P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 21:42:01 +02:00
Code Releases Activity

(v0.9.0.9020) as.mo() improvement

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-02-09 22:04:29 +01:00
parent 4e1c16c5a5
commit c7a76ba713
35 changed files with 70179 additions and 70116 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
docs/404.html
View File

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -84,7 +84,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>

100
docs/articles/benchmarks.html
View File

@ -41,7 +41,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">01 February 2020</h4>
<h4 class="date">09 February 2020</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -221,21 +221,21 @@
<a class="sourceLine" id="cb2-16" data-line-number="16"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb2-18" data-line-number="18"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 8.3 8.3 11.0 8.8 9.4 34.0</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 37.0 46.0 76.0 62.0 70.0 160.0</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 37.0 38.0 48.0 44.0 61.0 65.0</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 8.3 8.4 8.9 8.6 9.2 10.0</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.2 8.2 8.5 8.5 8.6 9.3</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 14.0 14.0 23.0 15.0 37.0 46.0</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 14.0 14.0 18.0 14.0 15.0 46.0</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 4.9 4.9 5.4 5.1 5.4 7.7</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 630.0 660.0 700.0 690.0 700.0 830.0</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 330.0 380.0 380.0 380.0 390.0 440.0</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.3 8.4 14.0 8.9 12.0 37.0</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 23.0 25.0 35.0 31.0 49.0 53.0</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 24.0 25.0 65.0 26.0 51.0 270.0</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 130.0 140.0 150.0 140.0 160.0 170.0</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 8.0 8.3 14 8.5 9.2 38.0</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 36.0 37.0 42 38.0 43.0 64.0</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 37.0 38.0 50 45.0 64.0 74.0</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 7.9 8.3 12 8.9 9.3 37.0</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 8.0 8.2 14 8.3 9.5 36.0</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 14.0 14.0 22 15.0 37.0 40.0</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 13.0 14.0 16 14.0 15.0 36.0</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 4.6 4.8 5 4.9 5.3 5.4</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 630.0 650.0 730 690.0 710.0 1100.0</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 350.0 370.0 400 380.0 420.0 500.0</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 8.0 8.2 11 8.3 9.3 33.0</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 24.0 25.0 46 36.0 49.0 140.0</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 23.0 25.0 37 37.0 48.0 49.0</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 120.0 130.0 140 140.0 150.0 150.0</span></a>
<a class="sourceLine" id="cb2-34" data-line-number="34"><span class="co"># neval</span></a>
<a class="sourceLine" id="cb2-35" data-line-number="35"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb2-36" data-line-number="36"><span class="co"># 10</span></a>
@ -262,18 +262,18 @@
<a class="sourceLine" id="cb3-6" data-line-number="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <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="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1444.000 1496.000 1539.00 1530.000 1573.000</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1451.000 1478.000 1521.00 1505.000 1555.000</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 14.140 14.370 17.22 14.790 14.970</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 14.460 14.690 20.25 14.850 15.800</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 5.014 5.383 11.53 5.566 5.831</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1412.000 1475.000 1514.00 1503.00 1553.000</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1348.000 1448.000 1470.00 1471.00 1512.000</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 14.410 14.600 20.03 14.84 16.170</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 14.640 15.070 26.61 18.52 41.270</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 5.289 5.508 11.34 5.63 5.837</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># max neval</span></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 1628.00 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 1658.00 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 39.56 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 42.11 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 38.03 10</span></a></code></pre></div>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 1634.00 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 1554.00 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 41.27 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 45.83 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 35.94 10</span></a></code></pre></div>
<p>That takes 5.6 times as much time on average. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></p>
@ -308,8 +308,8 @@
<a class="sourceLine" id="cb4-24" data-line-number="24"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb4-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 568 612 633 626 649 774 100</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.63 seconds (626 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 574 626 649 644 660 787 100</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.64 seconds (643 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -321,11 +321,11 @@
<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb5-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.310 6.380 6.720 6.46 6.740 8.79 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 13.500 13.800 18.200 14.60 15.000 52.20 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.815 0.839 0.886 0.86 0.899 1.13 10</span></a></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 0.0009 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="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.370 6.460 9.890 6.53 6.900 39.400 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 13.400 13.500 13.800 13.60 14.100 14.500 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.795 0.825 0.851 0.84 0.849 0.973 10</span></a></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 0.0008 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"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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="cb6-2" data-line-number="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="cb6-3" data-line-number="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
@ -338,14 +338,14 @@
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb6-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.485 0.510 0.514 0.515 0.529 0.535 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.492 0.510 0.538 0.535 0.565 0.588 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.665 0.679 0.794 0.804 0.883 0.932 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.512 0.530 0.547 0.547 0.562 0.584 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.467 0.504 0.507 0.512 0.515 0.520 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.472 0.492 0.511 0.515 0.524 0.557 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.473 0.476 0.497 0.497 0.515 0.523 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.470 0.499 0.507 0.507 0.524 0.553 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.451 0.485 0.488 0.489 0.495 0.518 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.507 0.510 0.526 0.522 0.538 0.554 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.732 0.742 0.769 0.781 0.786 0.807 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.507 0.514 0.534 0.531 0.549 0.585 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.469 0.486 0.492 0.489 0.499 0.532 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.473 0.479 0.483 0.481 0.482 0.513 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.466 0.469 0.481 0.480 0.486 0.517 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.468 0.476 0.502 0.483 0.494 0.665 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> 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">
@ -372,13 +372,13 @@
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="kw"><a href="https://rdrr.io/r/base/print.html">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="cb7-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 23.40 25.17 29.92 25.55 26.50 62.94 100</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 24.69 26.72 31.90 27.14 29.34 159.90 100</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 31.03 32.69 40.33 33.21 39.65 73.05 100</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 25.22 26.61 32.78 27.11 31.04 61.09 100</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 24.68 26.52 30.28 26.99 27.93 61.03 100</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 24.97 26.48 29.79 26.86 27.88 59.57 100</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 25.19 26.65 33.03 27.15 28.42 161.00 100</span></a></code></pre></div>
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 24.62 25.46 32.22 25.95 27.72 146.70 100</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 25.97 26.93 33.24 27.52 29.66 64.41 100</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 31.00 32.90 37.58 33.48 35.16 69.10 100</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 25.86 26.98 32.09 27.47 28.42 67.33 100</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 25.71 26.95 33.87 27.67 31.49 62.06 100</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 25.80 27.00 31.05 27.41 28.07 72.99 100</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 25.80 27.02 33.26 27.51 31.44 63.41 100</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

BIN
docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 94 KiB

After

Width:  |  Height:  |  Size: 93 KiB

BIN
docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 75 KiB

After

Width:  |  Height:  |  Size: 54 KiB

2
docs/articles/index.html
View File

@ -84,7 +84,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>

2
docs/authors.html
View File

@ -84,7 +84,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>

BIN
docs/countries.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 67 KiB

After

Width:  |  Height:  |  Size: 67 KiB

BIN
docs/countries_large.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 1.4 MiB

After

Width:  |  Height:  |  Size: 1.4 MiB

4
docs/index.html
View File

@ -45,7 +45,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
@ -206,7 +206,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<p>
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
<strong>Used in almost 100 countries</strong><br>
Since its first public release in early 2018, this package has been downloaded over 25,000 times from 96 countries <small>(as of January 2020, <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge.</p>
Since its first public release in early 2018, this package has been downloaded over 25,000 times from 99 countries <small>(as of February 2020, <a href="https://cran-logs.rstudio.com" target="_blank">CRAN logs</a>)</small>. Click the map to enlarge.</p>
<br><br>
</div>
<div id="partners" class="section level4">

21
docs/news/index.html
View File

@ -84,7 +84,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
@ -231,13 +231,13 @@
</div>
<div id="amr-0-9-0-9019" class="section level1">
<div id="amr-0-9-0-9020" class="section level1">
<h1 class="page-header">
<a href="#amr-0-9-0-9019" class="anchor"></a>AMR 0.9.0.9019<small> Unreleased </small>
<a href="#amr-0-9-0-9020" class="anchor"></a>AMR 0.9.0.9020<small> Unreleased </small>
</h1>
<div id="last-updated-01-feb-2020" class="section level2">
<div id="last-updated-09-feb-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-01-feb-2020" class="anchor"></a><small>Last updated: 01-Feb-2020</small>
<a href="#last-updated-09-feb-2020" class="anchor"></a><small>Last updated: 09-Feb-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -275,9 +275,16 @@
<li>The <code><a href="../reference/as.mo.html">as.mo()</a></code> function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the function <code>clear_mo_history()</code> was removed.</li>
<li>Bugfix for some WHONET microorganism codes that were not interpreted correctly when using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
</li>
<li>Speed improvement for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally), especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K penumoniae</em>
<li>Improvements for the algorithm used by <code><a href="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally):
<ul>
<li>Support for missing spaces, e.g. in <code><a href="../reference/as.mo.html">as.mo("Methicillin-resistant S.aureus")</a></code>
</li>
<li>Better support for determination of <em>Salmonella</em> biovars</li>
<li>Speed improvements, especially for the <em>G. species</em> format (G for genus), like <em>E. coli</em> and <em>K pneumoniae</em>
</li>
<li>Support for more common codes used in laboratory information systems</li>
</ul>
</li>
<li>Input values for <code><a href="../reference/as.disk.html">as.disk()</a></code> limited to a maximum of 50 millimeters</li>
<li>Added a lifecycle state to every function, following <a href="https://www.tidyverse.org/lifecycle">the lifecycle circle of the <code>tidyverse</code></a>
</li>
@ -1460,7 +1467,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-9-0-9019">0.9.0.9019</a></li>
<li><a href="#amr-0-9-0-9020">0.9.0.9020</a></li>
<li><a href="#amr-0-9-0">0.9.0</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>

6
docs/reference/antibiotics.html
View File

@ -85,7 +85,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
@ -290,8 +290,8 @@
<p>These data sets are available as 'flat files' for use even without R - you can find the files here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/antibiotics.R</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/antivirals.R</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt</a></p></li>
</ul>

6
docs/reference/as.mo.html
View File

@ -85,7 +85,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
@ -309,7 +309,7 @@
</pre>
<p>Values that cannot be coered will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href='mo_property.html'>mo_property_*</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>The algorithm uses data from the Catalogue of Life (see below) and from one other source (see <a href='microorganisms.html'>microorganisms</a>).</p>
<p>The <code>as.mo()</code> function uses several coercion rules for fast and logical results. It assesses the input matching criteria in the following order:</p><ol>
<li><p>Human pathogenic prevalence: the function starts with more prevalent microorganisms, followed by less prevalent ones;</p></li>
@ -317,7 +317,7 @@
<li><p>Breakdown of input values to identify possible matches.</p></li>
</ol>
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a highly prevalent microorganism found in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a less prevalent microorganism in humans), although the latter would alphabetically come first.</p>
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
<h3>Coping with uncertain results</h3>

2
docs/reference/index.html
View File

@ -84,7 +84,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>

8
docs/reference/microorganisms.codes.html
View File

@ -51,7 +51,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Translation table for common microorganism codes — microorganisms.codes" />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source()." />
<meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -85,7 +85,7 @@
</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">0.9.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
@ -234,7 +234,7 @@
</div>
<div class="ref-description">
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>.</p>
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>. They will all be searched when using <code><a href='as.mo.html'>as.mo()</a></code> and consequently all the <code><a href='mo_property.html'>mo_*</a></code> functions.</p>
</div>
<pre class="usage"><span class='no'>microorganisms.codes</span></pre>
@ -242,7 +242,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,433 observations and 2 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,450 observations and 2 variables:</p><ul>
<li><p><code>code</code><br /> Commonly used code of a microorganism</p></li>
<li><p><code>mo</code><br /> ID of the microorganism in the <a href='microorganisms.html'>microorganisms</a> data set</p></li>
</ul>

4
docs/reference/microorganisms.html
View File

@ -85,7 +85,7 @@
</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">0.9.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9020</span>
</span>
</div>
@ -273,7 +273,7 @@
<p>This data set is available as 'flat file' for use even without R - you can find the file here:</p><ul>
<li><p><a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/microorganisms.R</a></p></li>
<li><p><a href='https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt'>https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt</a></p></li>
</ul>