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(v1.4.0.9044) mo tibble printing, mo_shortname() fix

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dr. M.S. (Matthijs) Berends
2020-12-24 23:29:10 +01:00
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commit df37584189
96 changed files with 1039 additions and 2847 deletions
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<title>Benchmarks • AMR (for R)</title>
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@ -56,7 +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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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@ -244,20 +227,20 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/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</span>
<span class="co"># as.mo("sau") 10.0 11.0 20.0 13.0 38.0 41.0</span>
<span class="co"># as.mo("stau") 100.0 110.0 120.0 110.0 140.0 140.0</span>
<span class="co"># as.mo("STAU") 100.0 110.0 130.0 140.0 140.0 160.0</span>
<span class="co"># as.mo("staaur") 10.0 12.0 23.0 14.0 38.0 58.0</span>
<span class="co"># as.mo("STAAUR") 10.0 11.0 18.0 13.0 14.0 42.0</span>
<span class="co"># as.mo("S. aureus") 26.0 30.0 46.0 44.0 58.0 78.0</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 32.0 31.0 31.0 56.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 2.0 2.4 2.6 2.7 2.8 3.1</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 890.0 910.0 920.0 920.0 930.0 960.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 380.0 390.0 400.0 390.0 400.0 430.0</span>
<span class="co"># as.mo("MRSA") 9.9 11.0 16.0 14.0 14.0 41.0</span>
<span class="co"># as.mo("VISA") 17.0 19.0 28.0 21.0 45.0 52.0</span>
<span class="co"># as.mo("VRSA") 17.0 19.0 26.0 21.0 22.0 53.0</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 9.9 12.0 15.0 13.0 13.0 42.0</span>
<span class="co"># as.mo("stau") 100.0 100.0 130.0 120.0 140.0 190.0</span>
<span class="co"># as.mo("STAU") 110.0 110.0 130.0 130.0 140.0 150.0</span>
<span class="co"># as.mo("staaur") 9.8 12.0 26.0 13.0 41.0 60.0</span>
<span class="co"># as.mo("STAAUR") 11.0 11.0 15.0 13.0 13.0 41.0</span>
<span class="co"># as.mo("S. aureus") 26.0 28.0 50.0 58.0 63.0 75.0</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 46.0 51.0 60.0 67.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.9 2.2 2.5 2.5 2.8 3.1</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870.0 880.0 1100.0 910.0 1000.0 2400.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 360.0 370.0 400.0 380.0 420.0 540.0</span>
<span class="co"># as.mo("MRSA") 9.7 11.0 17.0 12.0 13.0 66.0</span>
<span class="co"># as.mo("VISA") 19.0 19.0 36.0 35.0 53.0 56.0</span>
<span class="co"># as.mo("VRSA") 17.0 20.0 20.0 21.0 21.0 23.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -301,8 +284,8 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/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) 128 167 205 195 232 298 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.195 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 134 167 201 179 207 310 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.179 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -316,10 +299,10 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/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 7.35 7.70 8.15 8.11 8.68 8.96 10</span>
<span class="co"># B 22.50 22.80 28.10 24.30 25.70 62.60 10</span>
<span class="co"># C 1.84 1.98 2.13 2.13 2.17 2.43 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 0.0021 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>
<span class="co"># A 7.59 7.93 8.24 8.09 8.66 9.06 10</span>
<span class="co"># B 23.60 23.70 29.20 24.30 27.10 66.10 10</span>
<span class="co"># C 1.84 2.13 2.22 2.19 2.35 2.62 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 0.0022 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">microbenchmark</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>,
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -333,14 +316,14 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/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 1.60 1.63 1.74 1.70 1.83 2.02 10</span>
<span class="co"># B 1.37 1.40 1.62 1.54 1.74 2.07 10</span>
<span class="co"># C 1.39 1.45 1.63 1.65 1.77 1.86 10</span>
<span class="co"># D 1.37 1.40 1.58 1.51 1.62 2.27 10</span>
<span class="co"># E 1.44 1.64 1.70 1.66 1.81 2.13 10</span>
<span class="co"># F 1.38 1.42 1.57 1.58 1.67 1.81 10</span>
<span class="co"># G 1.38 1.62 1.64 1.63 1.70 1.82 10</span>
<span class="co"># H 1.44 1.65 1.84 1.82 1.99 2.60 10</span></code></pre></div>
<span class="co"># A 1.69 1.77 1.82 1.83 1.86 1.92 10</span>
<span class="co"># B 1.78 1.79 1.89 1.91 1.95 2.06 10</span>
<span class="co"># C 1.74 1.79 1.88 1.87 1.94 2.06 10</span>
<span class="co"># D 1.75 1.77 1.94 1.95 1.99 2.41 10</span>
<span class="co"># E 1.70 1.75 1.84 1.81 1.87 2.08 10</span>
<span class="co"># F 1.66 1.70 1.76 1.74 1.80 1.89 10</span>
<span class="co"># G 1.68 1.70 1.82 1.75 1.93 2.09 10</span>
<span class="co"># H 1.66 1.69 1.75 1.74 1.80 1.92 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 ‘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">
@ -367,14 +350,14 @@
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/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 15.77 16.36 18.40 16.85 17.50 53.58 100</span>
<span class="co"># de 19.03 19.70 24.60 20.14 21.06 59.83 100</span>
<span class="co"># nl 30.93 32.03 36.58 32.80 33.78 85.59 100</span>
<span class="co"># es 18.78 19.62 24.49 19.98 20.60 58.73 100</span>
<span class="co"># it 18.80 19.50 22.68 19.92 20.89 63.99 100</span>
<span class="co"># fr 18.78 19.59 21.99 19.90 20.75 58.87 100</span>
<span class="co"># pt 18.79 19.65 23.04 20.08 20.82 59.30 100</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 15.91 16.98 21.87 17.54 18.34 168.50 100</span>
<span class="co"># de 18.98 20.14 26.30 20.74 22.64 66.68 100</span>
<span class="co"># nl 31.02 32.71 37.56 33.84 35.81 82.77 100</span>
<span class="co"># es 19.13 20.06 22.96 20.54 21.42 65.26 100</span>
<span class="co"># it 18.90 19.84 24.26 20.59 22.80 60.30 100</span>
<span class="co"># fr 18.89 19.92 23.46 20.49 21.72 62.85 100</span>
<span class="co"># pt 18.90 19.99 23.80 20.70 22.17 61.42 100</span></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
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@ -392,7 +375,7 @@
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