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<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.93425 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.35068 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.50137 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.26575 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.59452 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.30685 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.29315 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.40274 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.77534 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.35890 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.95342 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.36986 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.52055 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.28493 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.61370 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.32603 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.31233 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.42192 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.79452 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.37808 21</span>
</code></pre></div>
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<img src="../logo.svg" class="logo" alt=""><h1>AMR Extensions for Tidymodels</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/tidymodels.R" class="external-link"><code>R/tidymodels.R</code></a></small>
<div class="d-none name"><code>amr-tidymodels.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>This family of functions allows using AMR-specific data types such as <code>&lt;mic&gt;</code> and <code>&lt;sir&gt;</code> inside <code>tidymodels</code> pipelines.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">all_mic</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">all_mic_predictors</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">all_sir</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">all_sir_predictors</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">step_mic_log2</span><span class="op">(</span><span class="va">recipe</span>, <span class="va">...</span>, role <span class="op">=</span> <span class="cn">NA</span>, trained <span class="op">=</span> <span class="cn">FALSE</span>, columns <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> skip <span class="op">=</span> <span class="cn">FALSE</span>, id <span class="op">=</span> <span class="fu">recipes</span><span class="fu">::</span><span class="fu"><a href="https://recipes.tidymodels.org/reference/rand_id.html" class="external-link">rand_id</a></span><span class="op">(</span><span class="st">"mic_log2"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">step_sir_numeric</span><span class="op">(</span><span class="va">recipe</span>, <span class="va">...</span>, role <span class="op">=</span> <span class="cn">NA</span>, trained <span class="op">=</span> <span class="cn">FALSE</span>, columns <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> skip <span class="op">=</span> <span class="cn">FALSE</span>, id <span class="op">=</span> <span class="fu">recipes</span><span class="fu">::</span><span class="fu"><a href="https://recipes.tidymodels.org/reference/rand_id.html" class="external-link">rand_id</a></span><span class="op">(</span><span class="st">"sir_numeric"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-recipe">recipe<a class="anchor" aria-label="anchor" href="#arg-recipe"></a></dt>
<dd><p>A recipe object. The step will be added to the sequence of
operations for this recipe.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>One or more selector functions to choose variables for this step.
See <code><a href="https://recipes.tidymodels.org/reference/selections.html" class="external-link">selections()</a></code> for more details.</p></dd>
<dt id="arg-role">role<a class="anchor" aria-label="anchor" href="#arg-role"></a></dt>
<dd><p>Not used by this step since no new variables are created.</p></dd>
<dt id="arg-trained">trained<a class="anchor" aria-label="anchor" href="#arg-trained"></a></dt>
<dd><p>A logical to indicate if the quantities for preprocessing have
been estimated.</p></dd>
<dt id="arg-skip">skip<a class="anchor" aria-label="anchor" href="#arg-skip"></a></dt>
<dd><p>A logical. Should the step be skipped when the recipe is baked by
<code><a href="https://recipes.tidymodels.org/reference/bake.html" class="external-link">bake()</a></code>? While all operations are baked when <code><a href="https://recipes.tidymodels.org/reference/prep.html" class="external-link">prep()</a></code> is run, some
operations may not be able to be conducted on new data (e.g. processing the
outcome variable(s)). Care should be taken when using <code>skip = TRUE</code> as it
may affect the computations for subsequent operations.</p></dd>
<dt id="arg-id">id<a class="anchor" aria-label="anchor" href="#arg-id"></a></dt>
<dd><p>A character string that is unique to this step to identify it.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>You can read more in our online <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">AMR with tidymodels introduction</a>.</p>
<p>Tidyselect helpers include:</p><ul><li><p><code>all_mic()</code> and <code>all_mic_predictors()</code> to select <code>&lt;mic&gt;</code> columns</p></li>
<li><p><code>all_sir()</code> and <code>all_sir_predictors()</code> to select <code>&lt;sir&gt;</code> columns</p></li>
</ul><p>Pre-processing pipeline steps include:</p><ul><li><p><code>step_mic_log2()</code> to convert MIC columns to numeric (via <code><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric()</a></code>) and apply a log2 transform, to be used with <code>all_mic_predictors()</code></p></li>
<li><p><code>step_sir_numeric()</code> to convert SIR columns to numeric (via <code><a href="https://rdrr.io/r/base/numeric.html" class="external-link">as.numeric()</a></code>), to be used with <code>all_sir_predictors()</code>: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code>. Keep this in mind for further processing, especially if the model does not allow for <code>NA</code> values.</p></li>
</ul><p>These steps integrate with <code><a href="https://recipes.tidymodels.org/reference/recipe.html" class="external-link">recipes::recipe()</a></code> and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.</p>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><code><a href="https://recipes.tidymodels.org/reference/recipe.html" class="external-link">recipes::recipe()</a></code>, <code><a href="as.mic.html">as.mic()</a></code>, <code><a href="as.sir.html">as.sir()</a></code></p></div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><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></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.3.0 ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.8 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble </span> 3.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.0.8 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 1.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.3.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.2.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.0.4 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.3.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.3.2</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703</span></span></span>
<span class="r-in"><span><span class="co"># Presence of ESBL genes was predicted based on raw MIC values.</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># example data set in the AMR package</span></span></span>
<span class="r-in"><span><span class="va">esbl_isolates</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 500 × 19</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #BBBBBB;">.00</span> 0.12 16 16 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #BBBBBB;">.00</span> 32<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #BBBBBB;">.00</span> 2<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #BBBBBB;">.00</span> 0.12 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #BBBBBB;">.00</span> 4<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #BBBBBB;">.00</span> 64<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 490 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: NIT &lt;mic&gt;, FOS &lt;mic&gt;, CIP &lt;mic&gt;, IPM &lt;mic&gt;, MEM &lt;mic&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># COL &lt;mic&gt;</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Prepare a binary outcome and convert to ordered factor</span></span></span>
<span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">esbl_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>esbl <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">esbl</span>, levels <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="cn">FALSE</span>, <span class="cn">TRUE</span><span class="op">)</span>, ordered <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Split into training and testing sets</span></span></span>
<span class="r-in"><span><span class="va">split</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">training_data</span> <span class="op">&lt;-</span> <span class="fu">training</span><span class="op">(</span><span class="va">split</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">testing_data</span> <span class="op">&lt;-</span> <span class="fu">testing</span><span class="op">(</span><span class="va">split</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Create and prep a recipe with MIC log2 transformation</span></span></span>
<span class="r-in"><span><span class="va">mic_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">training_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="r-in"><span> <span class="co"># Optionally remove non-predictive variables</span></span></span>
<span class="r-in"><span> <span class="fu">remove_role</span><span class="op">(</span><span class="va">genus</span>, old_role <span class="op">=</span> <span class="st">"predictor"</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="r-in"><span> <span class="co"># Apply the log2 transformation to all MIC predictors</span></span></span>
<span class="r-in"><span> <span class="fu">step_mic_log2</span><span class="op">(</span><span class="fu">all_mic_predictors</span><span class="op">(</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="r-in"><span> <span class="fu">prep</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># View prepped recipe</span></span></span>
<span class="r-in"><span><span class="va">mic_recipe</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── Inputs </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Number of variables by role</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> outcome: 1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> predictor: 17</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> undeclared role: 1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── Training information </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Training data contained 375 data points and no incomplete rows.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── Operations </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> Log2 transformation of MIC columns: <span style="color: #0000BB;">AMC</span>, <span style="color: #0000BB;">AMP</span>, <span style="color: #0000BB;">TZP</span>, <span style="color: #0000BB;">CXM</span>, <span style="color: #0000BB;">FOX</span>, ... | <span style="font-style: italic;">Trained</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Apply the recipe to training and testing data</span></span></span>
<span class="r-in"><span><span class="va">out_training</span> <span class="op">&lt;-</span> <span class="fu">bake</span><span class="op">(</span><span class="va">mic_recipe</span>, new_data <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">out_testing</span> <span class="op">&lt;-</span> <span class="fu">bake</span><span class="op">(</span><span class="va">mic_recipe</span>, new_data <span class="op">=</span> <span class="va">testing_data</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Fit a logistic regression model</span></span></span>
<span class="r-in"><span><span class="va">fitted</span> <span class="op">&lt;-</span> <span class="fu">logistic_reg</span><span class="op">(</span>mode <span class="op">=</span> <span class="st">"classification"</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="r-in"><span> <span class="fu">set_engine</span><span class="op">(</span><span class="st">"glm"</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="r-in"><span> <span class="fu">fit</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">out_training</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>glm.fit: fitted probabilities numerically 0 or 1 occurred</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Generate predictions on the test set</span></span></span>
<span class="r-in"><span><span class="va">predictions</span> <span class="op">&lt;-</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">fitted</span>, <span class="va">out_testing</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="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_cols.html" class="external-link">bind_cols</a></span><span class="op">(</span><span class="va">out_testing</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Evaluate predictions using standard classification metrics</span></span></span>
<span class="r-in"><span><span class="va">our_metrics</span> <span class="op">&lt;-</span> <span class="fu">metric_set</span><span class="op">(</span><span class="va">accuracy</span>, <span class="va">kap</span>, <span class="va">ppv</span>, <span class="va">npv</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">metrics</span> <span class="op">&lt;-</span> <span class="fu">our_metrics</span><span class="op">(</span><span class="va">predictions</span>, truth <span class="op">=</span> <span class="va">esbl</span>, estimate <span class="op">=</span> <span class="va">.pred_class</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Show performance:</span></span></span>
<span class="r-in"><span><span class="co"># - negative predictive value (NPV) of ~98%</span></span></span>
<span class="r-in"><span><span class="co"># - positive predictive value (PPV) of ~94%</span></span></span>
<span class="r-in"><span><span class="va">metrics</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .metric .estimator .estimate</span>
<span class="r-out co"><span class="r-pr">#&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;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> accuracy binary 0.912</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> kap binary 0.824</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> ppv binary 0.917</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> npv binary 0.908</span>
</code></pre></div>
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4
reference/antibiogram.html
View File

@ -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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -614,7 +614,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Syndromic Group |Piperacillin/tazobactam |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |:---------------|:-----------------------|</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical |73.5% (67.8-79%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical |73.5% (68-79%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU |57.7% (49.9-65.3%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient |56.9% (46.5-66.8%) |</span>
<span class="r-in"><span></span></span>

5
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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -670,6 +670,9 @@ my_data_with_all_these_columns %&amp;gt;%
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: data.table</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Attaching package: ‘data.table’</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> The following object is masked from ‘package:purrr’:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> transpose</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> The following objects are masked from ‘package:dplyr’:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> between, first, last</span>

2
reference/antimicrobials.html
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@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<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="">3.0.0.9002</small>
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2
reference/as.ab.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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2
reference/as.av.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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2
reference/as.disk.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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2
reference/as.mic.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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2
reference/as.mo.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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14
reference/as.sir.html
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@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -309,7 +309,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<p>The function <code>is.sir()</code> detects if the input contains class <code>sir</code>. If the input is 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>, it iterates over all columns/items and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code> . <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code>. <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% potentially invalid antimicrobial interpretations, and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
</div>
@ -414,10 +414,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-06-06 <span style="color: #949494;">07:43:11</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-06-06 <span style="color: #949494;">07:43:12</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-06-06 <span style="color: #949494;">07:43:12</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-06-06 <span style="color: #949494;">07:43:12</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-06-13 <span style="color: #949494;">15:10:25</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-06-13 <span style="color: #949494;">15:10:25</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-06-13 <span style="color: #949494;">15:10:26</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-06-13 <span style="color: #949494;">15:10:26</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@ -614,7 +614,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</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="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 3 results in index '20' truncated (38%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 3 results in index '21' truncated (38%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>

2
reference/atc_online.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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2
reference/av_from_text.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="">3.0.0.9002</small>
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2
reference/av_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="">3.0.0.9002</small>
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2
reference/availability.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="">3.0.0.9002</small>
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reference/bug_drug_combinations.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="">3.0.0.9002</small>
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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>
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reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
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reference/custom_mdro_guideline.html
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@ -7,7 +7,7 @@
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reference/dosage.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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112
reference/esbl_isolates.html Normal file
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@ -0,0 +1,112 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 500 ESBL Isolates — esbl_isolates • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 500 ESBL Isolates — esbl_isolates"><meta name="description" content="A data set containing 500 microbial isolates with MIC values of common antibiotics and a binary esbl column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with tidymodels."><meta property="og:description" content="A data set containing 500 microbial isolates with MIC values of common antibiotics and a binary esbl column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with tidymodels."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 500 ESBL Isolates</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>esbl_isolates.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>A data set containing 500 microbial isolates with MIC values of common antibiotics and a binary <code>esbl</code> column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">tidymodels</a>.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">esbl_isolates</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 500 observations and 19 variables:</p><ul><li><p><code>esbl</code><br> Logical indicator if the isolate is ESBL-producing</p></li>
<li><p><code>genus</code><br> Genus of the microorganism</p></li>
<li><p><code>AMC:COL</code><br> MIC values for 17 antimicrobial agents, transformed to class <code><a href="as.mic.html">mic</a></code> (see <code><a href="as.mic.html">as.mic()</a></code>)</p></li>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>See our <a href="amr-tidymodels.html">tidymodels integration</a> for an example using this data set.</p>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">esbl_isolates</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 500 × 19</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> esbl genus AMC AMP TZP CXM FOX CTX CAZ GEN TOB TMP SXT</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> FALSE Esch… 32 32 4 64 64 8<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> FALSE Esch… 32 32 4 64 64 4<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> FALSE Esch… 4 2 64 8 4 8<span style="color: #BBBBBB;">.00</span> 0.12 16 16 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb… 32 32 16 64 64 8<span style="color: #BBBBBB;">.00</span> 8<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FALSE Esch… 32 32 4 4 4 0.25 2<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> FALSE Citr… 32 32 16 64 64 64<span style="color: #BBBBBB;">.00</span> 32<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> FALSE Morg… 32 32 4 64 64 16<span style="color: #BBBBBB;">.00</span> 2<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> FALSE Prot… 16 32 4 1 4 8<span style="color: #BBBBBB;">.00</span> 0.12 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> FALSE Ente… 32 32 8 64 64 32<span style="color: #BBBBBB;">.00</span> 4<span style="color: #BBBBBB;">.00</span> 1 1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> FALSE Citr… 32 32 32 64 64 8<span style="color: #BBBBBB;">.00</span> 64<span style="color: #BBBBBB;">.00</span> 1 1 16<span style="color: #BBBBBB;">.0</span> 320</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 490 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: NIT &lt;mic&gt;, FOS &lt;mic&gt;, CIP &lt;mic&gt;, IPM &lt;mic&gt;, MEM &lt;mic&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># COL &lt;mic&gt;</span></span>
</code></pre></div>
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@ -154,27 +154,27 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 20 42 39 6 46 25 24 12 15 44 11 1 37 29 48 11 4 15 28 45 6 31 4 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 23 43 35 23 27 21 48 4 40 25 46 30 12 38 46 13 18 8 26 8 7 34 5 31 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 28 36 40 40 10 45 22 10 42 24 6 25 1 3 33 43 26 25 15 17 31 7 46 14 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 9 39 49 41 40 2 37 6 48 47 43 47 6 38 14 30 22 42 34 40 19 9 19 16 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 7 4 45 15 6 11 26 43 24 20 8 29 24 42 32 13 45 2 43 39 15 32 45 2 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 4 19 21 44 22 44 9 43 38 16 7 45 10 33 36 44 4 20 11 14 5 19 7 39 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 46 30 4 30 41 7 13 28 37 30 18 27 9 42 17 22 40 12 8 34 13 2 44 4 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 33 35 15 22 23 15 9 40 12 1 43 17 18 36 31 22 34 37 43 36 37 10 23 25 36</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&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;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-14 058917 76 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>HMNS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-06 894506 83 M ICU <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@ -208,19 +208,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [93]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 010257 2004-04-03 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 021368 2016-03-25 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 034010 2010-02-26 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 058917 2002-11-14 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 083080 2010-02-25 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 097186 2015-10-28 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0DBF93 2015-12-03 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 105248 2005-06-16 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 130252 2002-04-08 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 161740 2005-06-21 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 060287 2007-03-11 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 101305 2006-12-13 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 141061 2014-10-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 151041 2006-02-10 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 15D386 2004-08-01 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 187841 2008-04-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 189363 2004-06-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 208305 2015-09-14 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 257844 2011-05-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 284FFF 2010-03-31 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><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">)</span> <span class="op">{</span></span></span>
@ -234,19 +234,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2004-04-03 010257 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Outpatient 2016-03-25 021368 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2010-02-26 034010 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2002-11-14 058917 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2010-02-25 083080 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2015-10-28 097186 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2015-12-03 0DBF93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2005-06-16 105248 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2002-04-08 130252 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2005-06-21 161740 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [88]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-03-11 060287 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2006-12-13 101305 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2014-10-22 141061 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-02-10 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2004-08-01 15D386 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2008-04-22 187841 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-06-22 189363 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2015-09-14 208305 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2011-05-22 257844 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2010-03-31 284FFF 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><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">)</span> <span class="op">{</span></span></span>
@ -262,9 +262,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 51 13 34 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 36 11 26 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 7 6 7 7</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 55 12 34 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 27 10 24 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 5 6 6</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -282,7 +282,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
<span class="r-in"><span><span class="co"># since you can now group on anything that seems relevant:</span></span></span>
@ -293,19 +293,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E19253 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> CB6026 <span style="color: #949494;">B_</span>PSDMN<span style="color: #949494;">_</span>AERG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> D07D73 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PYGN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 972724 <span style="color: #949494;">B_</span>SPHNGB<span style="color: #949494;">_</span>SPRT ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 999565 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 7D1606 <span style="color: #949494;">B_</span>VLLNL<span style="color: #949494;">_</span>PRVL ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B26404 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AB0003 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 105248 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> F09078 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [92]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F24801 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>AGLC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A26548 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 422833 <span style="color: #949494;">B_</span>ENTRC<span style="color: #949494;">_</span>FCLS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> AFD3B1 <span style="color: #BB0000;"> UNKNOWN</span> Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> F35553 <span style="color: #949494;">B_</span>ENTRBC<span style="color: #949494;">_</span>CLOC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 316893 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B54813 <span style="color: #949494;">B_</span>ENTRC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E06844 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B65162 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 43F266 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/ggplot_sir.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/guess_ab_col.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">

8
reference/index.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -388,6 +388,12 @@
<dd>Data Set with 2 000 Example Isolates</dd>
</dl><dl><dt>
<code><a href="esbl_isolates.html">esbl_isolates</a></code>
</dt>
<dd>Data Set with 500 ESBL Isolates</dd>
</dl><dl><dt>
<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
</dt>

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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/join.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/key_antimicrobials.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/kurtosis.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -91,9 +91,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.082227</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.072546</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02736212</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.024332</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

4
reference/like.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -107,6 +107,8 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># data.table has a more limited version of %like%, so unload it:</span></span></span>
<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/try.html" class="external-link">try</a></span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/detach.html" class="external-link">detach</a></span><span class="op">(</span><span class="st">"package:data.table"</span>, unload <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, silent <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>‘data.table’ namespace cannot be unloaded:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> namespace ‘data.table’ is imported by ‘prodlim’ so cannot be unloaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">a</span> <span class="op">&lt;-</span> <span class="st">"This is a test"</span></span></span>
<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="st">"TEST"</span></span></span>

2
reference/mdro.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">

90
reference/mean_amr_distance.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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -110,31 +110,31 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R S S I R R R S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R S R I I R R R S R</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7745967 1.1618950 -0.7745967 -0.7745967 -0.7745967 1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.1618950 1.1618950 -0.7745967 -0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.7745967 -1.1618950 0.7745967 -1.1618950 -1.1618950 0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.7745967 0.7745967 -1.1618950 0.7745967</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01 &lt;=0.001 &gt;=64 2 0.25 &lt;=0.001 32 0.025 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 0.0005 0.001 0.0002 8 &lt;=0.0001 &lt;=0.0001 0.004 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 0.016 0.002 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.52636230 -1.08012768 1.58136840 0.74786845 0.24776848 -1.08012768</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.41466841 -0.30599690 0.08106849 -1.08012768</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.17346160 -0.53194487 -0.34173212 -0.78339244 2.12452534 -0.97360519</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.97360519 0.03869338 0.41911887 -0.15151937</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.52636230 -1.08012768 1.58136840 0.74786845 0.24776848 -1.08012768</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.41466841 -0.30599690 0.08106849 -1.08012768</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.17346160 -0.53194487 -0.34173212 -0.78339244 2.12452534 -0.97360519</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.97360519 0.03869338 0.41911887 -0.15151937</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 46 7 16 44 16 16 12 41 13 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 31 26 23 38 44 41 20 49 32 16</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.2329916 -1.1475367 -0.5981840 1.1109132 -0.5981840 -0.5981840</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.8423408 0.9277957 -0.7813016 1.2940308</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.09179851 -0.55079106 -0.82618658 0.55079106 1.10158211 0.82618658</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.10158211 1.56057466 0.00000000 -1.46877615</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -145,35 +145,35 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 30 1 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 21 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 20 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 30 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 25 16 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 31 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 31 1 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 18 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 17 0.5 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 17 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 27 8 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 33 2 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 22 1 &lt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 32 0.25 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 31 8 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 31 2 &lt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 28 2 &lt;=4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 22 16 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 22 8 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 24 0.25 32</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.58987341 -0.03053318 -0.04319558 -0.40303919 0.28644445 0.01028759</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.63115955 -0.11068385 -0.58280241 -0.34751080</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.42546514 0.31178268 -0.85243112 0.27789744 0.43759204 -0.22674498</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.19734764 -0.16271414 -0.06891128 -0.33928341</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span></span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 30 2 1 -0.9142137</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 20 1 4 -0.3370495</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 18 8 1 -0.3068815</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 17 0.5 &gt;=8 -0.2003005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 31 4 2 -0.1701325</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 30 1 &gt;=8 0.1033656</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 31 1 &gt;=8 0.1033656</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 17 4 4 0.2702827</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 21 8 4 0.5739488</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 25 16 4 0.8776150</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 32 0.25 8 -0.93315862</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 22 1 &lt;=4 -0.88239870</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 31 2 &lt;=4 -0.64403306</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 28 2 &lt;=4 -0.64403306</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 24 0.25 32 -0.08121587</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 33 2 16 0.20790970</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 22 16 8 0.49703526</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 31 8 16 0.68464099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 22 8 16 0.68464099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 27 8 32 1.11061237</span>
<span class="r-in"><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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -186,16 +186,16 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 20 1 4 -0.04319558 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 21 8 4 -0.03053318 0.01266241</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 F I 31 4 2 0.01028759 0.05348318</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H R 18 8 1 -0.11068385 0.06748826</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J S 17 4 4 -0.34751080 0.30431522</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E S 25 16 4 0.28644445 0.32964004</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D S 30 2 1 -0.40303919 0.35984361</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 I S 17 0.5 &gt;=8 -0.58280241 0.53960682</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A R 30 1 &gt;=8 0.58987341 0.63306899</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G R 31 1 &gt;=8 0.63115955 0.67435514</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C I 22 1 &lt;=4 -0.85243112 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 J I 24 0.25 32 -0.33928341 0.5131477</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 F I 31 2 &lt;=4 -0.22674498 0.6256861</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H S 22 16 8 -0.16271414 0.6897170</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I I 22 8 16 -0.06891128 0.7835198</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 G R 28 2 &lt;=4 0.19734764 1.0497788</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D R 32 0.25 8 0.27789744 1.1303286</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B I 33 2 16 0.31178268 1.1642138</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A S 27 8 32 0.42546514 1.2778963</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 E S 31 8 16 0.43759204 1.2900232</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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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/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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">

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2
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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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2
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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">

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70
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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</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">
@ -55,9 +55,11 @@
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">random_mic</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">random_mic</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, skew <span class="op">=</span> <span class="st">"right"</span>,</span>
<span> severity <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">random_disk</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">random_disk</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, skew <span class="op">=</span> <span class="st">"left"</span>,</span>
<span> severity <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">random_sir</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, prob_SIR <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="fl">0.33</span>, <span class="fl">0.33</span>, <span class="fl">0.33</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
@ -71,13 +73,21 @@
<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>. Can be the same length as <code>size</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>
<dt id="arg-skew">skew<a class="anchor" aria-label="anchor" href="#arg-skew"></a></dt>
<dd><p>Direction of skew for MIC or disk values, either <code>"right"</code> or <code>"left"</code>. A left-skewed distribution has the majority of the data on the right.</p></dd>
<dt id="arg-severity">severity<a class="anchor" aria-label="anchor" href="#arg-severity"></a></dt>
<dd><p>Skew severity; higher values will increase the skewedness. Default is <code>2</code>; use <code>0</code> to prevent skewedness.</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>
@ -92,51 +102,61 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The base <span style="R">R</span> function <code><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample()</a></code> is used for generating values.</p>
<p>Generated values are based on the EUCAST 2025 guideline as implemented in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
</div>
<p>Internally, MIC and disk zone values are sampled based on clinical breakpoints defined in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument. The MICs are sampled on a log2 scale and disks linearly, using weighted probabilities. The weights are based on the <code>skew</code> and <code>severity</code> arguments:</p><ul><li><p><code>skew = "right"</code> places more emphasis on lower MIC or higher disk values.</p></li>
<li><p><code>skew = "left"</code> places more emphasis on higher MIC or lower disk values.</p></li>
<li><p><code>severity</code> controls the exponential bias applied.</p></li>
</ul></div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.001 8 0.002 256 256 256 0.125 0.25 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 0.01 32 32 256 0.01 32 8 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.0625 0.5 0.0625 0.5 0.01 0.125 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 2 16 1 0.004 0.008 0.0005 0.125 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 2 0.008 0.008 0.016 0.064 0.064 &lt;=0.0002 0.001 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 0.0005 0.5 0.002 0.002 0.125 8 &lt;=0.0002 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.064 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 48 46 26 46 17 46 15 50 20 13 48 44 6 47 26 15 12 20 11 45 8 41 45 14 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 24 47 38 28 36 33 31 50 41 29 40 31 44 45 37 40 44 49 9 48 20 37 47 28</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R S R I S S I S R S R I R S S S S I R S S S S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R R S S I S I S S I S R I I I I S I R I I I I R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># add more skewedness, make more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="va">disks</span> <span class="op">&lt;-</span> <span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span>, severity <span class="op">=</span> <span class="fl">2</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"CIP"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">disks</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="random-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set</span></span></span>
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">disks</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"CIP"</span>, guideline <span class="op">=</span> <span class="st">"CLSI 2025"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="random-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 0.25 0.002 0.025 0.01 0.0625 0.25 0.01 0.0625 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 0.01 0.125 8 0.002 0.0625 0.002 &gt;=256 &gt;=256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5 &gt;=256 1 0.125 64 64 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0005 8 0.008 0.0002 0.0002 0.0002 0.0002 &lt;=0.0001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 64 &lt;=0.0001 1 0.5 0.001 0.5 0.001 0.0005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 0.016 0.008 0.002 0.032 &lt;=0.0001 0.0002 0.001 0.0005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.001 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 &lt;=0.5 8 8 &lt;=0.5 2 2 8 2 8 8 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 1 &lt;=0.5 &gt;=16 1 4 2 1 &lt;=0.5 &gt;=16 4 4 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.5 &lt;=0.5 2 &lt;=0.5 1 &lt;=0.5 &lt;=0.5 &lt;=0.5 &lt;=0.5 1 &lt;=0.5 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] &lt;=0.5 1 &lt;=0.5 1 &lt;=0.5 &lt;=0.5 &lt;=0.5 &lt;=0.5 &lt;=0.5 &lt;=0.5 2 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.5 2 0.125 &lt;=0.025 0.25 0.0625 2 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 0.5 16 0.5 1 8 &lt;=0.025 2 &lt;=0.025</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.125 8 1 0.0625 2 1 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 0.125 1 0.25 0.5 0.125 0.125 0.125 0.125 0.125 0.125 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 1 0.125 0.5 1 0.125 0.25 0.5 0.25 0.5 0.5 0.5 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.25 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 39 19 39 20 37 11 18 10 46 46 9 40 46 24 30 31 13 12 42 50 43 12 34 22 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 21 23 21 14 22 25 29 29 28 34 34 34 33 13 28 33 34 32 25 18 26 13 21 33</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 11 17 12 11 16 13 14 15 13 17 15 11 13 16 15 14 13 12 16 14 11 12 14 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 21 15 22 16 22 16 14 21 17 15 19 20 17 18 21 16 20 11 22 19 18 19 11 21</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 19 20 27 27 20 21 16 23 20 22 17 27 20 23 22 22 16 16 24 24 19 25 17 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 29 25 31 17 29 21 31 34 33 31 29 30 23 20 33 20 34 32 35 26 26 26 34 30 33</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

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@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<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="">3.0.0.9002</small>
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@ -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="">3.0.0.9002</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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@ -90,7 +90,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.008140368</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.08600633</span>
</code></pre></div>
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