mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 00:02:38 +02:00
(v0.7.1.9076) mo codes
This commit is contained in:
@ -78,7 +78,7 @@
|
||||
</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">0.7.1.9075</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9076</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -225,11 +225,11 @@
|
||||
|
||||
</div>
|
||||
|
||||
<div id="amr-0-7-1-9075" class="section level1">
|
||||
<div id="amr-0-7-1-9076" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0-7-1-9075" class="anchor"></a>AMR 0.7.1.9075<small> Unreleased </small>
|
||||
<a href="#amr-0-7-1-9076" class="anchor"></a>AMR 0.7.1.9076<small> Unreleased </small>
|
||||
</h1>
|
||||
<p><small>Last updated: 18-Sep-2019</small></p>
|
||||
<p><small>Last updated: 20-Sep-2019</small></p>
|
||||
<div id="breaking" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#breaking" class="anchor"></a>Breaking</h3>
|
||||
@ -250,7 +250,7 @@ For WHONET users, this means that all records/isolates with organism code <code>
|
||||
<a class="sourceLine" id="cb2-8" data-line-number="8">x <-<span class="st"> </span><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-9" data-line-number="9">x[<span class="dv">1</span>] <-<span class="st"> "testvalue"</span></a>
|
||||
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#> invalid microbial code, NA generated</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#> invalid microorganism code, NA generated</span></a></code></pre></div>
|
||||
This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</li>
|
||||
<li><p>Function <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
</ul>
|
||||
@ -263,12 +263,13 @@ This is important, because a value like <code>"testvalue"</code> could never be
|
||||
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the antimicrobial resistance of any bug-drug combination in a data set:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</a>
|
||||
<a class="sourceLine" id="cb3-2" data-line-number="2">x</a>
|
||||
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co">#> ab mo S I R total</span></a>
|
||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#> 1 AMC B_ESCHR_COL 332 74 61 467</span></a>
|
||||
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co">#> 2 AMC B_KLBSL_PNE 49 3 6 58</span></a>
|
||||
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#> 3 AMC B_PROTS_MIR 28 7 1 36</span></a>
|
||||
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co">#> 4 AMC B_PSDMN_AER 0 0 30 30</span></a>
|
||||
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#> 5 AMC B_STPHY_AUR 234 0 1 235</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#> ab mo S I R total</span></a>
|
||||
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co">#> 1 AMC B_ESCHR_COLI 332 74 61 467</span></a>
|
||||
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#> 2 AMC B_KLBSL_PNMN 49 3 6 58</span></a>
|
||||
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co">#> 3 AMC B_PROTS_MRBL 28 7 1 36</span></a>
|
||||
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#> 4 AMC B_PSDMN_AERG 0 0 30 30</span></a>
|
||||
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#> 5 AMC B_STPHY_AURS 234 0 1 235</span></a></code></pre></div>
|
||||
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://www.rdocumentation.org/packages/base/topics/format">format()</a></code> function:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/format">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
|
||||
</li>
|
||||
@ -1266,7 +1267,7 @@ 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-0-7-1-9075">0.7.1.9075</a></li>
|
||||
<li><a href="#amr-0-7-1-9076">0.7.1.9076</a></li>
|
||||
<li><a href="#amr-0-7-1">0.7.1</a></li>
|
||||
<li><a href="#amr-0-7-0">0.7.0</a></li>
|
||||
<li><a href="#amr-0-6-1">0.6.1</a></li>
|
||||
|
||||
Reference in New Issue
Block a user