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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Check Availability of Columns — availability • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Check Availability of Columns — availability"><meta name="description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()."><meta property="og:description" content="Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. susceptibility() and resistance()."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9021</small>
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<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
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<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<li><a class="dropdown-item" href="../reference/mdro.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Check Availability of Columns</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/availability.R" class="external-link"><code>R/availability.R</code></a></small>
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<div class="d-none name"><code>availability.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. <code><a href="proportion.html">susceptibility()</a></code> and <code><a href="proportion.html">resistance()</a></code>.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">availability</span><span class="op">(</span><span class="va">tbl</span>, width <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> or <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>.</p></dd>
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<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a></dt>
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<dd><p>Number of characters to present the visual availability - the default is filling the width of the console.</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with column names of <code>tbl</code> as row names</p>
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>The function returns a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with columns <code>"resistant"</code> and <code>"visual_resistance"</code>. The values in that columns are calculated with <code><a href="proportion.html">resistance()</a></code>.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">availability</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ </span><span style="color: #0000BB; background-color: #444444;">`resistance()`</span><span style="color: #0000BB;"> assumes the EUCAST guideline and thus considers the 'I'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> category susceptible. Set the </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</span><span style="color: #0000BB;">.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
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<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
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<span class="r-out co"><span class="r-pr">#></span> date 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> patient 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> age 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> gender 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> ward 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> mo 2000 100.0% |####################| </span>
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<span class="r-out co"><span class="r-pr">#></span> PEN 1629 81.5% |################----| 73.7% |##############------|</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA 365 18.3% |###-----------------| 31.2% |######--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FLC 943 47.2% |#########-----------| 29.5% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMX 1350 67.5% |#############-------| 59.6% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMC 1879 94.0% |##################--| 23.7% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMP 1350 67.5% |#############-------| 59.6% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TZP 1001 50.0% |##########----------| 12.6% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CZO 446 22.3% |####----------------| 44.6% |########------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FEP 724 36.2% |#######-------------| 14.2% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CXM 1789 89.5% |#################---| 26.3% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FOX 818 40.9% |########------------| 27.4% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CTX 943 47.2% |#########-----------| 15.5% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CAZ 1811 90.6% |##################--| 66.5% |#############-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CRO 943 47.2% |#########-----------| 15.5% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> GEN 1855 92.8% |##################--| 24.6% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TOB 1351 67.6% |#############-------| 34.4% |######--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMK 692 34.6% |######--------------| 63.7% |############--------|</span>
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<span class="r-out co"><span class="r-pr">#></span> KAN 471 23.6% |####----------------| 100.0% |####################|</span>
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<span class="r-out co"><span class="r-pr">#></span> TMP 1499 75.0% |###############-----| 38.1% |#######-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> SXT 1759 88.0% |#################---| 20.5% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> NIT 743 37.2% |#######-------------| 17.1% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FOS 351 17.6% |###-----------------| 42.2% |########------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> LNZ 1023 51.2% |##########----------| 69.3% |#############-------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CIP 1409 70.5% |#############-------| 16.2% |###-----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MFX 211 10.6% |##------------------| 33.6% |######--------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> VAN 1861 93.1% |##################--| 38.3% |#######-------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TEC 976 48.8% |#########-----------| 75.7% |###############-----|</span>
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<span class="r-out co"><span class="r-pr">#></span> TCY 1200 60.0% |###########---------| 29.8% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TGC 798 39.9% |########------------| 12.7% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> DOX 1136 56.8% |###########---------| 27.7% |#####---------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> ERY 1894 94.7% |##################--| 57.2% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CLI 1520 76.0% |###############-----| 61.2% |############--------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AZM 1894 94.7% |##################--| 57.2% |###########---------|</span>
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<span class="r-out co"><span class="r-pr">#></span> IPM 889 44.5% |########------------| 6.2% |#-------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MEM 829 41.5% |########------------| 5.9% |#-------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> MTR 34 1.7% |--------------------| 14.7% |##------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CHL 154 7.7% |#-------------------| 21.4% |####----------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> COL 1640 82.0% |################----| 81.2% |################----|</span>
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<span class="r-out co"><span class="r-pr">#></span> MUP 270 13.5% |##------------------| 5.9% |#-------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> RIF 1003 50.2% |##########----------| 69.6% |#############-------|</span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">mo</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select_all.html" class="external-link">select_if</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu">availability</span><span class="op">(</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> count available visual_availabilty resistant visual_resistance</span>
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<span class="r-out co"><span class="r-pr">#></span> PEN 467 100.0% |######################| 100.0% |######################|</span>
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<span class="r-out co"><span class="r-pr">#></span> OXA 0 0.0% |----------------------| </span>
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<span class="r-out co"><span class="r-pr">#></span> FLC 0 0.0% |----------------------| </span>
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<span class="r-out co"><span class="r-pr">#></span> AMX 392 83.9% |##################----| 50.0% |###########-----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMC 467 100.0% |######################| 13.1% |##--------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMP 392 83.9% |##################----| 50.0% |###########-----------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TZP 416 89.1% |###################---| 5.5% |#---------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CZO 82 17.6% |###-------------------| 2.4% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FEP 317 67.9% |##############--------| 2.8% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CXM 465 99.6% |######################| 5.4% |#---------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> FOX 377 80.7% |#################-----| 6.9% |#---------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CTX 459 98.3% |#####################-| 2.4% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CAZ 460 98.5% |#####################-| 2.4% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> CRO 459 98.3% |#####################-| 2.4% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> GEN 460 98.5% |#####################-| 2.0% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> TOB 462 98.9% |#####################-| 2.6% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> AMK 171 36.6% |########--------------| 0.0% |----------------------|</span>
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<span class="r-out co"><span class="r-pr">#></span> KAN 0 0.0% |----------------------| </span>
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<span class="r-out co"><span class="r-pr">#></span> TMP 396 84.8% |##################----| 39.1% |########--------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> SXT 465 99.6% |######################| 31.6% |######----------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> NIT 458 98.1% |#####################-| 2.8% |----------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> FOS 61 13.1% |##--------------------| 0.0% |----------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> LNZ 467 100.0% |######################| 100.0% |######################|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> CIP 456 97.6% |#####################-| 12.5% |##--------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> MFX 57 12.2% |##--------------------| 100.0% |######################|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> VAN 467 100.0% |######################| 100.0% |######################|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> TEC 467 100.0% |######################| 100.0% |######################|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> TCY 3 0.6% |----------------------| 66.7% |##############--------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> TGC 68 14.6% |###-------------------| 0.0% |----------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> DOX 0 0.0% |----------------------| </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> ERY 467 100.0% |######################| 100.0% |######################|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> CLI 467 100.0% |######################| 100.0% |######################|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> AZM 467 100.0% |######################| 100.0% |######################|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> IPM 422 90.4% |###################---| 0.0% |----------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> MEM 418 89.5% |###################---| 0.0% |----------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> MTR 2 0.4% |----------------------| 0.0% |----------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> CHL 0 0.0% |----------------------| </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> COL 240 51.4% |###########-----------| 0.0% |----------------------|</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> MUP 0 0.0% |----------------------| </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> RIF 467 100.0% |######################| 100.0% |######################|</span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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</div>
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|
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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