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v1.2.0

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dr. M.S. (Matthijs) Berends
2020-05-28 16:48:55 +02:00
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commit b44e2c9202
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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">1.1.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0</span>
</span>
</div>
@ -221,21 +221,21 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">S.aureus</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">2</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 8.2 9.7 22.0 14.0 38.0 43</span>
<span class="co"># as.mo("stau") 130.0 130.0 160.0 170.0 170.0 190</span>
<span class="co"># as.mo("STAU") 120.0 130.0 150.0 150.0 180.0 190</span>
<span class="co"># as.mo("staaur") 8.3 9.1 13.0 9.4 10.0 40</span>
<span class="co"># as.mo("STAAUR") 8.0 9.3 15.0 10.0 13.0 35</span>
<span class="co"># as.mo("S. aureus") 9.3 11.0 26.0 14.0 15.0 120</span>
<span class="co"># as.mo("S aureus") 10.0 12.0 22.0 13.0 38.0 49</span>
<span class="co"># as.mo("Staphylococcus aureus") 6.6 7.7 8.5 8.6 9.1 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 820.0 860.0 890.0 880.0 930.0 1000</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 350.0 350.0 370.0 370.0 370.0 380</span>
<span class="co"># as.mo("MRSA") 7.8 9.1 13.0 10.0 11.0 42</span>
<span class="co"># as.mo("VISA") 11.0 12.0 19.0 13.0 15.0 47</span>
<span class="co"># as.mo("VRSA") 11.0 12.0 21.0 14.0 39.0 42</span>
<span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 150.0 190</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 8.5 11.0 17.0 12.0 12.0 43.0</span>
<span class="co"># as.mo("stau") 120.0 130.0 150.0 140.0 160.0 180.0</span>
<span class="co"># as.mo("STAU") 130.0 140.0 150.0 150.0 160.0 170.0</span>
<span class="co"># as.mo("staaur") 7.7 9.1 13.0 11.0 12.0 38.0</span>
<span class="co"># as.mo("STAAUR") 8.3 9.3 15.0 10.0 11.0 37.0</span>
<span class="co"># as.mo("S. aureus") 11.0 12.0 18.0 13.0 14.0 41.0</span>
<span class="co"># as.mo("S aureus") 8.8 11.0 17.0 12.0 13.0 41.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 6.4 6.6 7.4 7.6 7.8 9.1</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 810.0 870.0 890.0 890.0 900.0 1000.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 320.0 340.0 370.0 350.0 400.0 490.0</span>
<span class="co"># as.mo("MRSA") 9.2 10.0 13.0 11.0 12.0 37.0</span>
<span class="co"># as.mo("VISA") 12.0 12.0 22.0 13.0 43.0 44.0</span>
<span class="co"># as.mo("VRSA") 11.0 13.0 21.0 14.0 38.0 41.0</span>
<span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 170.0 200.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -262,12 +262,12 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">M.semesiae</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 135.600 143.500 157.800 153.400 175.70 191.40</span>
<span class="co"># as.mo("METSEM") 139.700 140.800 158.100 148.300 176.10 188.50</span>
<span class="co"># as.mo("M. semesiae") 9.010 9.317 13.280 9.802 12.51 40.46</span>
<span class="co"># as.mo("M. semesiae") 9.155 9.321 9.665 9.557 10.07 10.37</span>
<span class="co"># as.mo("Methanosarcina semesiae") 6.737 7.160 16.020 8.413 33.21 37.10</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("metsem") 143.400 146.300 156.10 155.400 164.900 176.40</span>
<span class="co"># as.mo("METSEM") 141.600 146.900 167.00 170.700 185.000 188.00</span>
<span class="co"># as.mo("M. semesiae") 9.665 9.879 16.50 10.090 11.960 44.29</span>
<span class="co"># as.mo("M. semesiae") 10.000 10.080 14.46 11.660 13.140 42.01</span>
<span class="co"># as.mo("Methanosarcina semesiae") 7.161 7.389 10.40 7.542 9.294 33.00</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -307,7 +307,7 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</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) 1670 1740 1800 1790 1880 1900 10</span></pre></body></html></div>
<span class="co"># mo_name(x) 1650 1730 1790 1790 1840 1900 10</span></pre></body></html></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.79 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
@ -320,10 +320,10 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">10</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 5.630 5.900 6.420 6.480 6.910 7.120 10</span>
<span class="co"># B 9.940 11.300 15.000 11.800 12.300 45.300 10</span>
<span class="co"># C 0.247 0.277 0.315 0.295 0.358 0.386 10</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 5.680 5.820 9.61 6.36 6.850 39.500 10</span>
<span class="co"># B 9.790 10.000 10.60 10.40 10.900 11.900 10</span>
<span class="co"># C 0.229 0.259 0.27 0.27 0.286 0.311 10</span></pre></body></html></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0003 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="cb6"><html><body><pre class="r"><span class="no">run_it</span> <span class="kw">&lt;-</span> <span class="fu">microbenchmark</span>(<span class="kw">A</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),
<span class="kw">B</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),
@ -337,14 +337,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">3</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 0.207 0.214 0.241 0.218 0.240 0.412 10</span>
<span class="co"># B 0.178 0.207 0.215 0.211 0.219 0.272 10</span>
<span class="co"># C 0.218 0.221 0.234 0.233 0.240 0.264 10</span>
<span class="co"># D 0.203 0.211 0.221 0.214 0.218 0.290 10</span>
<span class="co"># E 0.208 0.209 0.223 0.214 0.227 0.279 10</span>
<span class="co"># F 0.172 0.203 0.222 0.212 0.222 0.302 10</span>
<span class="co"># G 0.200 0.202 0.212 0.208 0.213 0.253 10</span>
<span class="co"># H 0.193 0.194 0.208 0.200 0.215 0.261 10</span></pre></body></html></div>
<span class="co"># A 0.209 0.221 0.236 0.225 0.244 0.311 10</span>
<span class="co"># B 0.197 0.201 0.215 0.212 0.222 0.266 10</span>
<span class="co"># C 0.205 0.224 0.243 0.229 0.242 0.383 10</span>
<span class="co"># D 0.199 0.207 0.216 0.211 0.214 0.270 10</span>
<span class="co"># E 0.196 0.206 0.218 0.215 0.221 0.270 10</span>
<span class="co"># F 0.188 0.197 0.212 0.210 0.216 0.269 10</span>
<span class="co"># G 0.195 0.198 0.213 0.203 0.215 0.299 10</span>
<span class="co"># H 0.184 0.193 0.205 0.201 0.207 0.252 10</span></pre></body></html></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">
@ -370,14 +370,14 @@
<span class="kw">times</span> <span class="kw">=</span> <span class="fl">100</span>)
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">run_it</span>, <span class="kw">unit</span> <span class="kw">=</span> <span class="st">"ms"</span>, <span class="kw">signif</span> <span class="kw">=</span> <span class="fl">4</span>)
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 11.24 11.97 16.09 13.31 13.71 48.40 100</span>
<span class="co"># de 12.18 12.84 19.63 14.33 15.00 55.14 100</span>
<span class="co"># nl 16.24 17.07 24.36 18.61 19.83 55.70 100</span>
<span class="co"># es 12.23 12.77 17.38 13.71 14.72 51.57 100</span>
<span class="co"># it 12.15 13.01 18.55 14.03 14.81 146.90 100</span>
<span class="co"># fr 12.23 13.08 16.81 14.30 14.86 49.30 100</span>
<span class="co"># pt 12.30 12.85 18.13 14.24 14.88 49.70 100</span></pre></body></html></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 9.303 11.59 14.90 12.40 13.63 45.92 100</span>
<span class="co"># de 10.080 12.39 15.77 13.11 14.45 46.27 100</span>
<span class="co"># nl 13.200 16.26 20.88 17.80 19.52 49.93 100</span>
<span class="co"># es 9.957 12.23 15.57 13.12 14.59 51.99 100</span>
<span class="co"># it 10.210 12.44 19.02 13.34 14.74 52.96 100</span>
<span class="co"># fr 10.040 12.40 18.90 13.26 15.07 54.40 100</span>
<span class="co"># pt 10.450 12.67 16.91 13.46 14.68 51.47 100</span></pre></body></html></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>