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(v1.6.0.9009) key_antibiotics update

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dr. M.S. (Matthijs) Berends
2021-04-23 16:13:26 +02:00
parent 70b803dbb6
commit 5f9e7bd3ee
20 changed files with 100 additions and 98 deletions
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2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

15
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1609008" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9008">
<a href="#amr-1609008" class="anchor"></a>AMR 1.6.0.9008<small> Unreleased </small>
<div id="amr-1609009" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9009">
<a href="#amr-1609009" class="anchor"></a>AMR 1.6.0.9009<small> Unreleased </small>
</h1>
<div id="last-updated-23-april-2021" class="section level2">
<h2 class="hasAnchor">
@ -287,6 +287,13 @@
<li>Fixed an installation error on R-3.0</li>
<li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li>
<li>Fixed a bug that <code>col_mo</code> for some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be column names of the <code>microorganisms</code> data set as it would throw an error</li>
<li>Using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> with key antibiotics:
<ul>
<li>Fixed a bug in the algorithm when using <code>type == "points"</code>, that now leads to inclusion of slightly more isolates</li>
<li>Big speed improvement for <code><a href="../reference/key_antibiotics.html">key_antibiotics_equal()</a></code> when using <code>type == "points"</code>
</li>
</ul>
</li>
</ul>
</div>
</div>

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-04-23T07:52Z
last_built: 2021-04-23T14:13Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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docs/reference/first_isolate.html
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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>
@ -346,7 +346,7 @@
</tr>
<tr>
<th>info</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
</tr>
<tr>
<th>include_unknown</th>

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docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

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docs/reference/key_antibiotics.html
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@ -82,7 +82,7 @@
</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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>
@ -273,7 +273,9 @@
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span><span class='op'>)</span>,
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span>
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -325,7 +327,11 @@
</tr>
<tr>
<th>info</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
<td><p>unused - previously used to indicate whether a progress bar should print</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether comparison with <code>NA</code> should return <code>FALSE</code> (defaults to <code>TRUE</code> for backwards compatibility)</p></td>
</tr>
</table>

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docs/survey.html
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@ -81,7 +81,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>