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@ -218,16 +218,25 @@
<a class="sourceLine" id="cb2-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("sau") 42.00 43.00 47.00 43.00 44.0 81.00 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("stau") 86.00 87.00 93.00 88.00 89.0 130.00 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("staaur") 43.00 43.00 45.00 43.00 43.0 64.00 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 23.00 23.00 27.00 23.00 24.0 60.00 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 23.00 23.00 29.00 24.00 24.0 73.00 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("STAAUR") 43.00 43.00 43.00 43.00 44.0 46.00 10</span></a>
<a class="sourceLine" id="cb2-19" title="19"><span class="co">#&gt; as.mo("Staphylococcus aureus") 14.00 15.00 19.00 15.00 16.0 53.00 10</span></a>
<a class="sourceLine" id="cb2-20" title="20"><span class="co">#&gt; as.mo("B_STPHY_AUR") 0.34 0.42 0.47 0.49 0.5 0.58 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of <code><a href="../reference/as.mo.html">as.mo("B_STPHY_AUR")</a></code>, the input is already a valid MO code, so it only almost takes no time at all (494 millionths of a second).</p>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("sau") 100.00 100.00 110.00 100.00 100.00 160.00</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("stau") 140.00 140.00 170.00 160.00 190.00 200.00</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("staaur") 99.00 100.00 100.00 100.00 100.00 110.00</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 64.00 64.00 65.00 65.00 66.00 67.00</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 65.00 65.00 70.00 66.00 66.00 110.00</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("STAAUR") 97.00 98.00 100.00 100.00 100.00 100.00</span></a>
<a class="sourceLine" id="cb2-19" title="19"><span class="co">#&gt; as.mo("Staphylococcus aureus") 35.00 35.00 36.00 36.00 37.00 38.00</span></a>
<a class="sourceLine" id="cb2-20" title="20"><span class="co">#&gt; as.mo("B_STPHY_AUR") 0.34 0.47 0.52 0.48 0.56 0.89</span></a>
<a class="sourceLine" id="cb2-21" title="21"><span class="co">#&gt; neval</span></a>
<a class="sourceLine" id="cb2-22" title="22"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-23" title="23"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-24" title="24"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-25" title="25"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-26" title="26"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-27" title="27"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-28" title="28"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-29" title="29"><span class="co">#&gt; 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of <code><a href="../reference/as.mo.html">as.mo("B_STPHY_AUR")</a></code>, the input is already a valid MO code, so it only almost takes no time at all (476 millionths of a second).</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Mycoplasma leonicaptivi</em> (<code>B_MYCPL_LEO</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">M.leonicaptivi &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"myle"</span>),</a>
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"mycleo"</span>),</a>
@ -239,14 +248,14 @@
<a class="sourceLine" id="cb3-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(M.leonicaptivi, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("myle") 140.00 140.00 150.0 140.00 140.00 180.00</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("mycleo") 470.00 480.00 500.0 510.00 520.00 560.00</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 240.00 240.00 250.0 240.00 280.00 290.00</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("M. leonicaptivi") 240.00 240.00 250.0 240.00 280.00 280.00</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("MYCLEO") 470.00 510.00 510.0 520.00 520.00 540.00</span></a>
<a class="sourceLine" id="cb3-17" title="17"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 150.00 150.00 170.0 180.00 190.00 200.00</span></a>
<a class="sourceLine" id="cb3-18" title="18"><span class="co">#&gt; as.mo("B_MYCPL_LEO") 0.32 0.58 0.6 0.59 0.61 0.97</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("myle") 210.00 220.00 240.0 230.00 260.00 310</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("mycleo") 610.00 630.00 680.0 680.00 720.00 770</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 370.00 370.00 390.0 390.00 410.00 410</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("M. leonicaptivi") 350.00 350.00 390.0 390.00 410.00 480</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("MYCLEO") 630.00 650.00 680.0 670.00 680.00 880</span></a>
<a class="sourceLine" id="cb3-17" title="17"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 250.00 250.00 260.0 250.00 260.00 290</span></a>
<a class="sourceLine" id="cb3-18" title="18"><span class="co">#&gt; as.mo("B_MYCPL_LEO") 0.35 0.43 5.6 0.69 0.75 50</span></a>
<a class="sourceLine" id="cb3-19" title="19"><span class="co">#&gt; neval</span></a>
<a class="sourceLine" id="cb3-20" title="20"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-21" title="21"><span class="co">#&gt; 10</span></a>
@ -255,7 +264,7 @@
<a class="sourceLine" id="cb3-24" title="24"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-25" title="25"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb3-26" title="26"><span class="co">#&gt; 10</span></a></code></pre></div>
<p>That takes 6.9 times as much time on average! A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance:</p>
<p>That takes 4.7 times as much time on average! A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="co"># highest value on y axis</span></a>
@ -292,8 +301,8 @@
<a class="sourceLine" id="cb6-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-21" title="21"><span class="co">#&gt; mo_fullname(x) 445 466 497 491 536 543 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.49 seconds (490 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb6-21" title="21"><span class="co">#&gt; mo_fullname(x) 487 499 527 535 538 573 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.54 seconds (535 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -305,11 +314,11 @@
<a class="sourceLine" id="cb7-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb7-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-6" title="6"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-8" title="8"><span class="co">#&gt; A 38.70 39.100 40.200 40.000 40.100 45.300 10</span></a>
<a class="sourceLine" id="cb7-9" title="9"><span class="co">#&gt; B 24.50 24.600 24.800 24.700 24.700 25.500 10</span></a>
<a class="sourceLine" id="cb7-10" title="10"><span class="co">#&gt; C 0.26 0.392 0.434 0.447 0.516 0.561 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0004 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>
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-8" title="8"><span class="co">#&gt; A 65.500 66.100 66.200 66.300 66.500 66.700 10</span></a>
<a class="sourceLine" id="cb7-9" title="9"><span class="co">#&gt; B 61.000 61.200 61.900 61.700 62.300 64.500 10</span></a>
<a class="sourceLine" id="cb7-10" title="10"><span class="co">#&gt; C 0.329 0.335 0.461 0.527 0.551 0.556 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0005 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="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
@ -322,14 +331,14 @@
<a class="sourceLine" id="cb8-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb8-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-13" title="13"><span class="co">#&gt; A 0.297 0.329 0.400 0.416 0.453 0.459 10</span></a>
<a class="sourceLine" id="cb8-14" title="14"><span class="co">#&gt; B 0.277 0.304 0.349 0.363 0.382 0.407 10</span></a>
<a class="sourceLine" id="cb8-15" title="15"><span class="co">#&gt; C 0.281 0.430 0.436 0.440 0.471 0.493 10</span></a>
<a class="sourceLine" id="cb8-16" title="16"><span class="co">#&gt; D 0.249 0.277 0.310 0.316 0.337 0.347 10</span></a>
<a class="sourceLine" id="cb8-17" title="17"><span class="co">#&gt; E 0.214 0.252 0.300 0.306 0.338 0.403 10</span></a>
<a class="sourceLine" id="cb8-18" title="18"><span class="co">#&gt; F 0.237 0.270 0.300 0.311 0.326 0.335 10</span></a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; G 0.245 0.282 0.297 0.298 0.314 0.348 10</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; H 0.241 0.282 0.308 0.312 0.328 0.373 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-13" title="13"><span class="co">#&gt; A 0.288 0.372 0.440 0.418 0.481 0.662 10</span></a>
<a class="sourceLine" id="cb8-14" title="14"><span class="co">#&gt; B 0.281 0.294 0.364 0.369 0.411 0.461 10</span></a>
<a class="sourceLine" id="cb8-15" title="15"><span class="co">#&gt; C 0.390 0.493 0.563 0.550 0.645 0.731 10</span></a>
<a class="sourceLine" id="cb8-16" title="16"><span class="co">#&gt; D 0.244 0.269 0.733 0.337 0.347 4.420 10</span></a>
<a class="sourceLine" id="cb8-17" title="17"><span class="co">#&gt; E 0.283 0.344 0.368 0.363 0.410 0.434 10</span></a>
<a class="sourceLine" id="cb8-18" title="18"><span class="co">#&gt; F 0.250 0.319 0.343 0.339 0.354 0.492 10</span></a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; G 0.286 0.329 0.363 0.340 0.392 0.496 10</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; H 0.292 0.305 0.365 0.359 0.421 0.459 10</span></a></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> too, 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">
@ -356,13 +365,13 @@
<a class="sourceLine" id="cb9-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb9-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb9-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb9-21" title="21"><span class="co">#&gt; en 10.85 10.89 11.10 11.03 11.23 11.83 10</span></a>
<a class="sourceLine" id="cb9-22" title="22"><span class="co">#&gt; de 19.43 19.50 19.86 19.58 20.35 20.99 10</span></a>
<a class="sourceLine" id="cb9-23" title="23"><span class="co">#&gt; nl 19.08 19.17 19.40 19.48 19.56 19.63 10</span></a>
<a class="sourceLine" id="cb9-24" title="24"><span class="co">#&gt; es 19.35 19.44 26.07 19.48 20.06 52.36 10</span></a>
<a class="sourceLine" id="cb9-25" title="25"><span class="co">#&gt; it 19.23 19.40 22.91 19.49 19.91 52.92 10</span></a>
<a class="sourceLine" id="cb9-26" title="26"><span class="co">#&gt; fr 19.10 19.22 19.40 19.45 19.54 19.68 10</span></a>
<a class="sourceLine" id="cb9-27" title="27"><span class="co">#&gt; pt 19.01 19.46 29.32 19.55 52.32 52.50 10</span></a></code></pre></div>
<a class="sourceLine" id="cb9-21" title="21"><span class="co">#&gt; en 24.41 25.27 26.34 25.41 26.92 30.60 10</span></a>
<a class="sourceLine" id="cb9-22" title="22"><span class="co">#&gt; de 35.53 35.76 36.76 35.98 37.20 41.19 10</span></a>
<a class="sourceLine" id="cb9-23" title="23"><span class="co">#&gt; nl 34.51 35.55 39.93 35.60 40.15 69.76 10</span></a>
<a class="sourceLine" id="cb9-24" title="24"><span class="co">#&gt; es 34.36 35.98 44.29 37.46 39.98 73.16 10</span></a>
<a class="sourceLine" id="cb9-25" title="25"><span class="co">#&gt; it 35.78 36.22 37.44 36.75 38.70 40.78 10</span></a>
<a class="sourceLine" id="cb9-26" title="26"><span class="co">#&gt; fr 35.45 35.71 36.09 35.79 36.15 37.93 10</span></a>
<a class="sourceLine" id="cb9-27" title="27"><span class="co">#&gt; pt 35.10 35.44 44.61 35.76 39.68 77.27 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>