="co"># de 19.93 20.26 22.60 20.48 20.97 81.27 100</span>
<span class="co"># nl 24.87 25.24 30.93 25.50 26.90 87.17 100</span>
<span class="co"># es 20.00 20.26 24.39 20.58 21.13 82.01 100</span>
<span class="co"># it 19.92 20.26 26.54 20.66 21.38 79.15 100</span>
<span class="co"># fr 19.62 19.90 24.74 20.10 21.04 77.20 100</span>
<span class="co"># pt 19.74 20.02 26.76 20.41 22.68 82.61 100</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 17.05 17.38 21.26 17.74 18.50 97.23 100</span>
<span class="co"># de 19.90 20.33 24.80 20.67 21.06 93.34 100</span>
<span class="co"># nl 24.86 25.30 31.21 25.65 26.34 102.20 100</span>
<span class="co"># es 19.83 20.22 26.56 20.49 21.20 97.59 100</span>
<span class="co"># it 19.79 20.20 26.82 20.63 21.31 94.85 100</span>
<span class="co"># fr 19.61 19.87 24.26 20.21 20.68 92.42 100</span>
<span class="co"># pt 19.64 20.06 23.78 20.40 21.05 92.91 100</span></code></pre></div>
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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</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">1.5.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9025</span>
</span>
</div>