P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-03 16:39:37 +02:00
Code Releases Activity

(v1.7.1.9070) Better WHONET support

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-13 10:18:28 +01:00
parent f90e27c1b0
commit 578e7dfee9
74 changed files with 20758 additions and 47402 deletions
Download Patch File Download Diff File Expand all files Collapse all files

125
docs/articles/benchmarks.html
View File

@@ -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">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9070</span>
</span>
</div>
@@ -222,23 +222,23 @@
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>, <span class="co"># Methicillin Resistant S. aureus</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span>, <span class="co"># Vancomycin Intermediate S. aureus</span>
times <span class="op">=</span> <span class="fl">25</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/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="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") 12.0 14.0 24.0 15.0 42 64 25</span>
<span class="co"># as.mo("stau") 49.0 62.0 79.0 77.0 98 120 25</span>
<span class="co"># as.mo("STAU") 53.0 59.0 76.0 66.0 92 120 25</span>
<span class="co"># as.mo("staaur") 12.0 14.0 19.0 15.0 17 53 25</span>
<span class="co"># as.mo("STAAUR") 12.0 13.0 18.0 14.0 16 54 25</span>
<span class="co"># as.mo("S. aureus") 27.0 32.0 41.0 33.0 39 79 25</span>
<span class="co"># as.mo("S aureus") 26.0 31.0 45.0 34.0 67 79 25</span>
<span class="co"># as.mo("Staphylococcus aureus") 3.7 4.4 8.8 4.7 5 45 25</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 280.0 280.0 300 330 25</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 170.0 200.0 230.0 220.0 240 330 25</span>
<span class="co"># as.mo("MRSA") 12.0 13.0 18.0 15.0 16 53 25</span>
<span class="co"># as.mo("VISA") 21.0 26.0 44.0 33.0 62 78 25</span></code></pre></div>
<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>
<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 200 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 66 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 &lt;mo&gt;:</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 &lt;mo&gt;</span>
<span class="co"># [1] B_STPHY_EPDR B_STRPT_GRPA B_STPHY_AURS F_CANDD_GLBR F_CANDD </span>
<span class="co"># [6] B_STRPT_ANGN</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"># 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>
@@ -272,11 +272,11 @@
<span class="co"># now let's see:</span>
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>,
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" 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="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) 232 245 327 353 384 449 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.353 seconds. That is 177 nanoseconds on average. You only lose time on your unique input values.</p>
<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>
</div>
<div class="section level3">
<h3 id="precalculated-results">Precalculated results<a class="anchor" aria-label="anchor" href="#precalculated-results"></a>
@@ -287,13 +287,13 @@
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>,
C <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span><span class="op">)</span>,
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" 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="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 9.04 9.19 9.33 9.65 10.0 10</span>
<span class="co"># B 24.00 26.60 33.10 27.50 27.80 78.7 10</span>
<span class="co"># C 2.20 2.41 7.64 2.57 2.66 53.6 10</span></code></pre></div>
<p>So going from <code>mo_name("Staphylococcus aureus")</code> to <code>"Staphylococcus aureus"</code> takes 0.0026 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"># 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>
<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"><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>,
@@ -304,52 +304,63 @@
G <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_phylum</a></span><span class="op">(</span><span class="st">"Firmicutes"</span><span class="op">)</span>,
H <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="st">"Bacteria"</span><span class="op">)</span>,
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" 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="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 1.52 1.69 2.40 1.92 3.43 4.28 10</span>
<span class="co"># B 1.37 1.39 1.83 1.70 1.74 3.61 10</span>
<span class="co"># C 1.41 1.72 2.17 2.00 2.51 3.34 10</span>
<span class="co"># D 1.39 1.43 1.63 1.61 1.73 2.10 10</span>
<span class="co"># E 1.40 1.71 1.82 1.75 2.13 2.26 10</span>
<span class="co"># F 1.36 1.40 1.70 1.66 1.93 2.27 10</span>
<span class="co"># G 1.38 1.68 2.32 1.71 3.56 4.41 10</span>
<span class="co"># H 1.36 1.64 2.06 1.69 2.25 3.59 10</span></code></pre></div>
<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>
<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">
<h3 id="results-in-other-languages">Results in other languages<a class="anchor" aria-label="anchor" href="#results-in-other-languages"></a>
</h3>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time:</p>
<p>When the system language is non-English and supported by this <code>AMR</code> package, some functions will have a translated result. This almost does’t take extra time (compare “en” from the table below with the other languages):</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on an English system</span>
<code class="sourceCode R"><span class="va">CoNS</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"CoNS"</span><span class="op">)</span>
<span class="va">CoNS</span>
<span class="co"># Class &lt;mo&gt;</span>
<span class="co"># [1] B_STPHY_CONS</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span> <span class="co"># or just mo_name(CoNS) on an English system</span>
<span class="co"># [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on a Spanish system</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># or just mo_name(CoNS) on a Spanish system</span>
<span class="co"># [1] "Staphylococcus coagulasa negativo (SCN)"</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># or just mo_name("CoNS") on a Dutch system</span>
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span> <span class="co"># or just mo_name(CoNS) on a Dutch system</span>
<span class="co"># [1] "Coagulase-negatieve Staphylococcus (CNS)"</span>
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>en <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span>,
de <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>,
nl <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>,
es <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>,
it <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"it"</span><span class="op">)</span>,
fr <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"fr"</span><span class="op">)</span>,
pt <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span>,
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class="external-link">microbenchmark</a></span><span class="op">(</span>da <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"da"</span><span class="op">)</span>,
de <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span>,
en <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span>,
es <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>,
fr <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"fr"</span><span class="op">)</span>,
it <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"it"</span><span class="op">)</span>,
nl <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>,
pt <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span>,
ru <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"ru"</span><span class="op">)</span>,
sv <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">CoNS</span>, language <span class="op">=</span> <span class="st">"sv"</span><span class="op">)</span>,
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" 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="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"># en 18.80 19.08 23.94 19.62 21.69 83.41 100</span>
<span class="co"># de 30.37 30.79 39.01 31.75 35.07 112.40 100</span>
<span class="co"># nl 34.35 34.94 46.21 35.95 43.04 100.30 100</span>
<span class="co"># es 34.10 34.71 43.74 35.44 39.66 101.60 100</span>
<span class="co"># it 32.91 33.42 41.19 34.04 36.24 101.50 100</span>
<span class="co"># fr 32.18 32.87 42.84 33.76 40.21 92.48 100</span>
<span class="co"># pt 30.11 30.78 38.80 31.33 34.45 99.76 100</span></code></pre></div>
<p>Currently supported non-English languages are German, Dutch, Spanish, Italian, French and Portuguese.</p>
<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>
</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: 83 KiB

After

Width:  |  Height:  |  Size: 83 KiB

122
docs/articles/datasets.html
View File

@@ -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">1.7.1.9069</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9070</span>
</span>
</div>
@@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">12 December 2021</h4>
<h4 data-toc-skip class="date">13 December 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
@@ -493,12 +493,12 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div class="section level2">
<h2 id="antibiotic-agents">Antibiotic agents<a class="anchor" aria-label="anchor" href="#antibiotic-agents"></a>
</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>It was last updated on 13 December 2021 09:13:56 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (33 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
</li>
@@ -1055,49 +1055,51 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div class="section level2">
<h2 id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<a class="anchor" aria-label="anchor" href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
</h2>
<p>A data set with 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>A data set with 20,318 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 12 December 2021 10:27:59 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 13 December 2021 08:00:17 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R file</a> (39 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel file</a> (0.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.6 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.8 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.5 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).</p>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST (2011-2021).</p>
</div>
<div class="section level3">
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
</h3>
<table class="table">
<colgroup>
<col width="8%">
<col width="9%">
<col width="5%">
<col width="4%">
<col width="12%">
<col width="20%">
<col width="17%">
<col width="7%">
<col width="16%">
<col width="8%">
<col width="11%">
<col width="9%">
<col width="9%">
<col width="4%">
<col width="8%">
<col width="10%">
<col width="10%">
<col width="5%">
</colgroup>
<thead><tr class="header">
<th align="center">guideline</th>
<th align="center">method</th>
<th align="center">site</th>
<th align="center">mo</th>
<th align="center">rank_index</th>
<th align="center">ab</th>
<th align="center">ref_tbl</th>
<th align="center">disk_dose</th>
@@ -1108,74 +1110,80 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<tbody>
<tr class="odd">
<td align="center">EUCAST 2021</td>
<td align="center">DISK</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">Enterobacterales</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Enterobacterales</td>
<td align="center">20-10ug</td>
<td align="center">19</td>
<td align="center">19</td>
<td align="center">Aspergillus fumigatus</td>
<td align="center">2</td>
<td align="center">Amphotericin B</td>
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">4</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2021</td>
<td align="center">DISK</td>
<td align="center">UTI</td>
<td align="center">Enterobacterales</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Enterobacterales</td>
<td align="center">20-10ug</td>
<td align="center">16</td>
<td align="center">16</td>
<td align="center">TRUE</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">Aspergillus niger</td>
<td align="center">2</td>
<td align="center">Amphotericin B</td>
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">4</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">Enterobacterales</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Enterobacterales</td>
<td align="center">Candida</td>
<td align="center">3</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">8</td>
<td align="center">8</td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center">UTI</td>
<td align="center">Enterobacterales</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Enterobacterales</td>
<td align="center"></td>
<td align="center">32</td>
<td align="center">32</td>
<td align="center">TRUE</td>
<td align="center">Candida albicans</td>
<td align="center">2</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">Actinomyces</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Anaerobes, Grampositive</td>
<td align="center">Candida krusei</td>
<td align="center">2</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">4</td>
<td align="center">8</td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2021</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">Bacteroides</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Anaerobes, Gramnegative</td>
<td align="center">Candida parapsilosis</td>
<td align="center">2</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">4</td>
<td align="center">8</td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">FALSE</td>
</tr>
</tbody>

2
docs/articles/index.html
View File

@@ -17,7 +17,7 @@
</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">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9070</span>
</span>
</div>

4
docs/articles/welcome_to_AMR.html
View File

@@ -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">1.7.1.9068</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9070</span>
</span>
</div>
@@ -201,7 +201,7 @@
<p>Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: <a href="https://msberends.github.io/AMR/articles/" class="uri">https://msberends.github.io/AMR/articles/</a>.</p>
<hr>
<p><code>AMR</code> is a free, open-source and independent R package (see <a href="https://msberends.github.io/AMR/#copyright">Copyright</a>) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>The <code>AMR</code> package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
<p>This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.</p>
<p>This package can be used for:</p>