mirror of
https://github.com/msberends/AMR.git
synced 2025-07-17 23:13:14 +02:00
(v1.7.1.9073) as.rsi() fix for UTIs
This commit is contained in:
@ -44,7 +44,7 @@
|
||||
</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="Released version">1.7.1.9070</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9073</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -225,20 +225,20 @@
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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") 11.0 12.0 18.0 14 15.0 59 25</span>
|
||||
<span class="co"># as.mo("stau") 51.0 55.0 74.0 87 91.0 97 25</span>
|
||||
<span class="co"># as.mo("STAU") 51.0 55.0 78.0 65 92.0 200 25</span>
|
||||
<span class="co"># as.mo("staaur") 12.0 14.0 20.0 15 18.0 52 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 10.0 12.0 16.0 13 14.0 61 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 27.0 42.0 31 63.0 68 25</span>
|
||||
<span class="co"># as.mo("S aureus") 25.0 28.0 39.0 32 39.0 78 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.1 3.8 5.6 4 4.6 42 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 270.0 260 270.0 360 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 190.0 200.0 200 220.0 260 25</span>
|
||||
<span class="co"># as.mo("MRSA") 11.0 12.0 18.0 12 14.0 51 25</span>
|
||||
<span class="co"># as.mo("VISA") 21.0 22.0 32.0 23 54.0 69 25</span></code></pre></div>
|
||||
<span class="co"># as.mo("sau") 12.0 12.0 17.0 14.0 15.0 56 25</span>
|
||||
<span class="co"># as.mo("stau") 51.0 60.0 81.0 87.0 98.0 120 25</span>
|
||||
<span class="co"># as.mo("STAU") 51.0 64.0 83.0 90.0 98.0 130 25</span>
|
||||
<span class="co"># as.mo("staaur") 9.7 12.0 15.0 15.0 15.0 46 25</span>
|
||||
<span class="co"># as.mo("STAAUR") 11.0 14.0 17.0 15.0 16.0 45 25</span>
|
||||
<span class="co"># as.mo("S. aureus") 24.0 31.0 43.0 33.0 63.0 77 25</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 28.0 45.0 34.0 62.0 76 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 3.0 3.7 5.4 3.8 4.6 37 25</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 240.0 250.0 270.0 260.0 270.0 310 25</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 180.0 190.0 210.0 200.0 220.0 260 25</span>
|
||||
<span class="co"># as.mo("MRSA") 10.0 13.0 20.0 15.0 17.0 73 25</span>
|
||||
<span class="co"># as.mo("VISA") 20.0 23.0 38.0 26.0 49.0 150 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 66 times slower to determine.</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 69 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>
|
||||
<div class="section level3">
|
||||
<h3 id="repetitive-results">Repetitive results<a class="anchor" aria-label="anchor" href="#repetitive-results"></a>
|
||||
@ -258,8 +258,8 @@
|
||||
<span class="co"># what do these values look like? They are of class <mo>:</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="co"># Class <mo></span>
|
||||
<span class="co"># [1] B_STRPT_EQUI B_STPHY_CONS B_ESCHR_COLI B_ENTRC_FACM B_STPHY_CONS</span>
|
||||
<span class="co"># [6] B_ESCHR_COLI</span>
|
||||
<span class="co"># [1] B_STRPT_PNMN B_ESCHR_COLI B_STPHY_AURS B_STPHY_CONS B_ENTRC </span>
|
||||
<span class="co"># [6] B_STPHY_HMNS</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" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
@ -275,8 +275,8 @@
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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) 203 230 308 299 385 409 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.299 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 205 234 315 310 393 447 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.31 seconds. That is 155 nanoseconds on average. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div class="section level3">
|
||||
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
|
||||
@ -290,10 +290,10 @@
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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 8.02 8.23 8.77 8.88 9.17 9.32 10</span>
|
||||
<span class="co"># B 22.20 22.80 37.70 26.50 37.70 78.20 10</span>
|
||||
<span class="co"># C 2.15 2.20 2.39 2.39 2.49 2.74 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0024 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 7.89 8.95 14.80 9.21 10.50 64.60 10</span>
|
||||
<span class="co"># B 22.60 26.10 33.80 26.90 29.80 89.20 10</span>
|
||||
<span class="co"># C 1.76 2.04 2.44 2.49 2.73 3.37 10</span></code></pre></div>
|
||||
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0025 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"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">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>,
|
||||
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>,
|
||||
@ -307,14 +307,14 @@
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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 1.73 1.85 2.08 2.01 2.13 3.02 10</span>
|
||||
<span class="co"># B 1.68 1.76 2.00 1.99 2.11 2.43 10</span>
|
||||
<span class="co"># C 1.74 1.99 2.00 2.02 2.05 2.20 10</span>
|
||||
<span class="co"># D 1.73 1.86 1.99 2.03 2.08 2.22 10</span>
|
||||
<span class="co"># E 1.75 1.82 1.98 2.02 2.10 2.27 10</span>
|
||||
<span class="co"># F 1.74 1.95 1.93 1.97 1.97 2.02 10</span>
|
||||
<span class="co"># G 1.71 1.76 1.95 1.98 1.99 2.56 10</span>
|
||||
<span class="co"># H 1.72 1.83 1.93 1.98 2.00 2.05 10</span></code></pre></div>
|
||||
<span class="co"># A 1.62 1.67 1.81 1.71 1.75 2.45 10</span>
|
||||
<span class="co"># B 1.59 1.62 1.94 1.75 2.15 3.08 10</span>
|
||||
<span class="co"># C 1.61 1.64 1.74 1.70 1.73 2.09 10</span>
|
||||
<span class="co"># D 1.58 1.66 1.87 1.69 2.07 2.63 10</span>
|
||||
<span class="co"># E 1.59 1.61 1.70 1.64 1.72 2.15 10</span>
|
||||
<span class="co"># F 1.57 1.60 1.69 1.66 1.71 2.07 10</span>
|
||||
<span class="co"># G 1.56 1.60 1.75 1.67 1.73 2.21 10</span>
|
||||
<span class="co"># H 1.60 1.62 1.67 1.64 1.70 1.81 10</span></code></pre></div>
|
||||
<p>Of course, when running <code>mo_phylum("Firmicutes")</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 class="section level3">
|
||||
@ -349,18 +349,18 @@
|
||||
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" class="external-link">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"># da 1.8950 1.9550 2.702 2.0530 2.465 46.650 100</span>
|
||||
<span class="co"># de 1.9030 1.9750 3.182 2.1390 2.442 52.250 100</span>
|
||||
<span class="co"># en 0.8658 0.8927 1.045 0.9821 1.132 1.727 100</span>
|
||||
<span class="co"># es 1.9010 1.9960 4.028 2.2770 2.498 66.860 100</span>
|
||||
<span class="co"># fr 1.7650 1.8400 3.124 1.9680 2.277 54.110 100</span>
|
||||
<span class="co"># it 1.8780 1.9660 2.934 2.1150 2.479 64.780 100</span>
|
||||
<span class="co"># nl 1.9200 1.9780 3.355 2.0880 2.466 57.900 100</span>
|
||||
<span class="co"># pt 1.8540 1.9030 2.670 2.0280 2.386 47.620 100</span>
|
||||
<span class="co"># ru 1.8070 1.8950 2.240 2.2520 2.432 3.715 100</span>
|
||||
<span class="co"># sv 1.8310 1.8960 2.766 2.0890 2.359 57.690 100</span></code></pre></div>
|
||||
<p>Currently supported languages are “Danish”, “Dutch”, “English”, “French”, “German”, “Italian”, “Portuguese”, “Russian”, “Spanish” and “Swedish”.</p>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># da 1.9160 2.012 2.308 2.213 2.445 4.040 100</span>
|
||||
<span class="co"># de 1.9130 2.057 3.165 2.358 2.495 44.140 100</span>
|
||||
<span class="co"># en 0.8684 0.910 1.076 1.004 1.137 2.173 100</span>
|
||||
<span class="co"># es 1.9060 2.066 3.304 2.335 2.595 60.500 100</span>
|
||||
<span class="co"># fr 1.7950 1.888 2.169 2.104 2.338 3.366 100</span>
|
||||
<span class="co"># it 1.8830 2.025 2.809 2.342 2.536 45.730 100</span>
|
||||
<span class="co"># nl 1.9370 2.034 3.482 2.316 2.626 60.780 100</span>
|
||||
<span class="co"># pt 1.8450 1.983 3.125 2.293 2.447 43.830 100</span>
|
||||
<span class="co"># ru 1.8260 1.932 3.454 2.018 2.413 87.210 100</span>
|
||||
<span class="co"># sv 1.8260 1.930 3.428 2.207 2.441 72.080 100</span></code></pre></div>
|
||||
<p>Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user