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(v1.4.0.9032) auto-data guessing for functions

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dr. M.S. (Matthijs) Berends
2020-12-07 16:06:42 +01:00
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11
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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -285,7 +285,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates.</p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><a href='https://rdrr.io/r/stats/filter.html'>filter()</a></code>, <code>mutate()</code> and <code>summarise()</code>.</p></td>
</tr>
<tr>
<th>col_date</th>
@ -366,7 +366,8 @@
<p>A <code><a href='https://rdrr.io/r/base/logical.html'>logical</a></code> vector</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>first_isolate()</code> function is a wrapper around the <code><a href='is_new_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>The <code>first_isolate()</code> function is a wrapper around the <code><a href='is_new_episode.html'>is_new_episode()</a></code> function, but more efficient for data sets containing microorganism codes or names.</p>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Why this is so important</h3>
@ -378,7 +379,7 @@
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates.</p>
<p>The function <code>filter_first_isolate()</code> is essentially equal to either:</p><pre> <span class='va'>x</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='va'>x</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>x</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span><span class='op'>)</span>
</pre>
<p>The function <code>filter_first_weighted_isolate()</code> is essentially equal to:</p><pre> <span class='va'>x</span> <span class='op'>%&gt;%</span>
@ -433,6 +434,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='co'># short-hand versions:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'>filter_first_isolate</span><span class='op'>(</span><span class='op'>)</span>

2
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">1.4.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>

45
docs/reference/is_new_episode.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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -281,48 +281,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimen
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span><span class='op'>)</span>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># is_new_episode() can also be used in dplyr verbs to determine patient</span>
<span class='co'># episodes based on any (combination of) grouping variables:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>condition <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span><span class='op'>(</span>x <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'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span><span class='op'>)</span>,
size <span class='op'>=</span> <span class='fl'>2000</span>,
replace <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>condition</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>new_episode <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span>patients <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></span><span class='op'>(</span><span class='va'>patient_id</span><span class='op'>)</span>,
n_episodes_365 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>,
n_episodes_60 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span><span class='op'>)</span>,
n_episodes_30 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>30</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># grouping on patients and microorganisms leads to the same results</span>
<span class='co'># as first_isolate():</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span>, include_unknown <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>y</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>patient_id</span>, <span class='va'>mo</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>patient_id</span>, <span class='va'>y</span><span class='op'>$</span><span class='va'>patient_id</span><span class='op'>)</span>
<span class='co'># but is_new_episode() has a lot more flexibility than first_isolate(),</span>
<span class='co'># since you can now group on anything that seems relevant:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>patient_id</span>, <span class='va'>mo</span>, <span class='va'>hospital_id</span>, <span class='va'>ward_icu</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>flag_episode <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
</pre>
<pre class="examples"></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

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@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Key antibiotics for first weighted isolates — key_antibiotics" />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." />
<meta property="og:description" content="These function can be used to determine first isolates (see first_isolate()). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first weighted isolates." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -239,7 +239,7 @@
</div>
<div class="ref-description">
<p>These function can be used to determine first isolates (see <code><a href='first_isolate.html'>first_isolate()</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first <em>weighted</em> isolates.</p>
<p>These function can be used to determine first isolates (see <code><a href='first_isolate.html'>first_isolate()</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first <em>weighted</em> isolates.</p>
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span><span class='op'>(</span>
@ -281,7 +281,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a data.frame with antibiotics columns, like <code>AMX</code> or <code>amox</code></p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p></td>
</tr>
<tr>
<th>col_mo</th>
@ -331,7 +331,8 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>key_antibiotics()</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antibiotics()</code> and ignored by <code>key_antibiotics_equal()</code>.</p>
<p>The <code>key_antibiotics()</code> function is context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>The function <code>key_antibiotics()</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antibiotics()</code> and ignored by <code>key_antibiotics_equal()</code>.</p>
<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function only uses this function on the same microbial species from the same patient. Using this, e.g. an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) is found within the same patient episode. Without key antibiotic comparison it would not. See <code><a href='first_isolate.html'>first_isolate()</a></code> for more info.</p>
<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are:</p><ul>
<li><p>Amoxicillin</p></li>
@ -395,30 +396,30 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># output of the `key_antibiotics` function could be like this:</span>
<span class='co'># output of the `key_antibiotics()` function could be like this:</span>
<span class='va'>strainA</span> <span class='op'>&lt;-</span> <span class='st'>"SSSRR.S.R..S"</span>
<span class='va'>strainB</span> <span class='op'>&lt;-</span> <span class='st'>"SSSIRSSSRSSS"</span>
<span class='co'># can those strings can be compared with:</span>
<span class='co'># those strings can be compared with:</span>
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span><span class='op'>)</span>
<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span>, ignore_I <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># FALSE, because I is not ignored and so the 4th value differs</span>
<span class='co'># FALSE, because I is not ignored and so the 4th character differs</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># set key antibiotics to a new variable</span>
<span class='va'>my_patients</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>keyab <span class='op'>=</span> <span class='fu'>key_antibiotics</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>keyab <span class='op'>=</span> <span class='fu'>key_antibiotics</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='co'># no need to define `x`</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>
<span class='co'># now calculate first isolates</span>
first_regular <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span>, col_keyantibiotics <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
first_regular <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span>col_keyantibiotics <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
<span class='co'># and first WEIGHTED isolates</span>
first_weighted <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span>, col_keyantibiotics <span class='op'>=</span> <span class='st'>"keyab"</span><span class='op'>)</span>
first_weighted <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span>col_keyantibiotics <span class='op'>=</span> <span class='st'>"keyab"</span><span class='op'>)</span>
<span class='op'>)</span>
<span class='co'># Check the difference, in this data set it results in 7% more isolates:</span>
<span class='co'># Check the difference, in this data set it results in a lot more isolates:</span>
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>my_patients</span><span class='op'>$</span><span class='va'>first_regular</span>, na.rm <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>my_patients</span><span class='op'>$</span><span class='va'>first_weighted</span>, na.rm <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='op'>}</span>

39
docs/reference/mdro.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">1.4.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -268,7 +268,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p></td>
</tr>
<tr>
<th>guideline</th>
@ -319,20 +319,21 @@ Ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <cod
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>For the <code>pct_required_classes</code> argument, values above 1 will be divided by 100. This is to support both fractions (<code>0.75</code> or <code>3/4</code>) and percentages (<code>75</code>).</p>
<p>These functions are context-aware when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>. This means that then the <code>x</code> parameter can be omitted, please see <em>Examples</em>.</p>
<p>For the <code>pct_required_classes</code> argument, values above 1 will be divided by 100. This is to support both fractions (<code>0.75</code> or <code>3/4</code>) and percentages (<code>75</code>).</p>
<p>Currently supported guidelines are (case-insensitive):</p><ul>
<li><p><code>guideline = "CMI2012"</code><br />
Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href='https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext'>link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)<br />
The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.1"</code><br />
The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
<li><p><code>guideline = "TB"</code><br />
The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code><br />
The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p></li>
<li><p><code>guideline = "BRMO"</code><br />
The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href='https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh'>link</a>)</p></li>
<li><p><code>guideline = "CMI2012"</code> (default)</p>
<p>Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href='https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext'>link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
<p>The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>link</a>)</p></li>
<li><p><code>guideline = "EUCAST3.1"</code></p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
<li><p><code>guideline = "TB"</code></p>
<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
<li><p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p></li>
<li><p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href='https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh'>link</a>)</p></li>
</ul>
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://github.com/msberends/AMR/issues/new'>https://github.com/msberends/AMR/issues/new</a>.</p>
@ -380,10 +381,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class='fu'>mdro</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/table.html'>table</a></span><span class='op'>(</span><span class='op'>)</span>
<span class='co'># no need to define `x` when used inside dplyr verbs:</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>EUCAST <span class='op'>=</span> <span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span>,
BRMO <span class='op'>=</span> <span class='fu'>brmo</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span>,
MRGN <span class='op'>=</span> <span class='fu'>mrgn</span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>MDRO <span class='op'>=</span> <span class='fu'>mdro</span><span class='op'>(</span><span class='op'>)</span>,
EUCAST <span class='op'>=</span> <span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span><span class='op'>)</span>,
BRMO <span class='op'>=</span> <span class='fu'>brmo</span><span class='op'>(</span><span class='op'>)</span>,
MRGN <span class='op'>=</span> <span class='fu'>mrgn</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>

4
docs/reference/resistance_predict.html
View File

@ -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">1.4.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
</span>
</div>
@ -287,7 +287,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates.</p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be omitted when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>.</p></td>
</tr>
<tr>
<th>col_ab</th>