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(v1.3.0.9036) documentation fix

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dr. M.S. (Matthijs) Berends
2020-09-30 10:24:53 +02:00
parent 4e0374af29
commit ac1c78c793
19 changed files with 86 additions and 106 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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
</span>
</div>

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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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
</span>
</div>

12
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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
</span>
</div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309035" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9035">
<a href="#amr-1309035" class="anchor"></a>AMR 1.3.0.9035<small> Unreleased </small>
<div id="amr-1309036" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9036">
<a href="#amr-1309036" class="anchor"></a>AMR 1.3.0.9036<small> Unreleased </small>
</h1>
<div id="last-updated-29-september-2020" class="section level2">
<div id="last-updated-30-september-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-29-september-2020" class="anchor"></a><small>Last updated: 29 September 2020</small>
<a href="#last-updated-30-september-2020" class="anchor"></a><small>Last updated: 30 September 2020</small>
</h2>
<p>Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!</p>
<div id="breaking" class="section level3">

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docs/pkgdown.yml
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@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-09-29T21:35Z
last_built: 2020-09-30T08:23Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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docs/reference/as.rsi.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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
</span>
</div>
@ -413,6 +413,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>example_isolates</span>) <span class='co'># see all R/SI results at a glance</span>
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://docs.ropensci.org/skimr'>"skimr"</a></span>)) {
<span class='co'># support for skim() too:</span>
<span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span>(<span class='kw'>example_isolates</span>)
}
<span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
<span class='co'># a whole data set, even with combined MIC values and disk zones</span>
@ -442,7 +447,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='as.mic.html'>is.mic</a></span>(<span class='kw'>x</span>) <span class='op'>|</span> <span class='fu'><a href='as.disk.html'>is.disk</a></span>(<span class='kw'>x</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>))
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>)
<span class='kw'>df</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>, <span class='kw'>as.rsi</span>))
<span class='kw'>df</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='kw'>AMP</span><span class='op'>:</span><span class='kw'>TOB</span>), <span class='kw'>as.rsi</span>, mo = <span class='st'>"E. coli"</span>)
@ -485,7 +490,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># note: from dplyr 1.0.0 on, this will be: </span>
<span class='co'># example_isolates %&gt;%</span>
<span class='co'># mutate(across(is.rsi.eligible, as.rsi))</span>
<span class='co'># mutate(across(where(is.rsi.eligible), as.rsi))</span>
}
<span class='co'># }</span>
</pre>

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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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
</span>
</div>

2
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">1.3.0.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9036</span>
</span>
</div>