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@ -32,7 +32,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -134,23 +134,10 @@ package.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span> <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span>
<span><span class="co">#&gt; ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.3.0 ──</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.8 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dplyr </span> 1.1.4 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble </span> 3.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">ggplot2 </span> 3.5.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.0.7 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 1.3.0</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.2.0</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.3.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.0</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.0.4 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.3.2</span></span>
<span><span class="co">#&gt; ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span> masks <span style="color: #0000BB;">stats</span>::lag()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span> masks <span style="color: #0000BB;">stats</span>::step()</span></span>
<span></span>
<span><span class="co"># Your data could look like this:</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span> <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span></code></pre></div>
<p>Prepare the data:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Your data could look like this:</span></span>
<span><span class="va">example_isolates</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
<span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span>
@ -215,7 +202,7 @@ three steps: preprocessing, model specification, and fitting.</p>
<h4 id="preprocessing-with-a-recipe">1. Preprocessing with a Recipe<a class="anchor" aria-label="anchor" href="#preprocessing-with-a-recipe"></a>
</h4>
<p>We create a recipe to preprocess the data for modelling.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Define the recipe for data preprocessing</span></span>
<span><span class="va">resistance_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">mo</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">data</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">step_corr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, threshold <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></span>
@ -233,7 +220,7 @@ three steps: preprocessing, model specification, and fitting.</p>
<p>For a recipe that includes at least one preprocessing operation, like
we have with <code>step_corr()</code>, the necessary parameters can be
estimated from a training set using <code>prep()</code>:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">prep</span><span class="op">(</span><span class="va">resistance_recipe</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
@ -277,7 +264,7 @@ much with existing, other variables.</p>
</h4>
<p>We define a logistic regression model since resistance prediction is
a binary classification task.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Specify a logistic regression model</span></span>
<span><span class="va">logistic_model</span> <span class="op">&lt;-</span> <span class="fu">logistic_reg</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">set_engine</span><span class="op">(</span><span class="st">"glm"</span><span class="op">)</span> <span class="co"># Use the Generalised Linear Model engine</span></span>
@ -300,7 +287,7 @@ engine.</li>
</h4>
<p>We bundle the recipe and model together into a <code>workflow</code>,
which organises the entire modeling process.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Combine the recipe and model into a workflow</span></span>
<span><span class="va">resistance_workflow</span> <span class="op">&lt;-</span> <span class="fu">workflow</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">add_recipe</span><span class="op">(</span><span class="va">resistance_recipe</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Add the preprocessing recipe</span></span>
@ -328,7 +315,7 @@ which organises the entire modeling process.</p>
<p>To train the model, we split the data into training and testing sets.
Then, we fit the workflow on the training set and evaluate its
performance.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Split data into training and testing sets</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123</span><span class="op">)</span> <span class="co"># For reproducibility</span></span>
<span><span class="va">data_split</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data</span>, prop <span class="op">=</span> <span class="fl">0.8</span><span class="op">)</span> <span class="co"># 80% training, 20% testing</span></span>
@ -350,7 +337,7 @@ testing sets.</li>
functions are internally called again. For training, these functions are
called since they are stored in the recipe.</p>
<p>Next, we evaluate the model on the testing data.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Make predictions on the testing set</span></span>
<span><span class="va">predictions</span> <span class="op">&lt;-</span> <span class="va">fitted_workflow</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">testing_data</span><span class="op">)</span> <span class="co"># Generate predictions</span></span>
@ -417,7 +404,7 @@ kappa.</li>
<p>It appears we can predict the Gram stain with a 99.5% accuracy based
on AMR results of only aminoglycosides and beta-lactam antibiotics. The
ROC curve looks like this:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">predictions</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">roc_curve</span><span class="op">(</span><span class="va">mo</span>, <span class="va">`.pred_Gram-negative`</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
@ -466,7 +453,7 @@ model.</li>
</h3>
<p>We start by transforming the <code>example_isolates</code> dataset
into a structured time-series format.</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Load required libraries</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span></span>
@ -499,11 +486,18 @@ into a structured time-series format.</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> <span style="text-decoration: underline;">2</span>006 Gram-negative 0.379 0 0.1 </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="text-decoration: underline;">2</span>006 Gram-positive 0.778 0.333 0.353 </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 22 more rows</span></span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code>mo_name(mo)</code>: Converts
microbial codes into proper species names. - <code><a href="../reference/proportion.html">resistance()</a></code>:
Converts AMR results into numeric values (proportion of resistant
isolates). - <code>group_by(year, ward, species)</code>: Aggregates
resistance rates by year and ward.</p>
<p><strong>Explanation:</strong></p>
<ul>
<li>
<code>mo_name(mo)</code>: Converts microbial codes into proper
species names.</li>
<li>
<code><a href="../reference/proportion.html">resistance()</a></code>: Converts AMR results into numeric values
(proportion of resistant isolates).</li>
<li>
<code>group_by(year, ward, species)</code>: Aggregates resistance
rates by year and ward.</li>
</ul>
</div>
<div class="section level3">
<h3 id="defining-the-workflow-1">
@ -514,7 +508,7 @@ preprocessing step, a model specification, and the fitting process.</p>
<div class="section level4">
<h4 id="preprocessing-with-a-recipe-1">1. Preprocessing with a Recipe<a class="anchor" aria-label="anchor" href="#preprocessing-with-a-recipe-1"></a>
</h4>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Define the recipe</span></span>
<span><span class="va">resistance_recipe_time</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">res_AMX</span> <span class="op">~</span> <span class="va">year</span> <span class="op">+</span> <span class="va">gramstain</span>, data <span class="op">=</span> <span class="va">data_time</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">step_dummy</span><span class="op">(</span><span class="va">gramstain</span>, one_hot <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># Convert categorical to numerical</span></span>
@ -534,17 +528,23 @@ preprocessing step, a model specification, and the fitting process.</p>
<span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Dummy variables from: <span style="color: #0000BB;">gramstain</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Centering and scaling for: <span style="color: #0000BB;">year</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">•</span> Sparse, unbalanced variable filter on: <span style="color: #0000BB;">all_predictors()</span></span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code>step_dummy()</code>: Encodes
categorical variables (<code>ward</code>, <code>species</code>) as
numerical indicators. - <code>step_normalize()</code>: Normalises the
<code>year</code> variable. - <code>step_nzv()</code>: Removes near-zero
variance predictors.</p>
<p><strong>Explanation:</strong></p>
<ul>
<li>
<code>step_dummy()</code>: Encodes categorical variables
(<code>ward</code>, <code>species</code>) as numerical indicators.</li>
<li>
<code>step_normalize()</code>: Normalises the <code>year</code>
variable.</li>
<li>
<code>step_nzv()</code>: Removes near-zero variance predictors.</li>
</ul>
</div>
<div class="section level4">
<h4 id="specifying-the-model-1">2. Specifying the Model<a class="anchor" aria-label="anchor" href="#specifying-the-model-1"></a>
</h4>
<p>We use a linear regression model to predict resistance trends.</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Define the linear regression model</span></span>
<span><span class="va">lm_model</span> <span class="op">&lt;-</span> <span class="fu">linear_reg</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">set_engine</span><span class="op">(</span><span class="st">"lm"</span><span class="op">)</span> <span class="co"># Use linear regression</span></span>
@ -553,15 +553,20 @@ variance predictors.</p>
<span><span class="co">#&gt; Linear Regression Model Specification (regression)</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; Computational engine: lm</span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code>linear_reg()</code>: Defines a
linear regression model. - <code>set_engine("lm")</code>: Uses R’s
built-in linear regression engine.</p>
<p><strong>Explanation:</strong></p>
<ul>
<li>
<code>linear_reg()</code>: Defines a linear regression model.</li>
<li>
<code>set_engine("lm")</code>: Uses R’s built-in linear regression
engine.</li>
</ul>
</div>
<div class="section level4">
<h4 id="building-the-workflow-1">3. Building the Workflow<a class="anchor" aria-label="anchor" href="#building-the-workflow-1"></a>
</h4>
<p>We combine the preprocessing recipe and model into a workflow.</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Create workflow</span></span>
<span><span class="va">resistance_workflow_time</span> <span class="op">&lt;-</span> <span class="fu">workflow</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu">add_recipe</span><span class="op">(</span><span class="va">resistance_recipe_time</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -591,7 +596,7 @@ built-in linear regression engine.</p>
</h3>
<p>We split the data into training and testing sets, fit the model, and
evaluate performance.</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Split the data</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123</span><span class="op">)</span></span>
<span><span class="va">data_split_time</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data_time</span>, prop <span class="op">=</span> <span class="fl">0.8</span><span class="op">)</span></span>
@ -618,17 +623,25 @@ evaluate performance.</p>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> rmse standard 0.077<span style="text-decoration: underline;">4</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> rsq standard 0.711 </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> mae standard 0.070<span style="text-decoration: underline;">4</span></span></span></code></pre></div>
<p><strong>Explanation:</strong> - <code>initial_split()</code>: Splits
data into training and testing sets. - <code>fit()</code>: Trains the
workflow. - <code><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict()</a></code>: Generates resistance predictions. -
<code>metrics()</code>: Evaluates model performance.</p>
<p><strong>Explanation:</strong></p>
<ul>
<li>
<code>initial_split()</code>: Splits data into training and testing
sets.</li>
<li>
<code>fit()</code>: Trains the workflow.</li>
<li>
<code><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict()</a></code>: Generates resistance predictions.</li>
<li>
<code>metrics()</code>: Evaluates model performance.</li>
</ul>
</div>
<div class="section level3">
<h3 id="visualising-predictions">
<strong>Visualising Predictions</strong><a class="anchor" aria-label="anchor" href="#visualising-predictions"></a>
</h3>
<p>We plot resistance trends over time for amoxicillin.</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Plot actual vs predicted resistance over time</span></span>
@ -642,7 +655,7 @@ workflow. - <code><a href="https://rdrr.io/r/stats/predict.html" class="external
<p><img src="AMR_with_tidymodels_files/figure-html/unnamed-chunk-14-1.png" width="720"></p>
<p>Additionally, we can visualise resistance trends in
<code>ggplot2</code> and directly add linear models there:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">data_time</span>, <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">year</span>, y <span class="op">=</span> <span class="va">res_AMX</span>, color <span class="op">=</span> <span class="va">gramstain</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_path.html" class="external-link">geom_line</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"AMX Resistance Trends"</span>,</span>

2
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@ -31,7 +31,7 @@
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@ -34,7 +34,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
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@ -49,20 +49,20 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9232" id="amr-2119232">AMR 2.1.1.9232<a class="anchor" aria-label="anchor" href="#amr-2119232"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9233" id="amr-2119233">AMR 2.1.1.9233<a class="anchor" aria-label="anchor" href="#amr-2119233"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9232">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9232"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9233">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9233"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9232">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9232"></a></h3>
<h3 id="breaking-2-1-1-9233">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9233"></a></h3>
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
<li>Function <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> is now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9232">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9232"></a></h3>
<h3 id="new-2-1-1-9233">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9233"></a></h3>
<ul><li>
<strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -116,7 +116,7 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9232">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9232"></a></h3>
<h3 id="changed-2-1-1-9233">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9233"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -195,7 +195,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9232">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9232"></a></h3>
<h3 id="other-2-1-1-9233">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9233"></a></h3>
<ul><li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
<li>Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes</li>
@ -204,7 +204,7 @@
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9232">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9232"></a></h3>
<h3 id="older-versions-2-1-1-9233">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9233"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

2
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@ -11,7 +11,7 @@ articles:
PCA: PCA.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2025-03-31T08:57Z
last_built: 2025-03-31T13:00Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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12
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -65,15 +65,15 @@
<dl><dt id="arg-text">text<a class="anchor" aria-label="anchor" href="#arg-text"></a></dt>
<dd><p>Text to analyse</p></dd>
<dd><p>Text to analyse.</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>Type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></dd>
<dd><p>Type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em>.</p></dd>
<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em>.</p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
@ -85,11 +85,11 @@
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>Arguments passed on to <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
</dl></div>
<div class="section level2">

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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -92,7 +92,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Any (vector of) text that can be coerced to a valid antibiotic drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>Any (vector of) text that can be coerced to a valid antibiotic drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -104,19 +104,19 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>In case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: columns to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>In case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: columns to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg-only-first">only_first<a class="anchor" aria-label="anchor" href="#arg-only-first"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group).</p></dd>
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>Way of administration, either <code>"oral"</code> or <code>"iv"</code></p></dd>
<dd><p>Way of administration, either <code>"oral"</code> or <code>"iv"</code>.</p></dd>
<dt id="arg-open">open<a class="anchor" aria-label="anchor" href="#arg-open"></a></dt>
<dd><p>Browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code></p></dd>
<dd><p>Browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code>.</p></dd>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
@ -124,11 +124,11 @@
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> of which the columns need to be renamed, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector of column names</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> of which the columns need to be renamed, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector of column names.</p></dd>
<dt id="arg-snake-case">snake_case<a class="anchor" aria-label="anchor" href="#arg-snake-case"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the names should be in so-called <a href="https://en.wikipedia.org/wiki/Snake_case" class="external-link">snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the names should be in so-called <a href="https://en.wikipedia.org/wiki/Snake_case" class="external-link">snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>).</p></dd>
</dl></div>
<div class="section level2">

4
reference/add_custom_antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -65,7 +65,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="antimicrobials.html">antimicrobials</a> data set, at least containing columns "ab" and "name"</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="antimicrobials.html">antimicrobials</a> data set, at least containing columns "ab" and "name".</p></dd>
</dl></div>
<div class="section level2">

4
reference/add_custom_microorganisms.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -65,7 +65,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="microorganisms.html">microorganisms</a> data set, at least containing column "genus" (case-insensitive)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="microorganisms.html">microorganisms</a> data set, at least containing column "genus" (case-insensitive).</p></dd>
</dl></div>
<div class="section level2">

10
reference/age.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -63,11 +63,11 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Date(s), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dd><p>Date(s), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code>.</p></dd>
<dt id="arg-reference">reference<a class="anchor" aria-label="anchor" href="#arg-reference"></a></dt>
<dd><p>Reference date(s) (default is today), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code></p></dd>
<dd><p>Reference date(s) (default is today), <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vectors) will be coerced with <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code>.</p></dd>
<dt id="arg-exact">exact<a class="anchor" aria-label="anchor" href="#arg-exact"></a></dt>
@ -75,11 +75,11 @@
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether missing values should be removed</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether missing values should be removed.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code>, such as <code>origin</code></p></dd>
<dd><p>Arguments passed on to <code><a href="https://rdrr.io/r/base/as.POSIXlt.html" class="external-link">as.POSIXlt()</a></code>, such as <code>origin</code>.</p></dd>
</dl></div>
<div class="section level2">

6
reference/age_groups.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -63,7 +63,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Age, e.g. calculated with <code><a href="age.html">age()</a></code></p></dd>
<dd><p>Age, e.g. calculated with <code><a href="age.html">age()</a></code>.</p></dd>
<dt id="arg-split-at">split_at<a class="anchor" aria-label="anchor" href="#arg-split-at"></a></dt>
@ -71,7 +71,7 @@
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether missing values should be removed</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether missing values should be removed.</p></dd>
</dl></div>
<div class="section level2">

32
reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -101,11 +101,11 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see <code><a href="as.sir.html">as.sir()</a></code>).</p></dd>
<dt id="arg-antimicrobials">antimicrobials<a class="anchor" aria-label="anchor" href="#arg-antimicrobials"></a></dt>
<dd><p>A vector specifying the antimicrobials to include in the antibiogram (see <em>Examples</em>). Will be evaluated using <code><a href="guess_ab_col.html">guess_ab_col()</a></code>. This can be:</p><ul><li><p>Any antimicrobial name or code</p></li>
<dd><p>A vector specifying the antimicrobials to include in the antibiogram (see <em>Examples</em>). Will be evaluated using <code><a href="guess_ab_col.html">guess_ab_col()</a></code>. This can be:.</p><ul><li><p>Any antimicrobial name or code</p></li>
<li><p>A column name in <code>x</code> that contains SIR values</p></li>
<li><p>Any <a href="antimicrobial_selectors.html">antimicrobial selector</a>, such as <code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> or <code><a href="antimicrobial_selectors.html">carbapenems()</a></code></p></li>
<li><p>A combination of the above, using <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code>, e.g.:</p><ul><li><p><code>c(aminoglycosides(), "AMP", "AMC")</code></p></li>
@ -138,11 +138,11 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination antibiograms): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see <em>Details</em></p></dd>
<dd><p>(for combination antibiograms): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see <em>Details</em>.</p></dd>
<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt>
<dd><p>Number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise</p></dd>
<dd><p>Number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise.</p></dd>
<dt id="arg-formatting-type">formatting_type<a class="anchor" aria-label="anchor" href="#arg-formatting-type"></a></dt>
@ -154,7 +154,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>Language to translate text, which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dd><p>Language to translate text, which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>).</p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
@ -162,11 +162,11 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all susceptibility should be determined by results of either S, SDD, or I, instead of only S (default is <code>TRUE</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all susceptibility should be determined by results of either S, SDD, or I, instead of only S (default is <code>TRUE</code>).</p></dd>
<dt id="arg-sep">sep<a class="anchor" aria-label="anchor" href="#arg-sep"></a></dt>
<dd><p>A separating character for antimicrobial columns in combination antibiograms</p></dd>
<dd><p>A separating character for antimicrobial columns in combination antibiograms.</p></dd>
<dt id="arg-wisca">wisca<a class="anchor" aria-label="anchor" href="#arg-wisca"></a></dt>
@ -174,31 +174,31 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-simulations">simulations<a class="anchor" aria-label="anchor" href="#arg-simulations"></a></dt>
<dd><p>(for WISCA) a numerical value to set the number of Monte Carlo simulations</p></dd>
<dd><p>(for WISCA) a numerical value to set the number of Monte Carlo simulations.</p></dd>
<dt id="arg-conf-interval">conf_interval<a class="anchor" aria-label="anchor" href="#arg-conf-interval"></a></dt>
<dd><p>A numerical value to set confidence interval (default is <code>0.95</code>)</p></dd>
<dd><p>A numerical value to set confidence interval (default is <code>0.95</code>).</p></dd>
<dt id="arg-interval-side">interval_side<a class="anchor" aria-label="anchor" href="#arg-interval-side"></a></dt>
<dd><p>The side of the confidence interval, either <code>"two-tailed"</code> (default), <code>"left"</code> or <code>"right"</code></p></dd>
<dd><p>The side of the confidence interval, either <code>"two-tailed"</code> (default), <code>"left"</code> or <code>"right"</code>.</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>When used in <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">R Markdown or Quarto</a>: arguments passed on to <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> (otherwise, has no use)</p></dd>
<dd><p>When used in <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">R Markdown or Quarto</a>: arguments passed on to <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> (otherwise, has no use).</p></dd>
<dt id="arg-wisca-model">wisca_model<a class="anchor" aria-label="anchor" href="#arg-wisca-model"></a></dt>
<dd><p>The outcome of <code>wisca()</code> or <code>antibiogram(..., wisca = TRUE)</code></p></dd>
<dd><p>The outcome of <code>wisca()</code> or <code>antibiogram(..., wisca = TRUE)</code>.</p></dd>
<dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
<dd><p>An <code>antibiogram()</code> object</p></dd>
<dd><p>An <code>antibiogram()</code> object.</p></dd>
<dt id="arg-italicise">italicise<a class="anchor" aria-label="anchor" href="#arg-italicise"></a></dt>
@ -206,7 +206,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-na">na<a class="anchor" aria-label="anchor" href="#arg-na"></a></dt>
<dd><p>Character to use for showing <code>NA</code> values</p></dd>
<dd><p>Character to use for showing <code>NA</code> values.</p></dd>
</dl></div>
<div class="section level2">

10
reference/antimicrobial_selectors.html
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -164,11 +164,11 @@ my_data_with_all_these_columns %&amp;gt;%
<dl><dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>sir</code> must be selected (default is <code>FALSE</code>), see <code><a href="as.sir.html">as.sir()</a></code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>sir</code> must be selected (default is <code>FALSE</code>), see <code><a href="as.sir.html">as.sir()</a></code>.</p></dd>
<dt id="arg-only-treatable">only_treatable<a class="anchor" aria-label="anchor" href="#arg-only-treatable"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is <code>TRUE</code>), such as gentamicin-high (<code>GEH</code>) and imipenem/EDTA (<code>IPE</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is <code>TRUE</code>), such as gentamicin-high (<code>GEH</code>) and imipenem/EDTA (<code>IPE</code>).</p></dd>
<dt id="arg-return-all">return_all<a class="anchor" aria-label="anchor" href="#arg-return-all"></a></dt>
@ -176,7 +176,7 @@ my_data_with_all_these_columns %&amp;gt;%
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions</p></dd>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>
<dt id="arg-amr-class">amr_class<a class="anchor" aria-label="anchor" href="#arg-amr-class"></a></dt>
@ -184,7 +184,7 @@ my_data_with_all_these_columns %&amp;gt;%
<dt id="arg-filter">filter<a class="anchor" aria-label="anchor" href="#arg-filter"></a></dt>
<dd><p>An <a href="https://rdrr.io/r/base/expression.html" class="external-link">expression</a> to be evaluated in the <a href="antimicrobials.html">antimicrobials</a> data set, such as <code>name %like% "trim"</code></p></dd>
<dd><p>An <a href="https://rdrr.io/r/base/expression.html" class="external-link">expression</a> to be evaluated in the <a href="antimicrobials.html">antimicrobials</a> data set, such as <code>name %like% "trim"</code>.</p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>

2
reference/antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

10
reference/as.ab.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -68,7 +68,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector to determine to antibiotic ID</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector to determine to antibiotic ID.</p></dd>
<dt id="arg-flag-multiple-results">flag_multiple_results<a class="anchor" aria-label="anchor" href="#arg-flag-multiple-results"></a></dt>
@ -76,15 +76,15 @@
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>Language to coerce input values from any of the 20 supported languages - default to the system language if supported (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dd><p>Language to coerce input values from any of the 20 supported languages - default to the system language if supported (see <code><a href="translate.html">get_AMR_locale()</a></code>).</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to internal functions</p></dd>
<dd><p>Arguments passed on to internal functions.</p></dd>
</dl></div>
<div class="section level2">

8
reference/as.av.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -65,7 +65,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector to determine to antiviral drug ID</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector to determine to antiviral drug ID.</p></dd>
<dt id="arg-flag-multiple-results">flag_multiple_results<a class="anchor" aria-label="anchor" href="#arg-flag-multiple-results"></a></dt>
@ -73,11 +73,11 @@
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to internal functions</p></dd>
<dd><p>Arguments passed on to internal functions.</p></dd>
</dl></div>
<div class="section level2">

6
reference/as.disk.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -71,11 +71,11 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Vector</p></dd>
<dd><p>Vector.</p></dd>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether missing values should be removed</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether missing values should be removed.</p></dd>
</dl></div>
<div class="section level2">

8
reference/as.mic.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -76,11 +76,11 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> or <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> or <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector.</p></dd>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether missing values should be removed</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether missing values should be removed.</p></dd>
<dt id="arg-keep-operators">keep_operators<a class="anchor" aria-label="anchor" href="#arg-keep-operators"></a></dt>
@ -96,7 +96,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to methods</p></dd>
<dd><p>Arguments passed on to methods.</p></dd>
</dl></div>
<div class="section level2">

8
reference/as.mo.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -82,7 +82,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with one or two columns</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with one or two columns.</p></dd>
<dt id="arg-becker">Becker<a class="anchor" aria-label="anchor" href="#arg-becker"></a></dt>
@ -120,7 +120,7 @@
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>Language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dd><p>Language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>).</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
@ -128,7 +128,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Other arguments passed on to functions</p></dd>
<dd><p>Other arguments passed on to functions.</p></dd>
</dl></div>
<div class="section level2">

36
reference/as.sir.html
View File

@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -136,7 +136,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Vector of values (for class <code><a href="as.mic.html">mic</a></code>: MIC values in mg/L, for class <code><a href="as.disk.html">disk</a></code>: a disk diffusion radius in millimetres)</p></dd>
<dd><p>Vector of values (for class <code><a href="as.mic.html">mic</a></code>: MIC values in mg/L, for class <code><a href="as.disk.html">disk</a></code>: a disk diffusion radius in millimetres).</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@ -144,7 +144,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
<dd><p>Maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em></p></dd>
<dd><p>Maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em>.</p></dd>
<dt id="arg-s-i-r-ni-sdd">S, I, R, NI, SDD<a class="anchor" aria-label="anchor" href="#arg-s-i-r-ni-sdd"></a></dt>
@ -152,15 +152,15 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to print information about the process</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to print information about the process.</p></dd>
<dt id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></dt>
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to valid microorganism codes with <code><a href="as.mo.html">as.mo()</a></code>, can be left empty to determine it automatically</p></dd>
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to valid microorganism codes with <code><a href="as.mo.html">as.mo()</a></code>, can be left empty to determine it automatically.</p></dd>
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>A vector (or column name) with <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>s that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
@ -172,7 +172,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-capped-mic-handling">capped_mic_handling<a class="anchor" aria-label="anchor" href="#arg-capped-mic-handling"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> string that controls how MIC values with a cap (i.e., starting with <code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, or <code>&gt;=</code>) are interpreted. Supports the following options:</p>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> string that controls how MIC values with a cap (i.e., starting with <code>&lt;</code>, <code>&lt;=</code>, <code>&gt;</code>, or <code>&gt;=</code>) are interpreted. Supports the following options:.</p>
<p><code>"none"</code></p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> are treated as-is.</p></li>
<li><p><code>&lt;</code> and <code>&gt;</code> are treated as-is.</p></li>
</ul><p><code>"conservative"</code></p><ul><li><p><code>&lt;=</code> and <code>&gt;=</code> return <code>"NI"</code> (non-interpretable) if the MIC is within the breakpoint guideline range.</p></li>
@ -217,7 +217,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-conserve-capped-values">conserve_capped_values<a class="anchor" aria-label="anchor" href="#arg-conserve-capped-values"></a></dt>
<dd><p>Deprecated, use <code>capped_mic_handling</code> instead</p></dd>
<dd><p>Deprecated, use <code>capped_mic_handling</code> instead.</p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
@ -225,7 +225,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-clean">clean<a class="anchor" aria-label="anchor" href="#arg-clean"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether previously stored results should be forgotten after returning the 'logbook' with results</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether previously stored results should be forgotten after returning the 'logbook' with results.</p></dd>
</dl></div>
<div class="section level2">
@ -820,16 +820,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 65 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-31 <span style="color: #949494;">08:58:25</span> 1 ampicillin Strep p… human AMP <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-31 <span style="color: #949494;">08:58:25</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-31 <span style="color: #949494;">08:58:25</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-31 <span style="color: #949494;">13:01:25</span> 1 ampicillin Strep p… human AMP <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-31 <span style="color: #949494;">13:01:25</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-31 <span style="color: #949494;">13:01:25</span> 1 AMP Escheri… human AMP <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-31 <span style="color: #949494;">08:58:26</span> 1 GEN Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-31 <span style="color: #949494;">08:58:26</span> 1 TOB Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-31 <span style="color: #949494;">08:58:27</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-31 <span style="color: #949494;">08:58:27</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-31 <span style="color: #949494;">08:58:27</span> 2 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-31 <span style="color: #949494;">08:58:27</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-31 <span style="color: #949494;">13:01:25</span> 1 GEN Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-31 <span style="color: #949494;">13:01:26</span> 1 TOB Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBC…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-31 <span style="color: #949494;">13:01:26</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-31 <span style="color: #949494;">13:01:26</span> 1 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-31 <span style="color: #949494;">13:01:26</span> 2 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-31 <span style="color: #949494;">13:01:26</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

8
reference/atc_online.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -75,7 +75,7 @@
<dl><dt id="arg-atc-code">atc_code<a class="anchor" aria-label="anchor" href="#arg-atc-code"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) with ATC code(s) of antimicrobials, will be coerced with <code><a href="as.ab.html">as.ab()</a></code> and <code><a href="ab_property.html">ab_atc()</a></code> internally if not a valid ATC code</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) with ATC code(s) of antimicrobials, will be coerced with <code><a href="as.ab.html">as.ab()</a></code> and <code><a href="ab_property.html">ab_atc()</a></code> internally if not a valid ATC code.</p></dd>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
@ -83,7 +83,7 @@
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>Type of administration when using <code>property = "Adm.R"</code>, see <em>Details</em></p></dd>
<dd><p>Type of administration when using <code>property = "Adm.R"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-url">url<a class="anchor" aria-label="anchor" href="#arg-url"></a></dt>
@ -95,7 +95,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments to pass on to <code>atc_property</code></p></dd>
<dd><p>Arguments to pass on to <code>atc_property</code>.</p></dd>
</dl></div>
<div class="section level2">

12
reference/av_from_text.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -65,15 +65,15 @@
<dl><dt id="arg-text">text<a class="anchor" aria-label="anchor" href="#arg-text"></a></dt>
<dd><p>Text to analyse</p></dd>
<dd><p>Text to analyse.</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>Type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></dd>
<dd><p>Type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em>.</p></dd>
<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em>.</p></dd>
<dt id="arg-translate-av">translate_av<a class="anchor" aria-label="anchor" href="#arg-translate-av"></a></dt>
@ -85,11 +85,11 @@
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to <code><a href="as.av.html">as.av()</a></code></p></dd>
<dd><p>Arguments passed on to <code><a href="as.av.html">as.av()</a></code>.</p></dd>
</dl></div>
<div class="section level2">

10
reference/av_property.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -85,7 +85,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Any (vector of) text that can be coerced to a valid antiviral drug code with <code><a href="as.av.html">as.av()</a></code></p></dd>
<dd><p>Any (vector of) text that can be coerced to a valid antiviral drug code with <code><a href="as.av.html">as.av()</a></code>.</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -97,15 +97,15 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Other arguments passed on to <code><a href="as.av.html">as.av()</a></code></p></dd>
<dd><p>Other arguments passed on to <code><a href="as.av.html">as.av()</a></code>.</p></dd>
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>Way of administration, either <code>"oral"</code> or <code>"iv"</code></p></dd>
<dd><p>Way of administration, either <code>"oral"</code> or <code>"iv"</code>.</p></dd>
<dt id="arg-open">open<a class="anchor" aria-label="anchor" href="#arg-open"></a></dt>
<dd><p>Browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code></p></dd>
<dd><p>Browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code>.</p></dd>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>

6
reference/availability.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -63,11 +63,11 @@
<dl><dt id="arg-tbl">tbl<a class="anchor" aria-label="anchor" href="#arg-tbl"></a></dt>
<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>
<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>
<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a></dt>
<dd><p>Number of characters to present the visual availability - the default is filling the width of the console</p></dd>
<dd><p>Number of characters to present the visual availability - the default is filling the width of the console.</p></dd>
</dl></div>
<div class="section level2">

18
reference/bug_drug_combinations.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -71,7 +71,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dd><p>A data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code>.</p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
@ -79,19 +79,19 @@
<dt id="arg-fun">FUN<a class="anchor" aria-label="anchor" href="#arg-fun"></a></dt>
<dd><p>The function to call on the <code>mo</code> column to transform the microorganism codes - the default is <code><a href="mo_property.html">mo_shortname()</a></code></p></dd>
<dd><p>The function to call on the <code>mo</code> column to transform the microorganism codes - the default is <code><a href="mo_property.html">mo_shortname()</a></code>.</p></dd>
<dt id="arg-include-n-rows">include_n_rows<a class="anchor" aria-label="anchor" href="#arg-include-n-rows"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if the total number of rows must be included in the output</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if the total number of rows must be included in the output.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to <code>FUN</code></p></dd>
<dd><p>Arguments passed on to <code>FUN</code>.</p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antimicrobials.html">antimicrobials</a> data set</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antimicrobials.html">antimicrobials</a> data set.</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -103,15 +103,15 @@
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is <code>TRUE</code>.</p></dd>
<dt id="arg-add-ab-group">add_ab_group<a class="anchor" aria-label="anchor" href="#arg-add-ab-group"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate where the group of the antimicrobials must be included as a first column</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate where the group of the antimicrobials must be included as a first column.</p></dd>
<dt id="arg-remove-intrinsic-resistant">remove_intrinsic_resistant<a class="anchor" aria-label="anchor" href="#arg-remove-intrinsic-resistant"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table</p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table.</p></dd>
<dt id="arg-decimal-mark">decimal.mark<a class="anchor" aria-label="anchor" href="#arg-decimal-mark"></a></dt>

2
reference/clinical_breakpoints.html
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@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

10
reference/count.html
View File

@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -89,15 +89,15 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below</p></dd>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below.</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>).</p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>.</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -105,7 +105,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code>.</p></dd>
</dl></div>
<div class="section level2">

4
reference/custom_eucast_rules.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -63,7 +63,7 @@
<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Rules in <a href="https://rdrr.io/r/base/tilde.html" class="external-link">formula</a> notation, see below for instructions, and in <em>Examples</em></p></dd>
<dd><p>Rules in <a href="https://rdrr.io/r/base/tilde.html" class="external-link">formula</a> notation, see below for instructions, and in <em>Examples</em>.</p></dd>
</dl></div>
<div class="section level2">

2
reference/dosage.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

18
reference/eucast_rules.html
View File

@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -86,7 +86,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dd><p>A data set with antimicrobials columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code>.</p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
@ -94,7 +94,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.</p></dd>
<dt id="arg-rules">rules<a class="anchor" aria-label="anchor" href="#arg-rules"></a></dt>
@ -122,27 +122,27 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dt id="arg-custom-rules">custom_rules<a class="anchor" aria-label="anchor" href="#arg-custom-rules"></a></dt>
<dd><p>Custom rules to apply, created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code></p></dd>
<dd><p>Custom rules to apply, created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dt id="arg-overwrite">overwrite<a class="anchor" aria-label="anchor" href="#arg-overwrite"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite non-<code>NA</code> values (default: <code>FALSE</code>). When <code>FALSE</code>, only <code>NA</code> values are modified. To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant."</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> indicating whether to overwrite non-<code>NA</code> values (default: <code>FALSE</code>). When <code>FALSE</code>, only <code>NA</code> values are modified. To ensure compliance with EUCAST guidelines, <strong>this should remain</strong> <code>FALSE</code>, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant.".</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Column name of an antimicrobial, see section <em>Antimicrobials</em> below</p></dd>
<dd><p>Column name of an antimicrobial, see section <em>Antimicrobials</em> below.</p></dd>
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
<dd><p>Any (vector of) text that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>Any (vector of) text that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
<dd><p>Route of administration, either "im", "iv", or "oral"</p></dd>
<dd><p>Route of administration, either "im", "iv", or "oral".</p></dd>
</dl></div>
<div class="section level2">

2
reference/example_isolates.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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8
reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
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@ -65,15 +65,15 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A data set</p></dd>
<dd><p>A data set.</p></dd>
<dt id="arg-filename">filename<a class="anchor" aria-label="anchor" href="#arg-filename"></a></dt>
<dd><p>A character string specifying the file name</p></dd>
<dd><p>A character string specifying the file name.</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>A character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see <a href="https://www.ncbi.nlm.nih.gov/biosample/docs/" class="external-link">https://www.ncbi.nlm.nih.gov/biosample/docs/</a></p></dd>
<dd><p>A character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see <a href="https://www.ncbi.nlm.nih.gov/biosample/docs/" class="external-link">https://www.ncbi.nlm.nih.gov/biosample/docs/</a>.</p></dd>
</dl></div>

24
reference/first_isolate.html
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@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -86,11 +86,11 @@
<dt id="arg-col-date">col_date<a class="anchor" aria-label="anchor" href="#arg-col-date"></a></dt>
<dd><p>Column name of the result date (or date that is was received on the lab) - the default is the first column with a date class</p></dd>
<dd><p>Column name of the result date (or date that is was received on the lab) - the default is the first column with a date class.</p></dd>
<dt id="arg-col-patient-id">col_patient_id<a class="anchor" aria-label="anchor" href="#arg-col-patient-id"></a></dt>
<dd><p>Column name of the unique IDs of the patients - the default is the first column that starts with 'patient' or 'patid' (case insensitive)</p></dd>
<dd><p>Column name of the unique IDs of the patients - the default is the first column that starts with 'patient' or 'patid' (case insensitive).</p></dd>
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
@ -102,7 +102,7 @@
<dt id="arg-col-specimen">col_specimen<a class="anchor" aria-label="anchor" href="#arg-col-specimen"></a></dt>
<dd><p>Column name of the specimen type or group</p></dd>
<dd><p>Column name of the specimen type or group.</p></dd>
<dt id="arg-col-icu">col_icu<a class="anchor" aria-label="anchor" href="#arg-col-icu"></a></dt>
@ -118,19 +118,19 @@
<dt id="arg-testcodes-exclude">testcodes_exclude<a class="anchor" aria-label="anchor" href="#arg-testcodes-exclude"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector with test codes that should be excluded (case-insensitive)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector with test codes that should be excluded (case-insensitive).</p></dd>
<dt id="arg-icu-exclude">icu_exclude<a class="anchor" aria-label="anchor" href="#arg-icu-exclude"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether ICU isolates should be excluded (rows with value <code>TRUE</code> in the column set with <code>col_icu</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether ICU isolates should be excluded (rows with value <code>TRUE</code> in the column set with <code>col_icu</code>).</p></dd>
<dt id="arg-specimen-group">specimen_group<a class="anchor" aria-label="anchor" href="#arg-specimen-group"></a></dt>
<dd><p>Value in the column set with <code>col_specimen</code> to filter on</p></dd>
<dd><p>Value in the column set with <code>col_specimen</code> to filter on.</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>Type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dd><p>Type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
@ -138,15 +138,15 @@
<dt id="arg-ignore-i">ignore_I<a class="anchor" aria-label="anchor" href="#arg-ignore-i"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-points-threshold">points_threshold<a class="anchor" aria-label="anchor" href="#arg-points-threshold"></a></dt>
<dd><p>Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
<dd><p>Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
<dt id="arg-include-unknown">include_unknown<a class="anchor" aria-label="anchor" href="#arg-include-unknown"></a></dt>
@ -158,7 +158,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, otherwise arguments passed on to <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code> (such as <code>universal</code>, <code>gram_negative</code>, <code>gram_positive</code>)</p></dd>
<dd><p>Arguments passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, otherwise arguments passed on to <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code> (such as <code>universal</code>, <code>gram_negative</code>, <code>gram_positive</code>).</p></dd>
</dl></div>
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2
reference/g.test.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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10
reference/get_episode.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -65,19 +65,19 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Vector of dates (class <code>Date</code> or <code>POSIXt</code>), will be sorted internally to determine episodes</p></dd>
<dd><p>Vector of dates (class <code>Date</code> or <code>POSIXt</code>), will be sorted internally to determine episodes.</p></dd>
<dt id="arg-episode-days">episode_days<a class="anchor" aria-label="anchor" href="#arg-episode-days"></a></dt>
<dd><p>Episode length in days to specify the time period after which a new episode begins, can also be less than a day or <code>Inf</code>, see <em>Details</em></p></dd>
<dd><p>Episode length in days to specify the time period after which a new episode begins, can also be less than a day or <code>Inf</code>, see <em>Details</em>.</p></dd>
<dt id="arg-case-free-days">case_free_days<a class="anchor" aria-label="anchor" href="#arg-case-free-days"></a></dt>
<dd><p>(inter-epidemic) interval length in days after which a new episode will start, can also be less than a day or <code>Inf</code>, see <em>Details</em></p></dd>
<dd><p>(inter-epidemic) interval length in days after which a new episode will start, can also be less than a day or <code>Inf</code>, see <em>Details</em>.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions</p></dd>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>
</dl></div>
<div class="section level2">

36
reference/ggplot_pca.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -79,7 +79,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>An object returned by <code><a href="pca.html">pca()</a></code>, <code><a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">prcomp()</a></code> or <code><a href="https://rdrr.io/r/stats/princomp.html" class="external-link">princomp()</a></code></p></dd>
<dd><p>An object returned by <code><a href="pca.html">pca()</a></code>, <code><a href="https://rdrr.io/r/stats/prcomp.html" class="external-link">prcomp()</a></code> or <code><a href="https://rdrr.io/r/stats/princomp.html" class="external-link">princomp()</a></code>.</p></dd>
<dt id="arg-choices">choices<a class="anchor" aria-label="anchor" href="#arg-choices"></a></dt>
@ -108,11 +108,11 @@
<dt id="arg-labels-textsize">labels_textsize<a class="anchor" aria-label="anchor" href="#arg-labels-textsize"></a></dt>
<dd><p>The size of the text used for the labels</p></dd>
<dd><p>The size of the text used for the labels.</p></dd>
<dt id="arg-labels-text-placement">labels_text_placement<a class="anchor" aria-label="anchor" href="#arg-labels-text-placement"></a></dt>
<dd><p>Adjustment factor the placement of the variable names (<code>&gt;=1</code> means further away from the arrow head)</p></dd>
<dd><p>Adjustment factor the placement of the variable names (<code>&gt;=1</code> means further away from the arrow head).</p></dd>
<dt id="arg-groups">groups<a class="anchor" aria-label="anchor" href="#arg-groups"></a></dt>
@ -120,59 +120,59 @@
<dt id="arg-ellipse">ellipse<a class="anchor" aria-label="anchor" href="#arg-ellipse"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a normal data ellipse should be drawn for each group (set with <code>groups</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a normal data ellipse should be drawn for each group (set with <code>groups</code>).</p></dd>
<dt id="arg-ellipse-prob">ellipse_prob<a class="anchor" aria-label="anchor" href="#arg-ellipse-prob"></a></dt>
<dd><p>Statistical size of the ellipse in normal probability</p></dd>
<dd><p>Statistical size of the ellipse in normal probability.</p></dd>
<dt id="arg-ellipse-size">ellipse_size<a class="anchor" aria-label="anchor" href="#arg-ellipse-size"></a></dt>
<dd><p>The size of the ellipse line</p></dd>
<dd><p>The size of the ellipse line.</p></dd>
<dt id="arg-ellipse-alpha">ellipse_alpha<a class="anchor" aria-label="anchor" href="#arg-ellipse-alpha"></a></dt>
<dd><p>The alpha (transparency) of the ellipse line</p></dd>
<dd><p>The alpha (transparency) of the ellipse line.</p></dd>
<dt id="arg-points-size">points_size<a class="anchor" aria-label="anchor" href="#arg-points-size"></a></dt>
<dd><p>The size of the points</p></dd>
<dd><p>The size of the points.</p></dd>
<dt id="arg-points-alpha">points_alpha<a class="anchor" aria-label="anchor" href="#arg-points-alpha"></a></dt>
<dd><p>The alpha (transparency) of the points</p></dd>
<dd><p>The alpha (transparency) of the points.</p></dd>
<dt id="arg-arrows">arrows<a class="anchor" aria-label="anchor" href="#arg-arrows"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether arrows should be drawn</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether arrows should be drawn.</p></dd>
<dt id="arg-arrows-colour">arrows_colour<a class="anchor" aria-label="anchor" href="#arg-arrows-colour"></a></dt>
<dd><p>The colour of the arrow and their text</p></dd>
<dd><p>The colour of the arrow and their text.</p></dd>
<dt id="arg-arrows-size">arrows_size<a class="anchor" aria-label="anchor" href="#arg-arrows-size"></a></dt>
<dd><p>The size (thickness) of the arrow lines</p></dd>
<dd><p>The size (thickness) of the arrow lines.</p></dd>
<dt id="arg-arrows-textsize">arrows_textsize<a class="anchor" aria-label="anchor" href="#arg-arrows-textsize"></a></dt>
<dd><p>The size of the text at the end of the arrows</p></dd>
<dd><p>The size of the text at the end of the arrows.</p></dd>
<dt id="arg-arrows-textangled">arrows_textangled<a class="anchor" aria-label="anchor" href="#arg-arrows-textangled"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> whether the text at the end of the arrows should be angled</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> whether the text at the end of the arrows should be angled.</p></dd>
<dt id="arg-arrows-alpha">arrows_alpha<a class="anchor" aria-label="anchor" href="#arg-arrows-alpha"></a></dt>
<dd><p>The alpha (transparency) of the arrows and their text</p></dd>
<dd><p>The alpha (transparency) of the arrows and their text.</p></dd>
<dt id="arg-base-textsize">base_textsize<a class="anchor" aria-label="anchor" href="#arg-base-textsize"></a></dt>
<dd><p>The text size for all plot elements except the labels and arrows</p></dd>
<dd><p>The text size for all plot elements except the labels and arrows.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to functions</p></dd>
<dd><p>Arguments passed on to functions.</p></dd>
</dl></div>
<div class="section level2">

38
reference/ggplot_sir.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
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@ -74,39 +74,39 @@
<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with column(s) of class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with column(s) of class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>).</p></dd>
<dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a></dt>
<dd><p>Position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code></p></dd>
<dd><p>Position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code>.</p></dd>
<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Variable to show on x axis, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></dd>
<dd><p>Variable to show on x axis, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable.</p></dd>
<dt id="arg-fill">fill<a class="anchor" aria-label="anchor" href="#arg-fill"></a></dt>
<dd><p>Variable to categorise using the plots legend, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></dd>
<dd><p>Variable to categorise using the plots legend, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable.</p></dd>
<dt id="arg-facet">facet<a class="anchor" aria-label="anchor" href="#arg-facet"></a></dt>
<dd><p>Variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></dd>
<dd><p>Variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable.</p></dd>
<dt id="arg-breaks">breaks<a class="anchor" aria-label="anchor" href="#arg-breaks"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of positions</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of positions.</p></dd>
<dt id="arg-limits">limits<a class="anchor" aria-label="anchor" href="#arg-limits"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum.</p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>.</p></dd>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code>.</p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
@ -118,7 +118,7 @@
<dt id="arg-nrow">nrow<a class="anchor" aria-label="anchor" href="#arg-nrow"></a></dt>
<dd><p>(when using <code>facet</code>) number of rows</p></dd>
<dd><p>(when using <code>facet</code>) number of rows.</p></dd>
<dt id="arg-colours">colours<a class="anchor" aria-label="anchor" href="#arg-colours"></a></dt>
@ -126,35 +126,35 @@
<dt id="arg-datalabels">datalabels<a class="anchor" aria-label="anchor" href="#arg-datalabels"></a></dt>
<dd><p>Show datalabels using <code><a href="plot.html">labels_sir_count()</a></code></p></dd>
<dd><p>Show datalabels using <code><a href="plot.html">labels_sir_count()</a></code>.</p></dd>
<dt id="arg-datalabels-size">datalabels.size<a class="anchor" aria-label="anchor" href="#arg-datalabels-size"></a></dt>
<dd><p>Size of the datalabels</p></dd>
<dd><p>Size of the datalabels.</p></dd>
<dt id="arg-datalabels-colour">datalabels.colour<a class="anchor" aria-label="anchor" href="#arg-datalabels-colour"></a></dt>
<dd><p>Colour of the datalabels</p></dd>
<dd><p>Colour of the datalabels.</p></dd>
<dt id="arg-title">title<a class="anchor" aria-label="anchor" href="#arg-title"></a></dt>
<dd><p>Text to show as title of the plot</p></dd>
<dd><p>Text to show as title of the plot.</p></dd>
<dt id="arg-subtitle">subtitle<a class="anchor" aria-label="anchor" href="#arg-subtitle"></a></dt>
<dd><p>Text to show as subtitle of the plot</p></dd>
<dd><p>Text to show as subtitle of the plot.</p></dd>
<dt id="arg-caption">caption<a class="anchor" aria-label="anchor" href="#arg-caption"></a></dt>
<dd><p>Text to show as caption of the plot</p></dd>
<dd><p>Text to show as caption of the plot.</p></dd>
<dt id="arg-x-title">x.title<a class="anchor" aria-label="anchor" href="#arg-x-title"></a></dt>
<dd><p>Text to show as x axis description</p></dd>
<dd><p>Text to show as x axis description.</p></dd>
<dt id="arg-y-title">y.title<a class="anchor" aria-label="anchor" href="#arg-y-title"></a></dt>
<dd><p>Text to show as y axis description</p></dd>
<dd><p>Text to show as y axis description.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>

10
reference/guess_ab_col.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -64,19 +64,19 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>.</p></dd>
<dt id="arg-search-string">search_string<a class="anchor" aria-label="anchor" href="#arg-search-string"></a></dt>
<dd><p>A text to search <code>x</code> for, will be checked with <code><a href="as.ab.html">as.ab()</a></code> if this value is not a column in <code>x</code></p></dd>
<dd><p>A text to search <code>x</code> for, will be checked with <code><a href="as.ab.html">as.ab()</a></code> if this value is not a column in <code>x</code>.</p></dd>
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether additional info should be printed</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether additional info should be printed.</p></dd>
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
</dl></div>
<div class="section level2">

2
reference/index.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/intrinsic_resistant.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/italicise_taxonomy.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -65,11 +65,11 @@
<dl><dt id="arg-string">string<a class="anchor" aria-label="anchor" href="#arg-string"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector).</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>Type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see <em>Details</em></p></dd>
<dd><p>Type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see <em>Details</em>.</p></dd>
</dl></div>
<div class="section level2">

6
reference/join.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -77,7 +77,7 @@
<dt id="arg-by">by<a class="anchor" aria-label="anchor" href="#arg-by"></a></dt>
<dd><p>A variable to join by - if left empty will search for a column with class <code><a href="as.mo.html">mo</a></code> (created with <code><a href="as.mo.html">as.mo()</a></code>) or will be <code>"mo"</code> if that column name exists in <code>x</code>, could otherwise be a column name of <code>x</code> with values that exist in <code>microorganisms$mo</code> (such as <code>by = "bacteria_id"</code>), or another column in <a href="microorganisms.html">microorganisms</a> (but then it should be named, like <code>by = c("bacteria_id" = "fullname")</code>)</p></dd>
<dd><p>A variable to join by - if left empty will search for a column with class <code><a href="as.mo.html">mo</a></code> (created with <code><a href="as.mo.html">as.mo()</a></code>) or will be <code>"mo"</code> if that column name exists in <code>x</code>, could otherwise be a column name of <code>x</code> with values that exist in <code>microorganisms$mo</code> (such as <code>by = "bacteria_id"</code>), or another column in <a href="microorganisms.html">microorganisms</a> (but then it should be named, like <code>by = c("bacteria_id" = "fullname")</code>).</p></dd>
<dt id="arg-suffix">suffix<a class="anchor" aria-label="anchor" href="#arg-suffix"></a></dt>
@ -85,7 +85,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions</p></dd>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>
</dl></div>
<div class="section level2">

22
reference/key_antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -83,43 +83,43 @@
<dt id="arg-universal">universal<a class="anchor" aria-label="anchor" href="#arg-universal"></a></dt>
<dd><p>Names of <strong>broad-spectrum</strong> antimicrobial drugs, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antimicrobial drugs</p></dd>
<dd><p>Names of <strong>broad-spectrum</strong> antimicrobial drugs, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antimicrobial drugs.</p></dd>
<dt id="arg-gram-negative">gram_negative<a class="anchor" aria-label="anchor" href="#arg-gram-negative"></a></dt>
<dd><p>Names of antibiotic drugs for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dd><p>Names of antibiotic drugs for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs.</p></dd>
<dt id="arg-gram-positive">gram_positive<a class="anchor" aria-label="anchor" href="#arg-gram-positive"></a></dt>
<dd><p>Names of antibiotic drugs for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dd><p>Names of antibiotic drugs for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs.</p></dd>
<dt id="arg-antifungal">antifungal<a class="anchor" aria-label="anchor" href="#arg-antifungal"></a></dt>
<dd><p>Names of antifungal drugs for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antifungal drugs</p></dd>
<dd><p>Names of antifungal drugs for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antifungal drugs.</p></dd>
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions</p></dd>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>
<dt id="arg-y-z">y, z<a class="anchor" aria-label="anchor" href="#arg-y-z"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare</p></dd>
<dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare.</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>Type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dd><p>Type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-ignore-i">ignore_I<a class="anchor" aria-label="anchor" href="#arg-ignore-i"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em>.</p></dd>
<dt id="arg-points-threshold">points_threshold<a class="anchor" aria-label="anchor" href="#arg-points-threshold"></a></dt>
<dd><p>Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
<dd><p>Minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em>.</p></dd>
</dl></div>
<div class="section level2">

6
reference/kurtosis.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -72,11 +72,11 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A vector of values, a <a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a> or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></p></dd>
<dd><p>A vector of values, a <a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a> or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>.</p></dd>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether <code>NA</code> values should be stripped before the computation proceeds</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether <code>NA</code> values should be stripped before the computation proceeds.</p></dd>
<dt id="arg-excess">excess<a class="anchor" aria-label="anchor" href="#arg-excess"></a></dt>

2
reference/like.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

20
reference/mdro.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -95,31 +95,31 @@
<dt id="arg-esbl">esbl<a class="anchor" aria-label="anchor" href="#arg-esbl"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins)</p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins).</p></dd>
<dt id="arg-carbapenemase">carbapenemase<a class="anchor" aria-label="anchor" href="#arg-carbapenemase"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins)</p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins).</p></dd>
<dt id="arg-meca">mecA<a class="anchor" aria-label="anchor" href="#arg-meca"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecA</em> gene (or production of its proteins)</p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecA</em> gene (or production of its proteins).</p></dd>
<dt id="arg-mecc">mecC<a class="anchor" aria-label="anchor" href="#arg-mecc"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecC</em> gene (or production of its proteins)</p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>mecC</em> gene (or production of its proteins).</p></dd>
<dt id="arg-vana">vanA<a class="anchor" aria-label="anchor" href="#arg-vana"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanA</em> gene (or production of its proteins)</p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanA</em> gene (or production of its proteins).</p></dd>
<dt id="arg-vanb">vanB<a class="anchor" aria-label="anchor" href="#arg-vanb"></a></dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanB</em> gene (or production of its proteins)</p></dd>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> values, or a column name containing logical values, indicating the presence of a <em>vanB</em> gene (or production of its proteins).</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.</p></dd>
<dt id="arg-pct-required-classes">pct_required_classes<a class="anchor" aria-label="anchor" href="#arg-pct-required-classes"></a></dt>
@ -135,7 +135,7 @@
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@ -143,7 +143,7 @@
<dt id="arg-as-factor">as_factor<a class="anchor" aria-label="anchor" href="#arg-as-factor"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the returned value should be an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> (<code>TRUE</code>, default), or otherwise a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the returned value should be an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> (<code>TRUE</code>, default), or otherwise a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector.</p></dd>
</dl></div>
<div class="section level2">

12
reference/mean_amr_distance.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -71,23 +71,23 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A vector of class <a href="as.sir.html">sir</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
<dd><p>A vector of class <a href="as.sir.html">sir</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Variables to select. Supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> (such as <code>column1:column4</code> and <code>where(is.mic)</code>), and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a></p></dd>
<dd><p>Variables to select. Supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> (such as <code>column1:column4</code> and <code>where(is.mic)</code>), and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a>.</p></dd>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code>.</p></dd>
<dt id="arg-amr-distance">amr_distance<a class="anchor" aria-label="anchor" href="#arg-amr-distance"></a></dt>
<dd><p>The outcome of <code>mean_amr_distance()</code></p></dd>
<dd><p>The outcome of <code>mean_amr_distance()</code>.</p></dd>
<dt id="arg-row">row<a class="anchor" aria-label="anchor" href="#arg-row"></a></dt>
<dd><p>An index, such as a row number</p></dd>
<dd><p>An index, such as a row number.</p></dd>
</dl></div>
<div class="section level2">

2
reference/microorganisms.codes.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/mo_matching_score.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -63,11 +63,11 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Any user input value(s)</p></dd>
<dd><p>Any user input value(s).</p></dd>
<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
<dd><p>A full taxonomic name, that exists in <code><a href="microorganisms.html">microorganisms$fullname</a></code></p></dd>
<dd><p>A full taxonomic name, that exists in <code><a href="microorganisms.html">microorganisms$fullname</a></code>.</p></dd>
</dl></div>
<div class="section level2">

12
reference/mo_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -175,7 +175,7 @@
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>Language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dd><p>Language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>).</p></dd>
<dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt>
@ -183,19 +183,19 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'</p></dd>
<dd><p>Other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'.</p></dd>
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
<dd><p>Any (vector of) text that can be coerced to a valid antibiotic drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>Any (vector of) text that can be coerced to a valid antibiotic drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg-open">open<a class="anchor" aria-label="anchor" href="#arg-open"></a></dt>
<dd><p>Browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">browseURL()</a></code></p></dd>
<dd><p>Browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">browseURL()</a></code>.</p></dd>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>
<dd><p>One of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be <code>"shortname"</code></p></dd>
<dd><p>One of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be <code>"shortname"</code>.</p></dd>
</dl></div>
<div class="section level2">

2
reference/mo_source.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

BIN
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24
reference/pca.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -64,7 +64,7 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> columns</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> columns.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@ -142,17 +142,8 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">pca_result</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># old base R plotting method:</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="co"># new ggplot2 plotting method using this package:</span></span></span>
<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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_colour_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Title here"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">}</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 73 warnings in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
@ -169,7 +160,18 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-plt img"><img src="pca-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># new ggplot2 plotting method using this package:</span></span></span>
<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">&amp;&amp;</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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="pca-2.png" alt="" width="700" height="433"></span>
<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">&amp;&amp;</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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/scale_viridis.html" class="external-link">scale_colour_viridis_d</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"Title here"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="pca-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

36
reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -161,7 +161,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to methods</p></dd>
<dd><p>Arguments passed on to methods.</p></dd>
<dt id="arg-colours-sir">colours_SIR<a class="anchor" aria-label="anchor" href="#arg-colours-sir"></a></dt>
@ -177,27 +177,27 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-x-object">x, object<a class="anchor" aria-label="anchor" href="#arg-x-object"></a></dt>
<dd><p>Values created with <code><a href="as.mic.html">as.mic()</a></code>, <code><a href="as.disk.html">as.disk()</a></code> or <code><a href="as.sir.html">as.sir()</a></code> (or their <code>random_*</code> variants, such as <code><a href="random.html">random_mic()</a></code>)</p></dd>
<dd><p>Values created with <code><a href="as.mic.html">as.mic()</a></code>, <code><a href="as.disk.html">as.disk()</a></code> or <code><a href="as.sir.html">as.sir()</a></code> (or their <code>random_*</code> variants, such as <code><a href="random.html">random_mic()</a></code>).</p></dd>
<dt id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></dt>
<dd><p>Any (vector of) text that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code></p></dd>
<dd><p>Any (vector of) text that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
<dd><p>Any (vector of) text that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>Any (vector of) text that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>Interpretation guideline to use - the default is the latest included EUCAST guideline, see <em>Details</em></p></dd>
<dd><p>Interpretation guideline to use - the default is the latest included EUCAST guideline, see <em>Details</em>.</p></dd>
<dt id="arg-main-title">main, title<a class="anchor" aria-label="anchor" href="#arg-main-title"></a></dt>
<dd><p>Title of the plot</p></dd>
<dd><p>Title of the plot.</p></dd>
<dt id="arg-xlab-ylab">xlab, ylab<a class="anchor" aria-label="anchor" href="#arg-xlab-ylab"></a></dt>
<dd><p>Axis title</p></dd>
<dd><p>Axis title.</p></dd>
<dt id="arg-expand">expand<a class="anchor" aria-label="anchor" href="#arg-expand"></a></dt>
@ -213,31 +213,31 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-facet">facet<a class="anchor" aria-label="anchor" href="#arg-facet"></a></dt>
<dd><p>Variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></dd>
<dd><p>Variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable.</p></dd>
<dt id="arg-nrow">nrow<a class="anchor" aria-label="anchor" href="#arg-nrow"></a></dt>
<dd><p>(when using <code>facet</code>) number of rows</p></dd>
<dd><p>(when using <code>facet</code>) number of rows.</p></dd>
<dt id="arg-breaks">breaks<a class="anchor" aria-label="anchor" href="#arg-breaks"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of positions</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of positions.</p></dd>
<dt id="arg-limits">limits<a class="anchor" aria-label="anchor" href="#arg-limits"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector of length two providing limits of the scale, use <code>NA</code> to refer to the existing minimum or maximum.</p></dd>
<dt id="arg-aesthetics">aesthetics<a class="anchor" aria-label="anchor" href="#arg-aesthetics"></a></dt>
<dd><p>Aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size"</p></dd>
<dd><p>Aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size".</p></dd>
<dt id="arg-position">position<a class="anchor" aria-label="anchor" href="#arg-position"></a></dt>
<dd><p>Position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code></p></dd>
<dd><p>Position adjustment of bars, either <code>"fill"</code>, <code>"stack"</code> or <code>"dodge"</code>.</p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>.</p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
@ -245,15 +245,15 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code>.</p></dd>
<dt id="arg-datalabels-size">datalabels.size<a class="anchor" aria-label="anchor" href="#arg-datalabels-size"></a></dt>
<dd><p>Size of the datalabels</p></dd>
<dd><p>Size of the datalabels.</p></dd>
<dt id="arg-datalabels-colour">datalabels.colour<a class="anchor" aria-label="anchor" href="#arg-datalabels-colour"></a></dt>
<dd><p>Colour of the datalabels</p></dd>
<dd><p>Colour of the datalabels.</p></dd>
</dl></div>
<div class="section level2">

14
reference/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -113,11 +113,11 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below</p></dd>
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antimicrobials, see section <em>Combination Therapy</em> below.</p></dd>
<dt id="arg-ab-result">ab_result<a class="anchor" aria-label="anchor" href="#arg-ab-result"></a></dt>
<dd><p>Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R"</p></dd>
<dd><p>Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".</p></dd>
<dt id="arg-confidence-level">confidence_level<a class="anchor" aria-label="anchor" href="#arg-confidence-level"></a></dt>
@ -129,15 +129,15 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-collapse">collapse<a class="anchor" aria-label="anchor" href="#arg-collapse"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing.</p></dd>
<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>).</p></dd>
<dt id="arg-translate-ab">translate_ab<a class="anchor" aria-label="anchor" href="#arg-translate-ab"></a></dt>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dd><p>A column name of the <a href="antimicrobials.html">antimicrobials</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code>.</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
@ -145,7 +145,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code>.</p></dd>
</dl></div>
<div class="section level2">

10
reference/random.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -71,19 +71,19 @@
<dt id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></dt>
<dd><p>Any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code></p></dd>
<dd><p>Any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></dt>
<dd><p>Any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dd><p>Any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions</p></dd>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>
<dt id="arg-prob-sir">prob_SIR<a class="anchor" aria-label="anchor" href="#arg-prob-sir"></a></dt>
<dd><p>A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value)</p></dd>
<dd><p>A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value).</p></dd>
</dl></div>
<div class="section level2">

20
reference/resistance_predict.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -84,23 +84,23 @@
<dt id="arg-col-ab">col_ab<a class="anchor" aria-label="anchor" href="#arg-col-ab"></a></dt>
<dd><p>Column name of <code>x</code> containing antimicrobial interpretations (<code>"R"</code>, <code>"I"</code> and <code>"S"</code>)</p></dd>
<dd><p>Column name of <code>x</code> containing antimicrobial interpretations (<code>"R"</code>, <code>"I"</code> and <code>"S"</code>).</p></dd>
<dt id="arg-col-date">col_date<a class="anchor" aria-label="anchor" href="#arg-col-date"></a></dt>
<dd><p>Column name of the date, will be used to calculate years if this column doesn't consist of years already - the default is the first column of with a date class</p></dd>
<dd><p>Column name of the date, will be used to calculate years if this column doesn't consist of years already - the default is the first column of with a date class.</p></dd>
<dt id="arg-year-min">year_min<a class="anchor" aria-label="anchor" href="#arg-year-min"></a></dt>
<dd><p>Lowest year to use in the prediction model, dafaults to the lowest year in <code>col_date</code></p></dd>
<dd><p>Lowest year to use in the prediction model, dafaults to the lowest year in <code>col_date</code>.</p></dd>
<dt id="arg-year-max">year_max<a class="anchor" aria-label="anchor" href="#arg-year-max"></a></dt>
<dd><p>Highest year to use in the prediction model - the default is 10 years after today</p></dd>
<dd><p>Highest year to use in the prediction model - the default is 10 years after today.</p></dd>
<dt id="arg-year-every">year_every<a class="anchor" aria-label="anchor" href="#arg-year-every"></a></dt>
<dd><p>Unit of sequence between lowest year found in the data and <code>year_max</code></p></dd>
<dd><p>Unit of sequence between lowest year found in the data and <code>year_max</code>.</p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
@ -124,19 +124,19 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Arguments passed on to functions</p></dd>
<dd><p>Arguments passed on to functions.</p></dd>
<dt id="arg-main">main<a class="anchor" aria-label="anchor" href="#arg-main"></a></dt>
<dd><p>Title of the plot</p></dd>
<dd><p>Title of the plot.</p></dd>
<dt id="arg-ribbon">ribbon<a class="anchor" aria-label="anchor" href="#arg-ribbon"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a ribbon should be shown (default) or error bars</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a ribbon should be shown (default) or error bars.</p></dd>
<dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
<dd><p>Model data to be plotted</p></dd>
<dd><p>Model data to be plotted.</p></dd>
</dl></div>
<div class="section level2">

6
reference/skewness.html
View File

@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -75,11 +75,11 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A vector of values, a <a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a> or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></p></dd>
<dd><p>A vector of values, a <a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a> or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>.</p></dd>
<dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value indicating whether <code>NA</code> values should be stripped before the computation proceeds</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value indicating whether <code>NA</code> values should be stripped before the computation proceeds.</p></dd>
</dl></div>
<div class="section level2">

6
reference/top_n_microorganisms.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -64,11 +64,11 @@
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>A data frame containing microbial data</p></dd>
<dd><p>A data frame containing microbial data.</p></dd>
<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
<dd><p>An integer specifying the maximum number of unique values of the <code>property</code> to include in the output</p></dd>
<dd><p>An integer specifying the maximum number of unique values of the <code>property</code> to include in the output.</p></dd>
<dt id="arg-property">property<a class="anchor" aria-label="anchor" href="#arg-property"></a></dt>

4
reference/translate.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -73,7 +73,7 @@
<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Text to translate</p></dd>
<dd><p>Text to translate.</p></dd>
</dl></div>
<div class="section level2">

2
search.json
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