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@@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9035</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</small>
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<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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@@ -179,14 +179,14 @@ package.</p>
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<span> mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</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">%>%</a></span></span>
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<span> <span class="co"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
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<span> <span class="fu">drop_na</span><span class="op">(</span><span class="op">)</span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">' (cefoxitin), '</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">' (cefotaxime), '</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">' (ceftazidime),</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> '</span><span style="color: #0000BB; font-weight: bold;">CRO</span><span style="color: #0000BB;">' (ceftriaxone), '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem), and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
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<span><span class="co">#> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span></span>
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<span><span class="co">#> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
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<span><span class="co">#> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
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<span><span class="co">#> (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
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<span><span class="co">#> (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
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<span><span class="co">#> '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span></code></pre></div>
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<p><strong>Explanation:</strong></p>
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<ul>
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<li>
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@@ -227,26 +227,37 @@ we have with <code>step_corr()</code>, the necessary parameters can be
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estimated from a training set using <code>prep()</code>:</p>
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<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu">prep</span><span class="op">(</span><span class="va">resistance_recipe</span><span class="op">)</span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ For `aminoglycosides()` using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ For `betalactams()` using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">' (cefoxitin), '</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">' (cefotaxime), '</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">' (ceftazidime),</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> '</span><span style="color: #0000BB; font-weight: bold;">CRO</span><span style="color: #0000BB;">' (ceftriaxone), '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem), and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span></span>
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<span><span class="co">#> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (kanamycin)</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns '<span style="font-weight: bold;">PEN</span>' (benzylpenicillin), '<span style="font-weight: bold;">OXA</span>'</span></span>
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<span><span class="co">#> (oxacillin), '<span style="font-weight: bold;">FLC</span>' (flucloxacillin), '<span style="font-weight: bold;">AMX</span>' (amoxicillin), '<span style="font-weight: bold;">AMC</span>'</span></span>
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<span><span class="co">#> (amoxicillin/clavulanic acid), '<span style="font-weight: bold;">AMP</span>' (ampicillin), '<span style="font-weight: bold;">TZP</span>'</span></span>
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<span><span class="co">#> (piperacillin/tazobactam), '<span style="font-weight: bold;">CZO</span>' (cefazolin), '<span style="font-weight: bold;">FEP</span>' (cefepime), '<span style="font-weight: bold;">CXM</span>'</span></span>
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<span><span class="co">#> (cefuroxime), '<span style="font-weight: bold;">FOX</span>' (cefoxitin), '<span style="font-weight: bold;">CTX</span>' (cefotaxime), '<span style="font-weight: bold;">CAZ</span>' (ceftazidime),</span></span>
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<span><span class="co">#> '<span style="font-weight: bold;">CRO</span>' (ceftriaxone), '<span style="font-weight: bold;">IPM</span>' (imipenem), and '<span style="font-weight: bold;">MEM</span>' (meropenem)</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> ── Inputs</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> ── Inputs </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> Number of variables by role</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> outcome: 1</span></span>
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<span><span class="co">#> predictor: 20</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> ── Training information</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> ── Training information </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> Training data contained 1968 data points and no incomplete rows.</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> ── Operations</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> ── Operations </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">•</span> Correlation filter on: <span style="color: #0000BB;">AMX</span> <span style="color: #0000BB;">CTX</span> | <span style="font-style: italic;">Trained</span></span></span></code></pre></div>
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<p><strong>Explanation:</strong></p>
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<ul>
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@@ -737,11 +748,12 @@ into a structured time-series format.</p>
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<span> .names <span class="op">=</span> <span class="st">"res_{.col}"</span><span class="op">)</span>, </span>
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<span> .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
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<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for `col_mo`.</span></span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span></span>
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<span><span class="co"><span style="color: #0000BB;">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span></span>
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<span><span class="co">#> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column '<span style="font-weight: bold;">mo</span>' as input for `col_mo`.</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` (`?AMR::resistance()`) assumes the EUCAST guideline and thus</span></span>
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<span><span class="co">#> considers the 'I' category susceptible. Set the `guideline` argument or the</span></span>
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<span><span class="co">#> `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span></span>
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<span><span class="co">#> (`?AMR::AMR-options`).</span></span>
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<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
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<span></span>
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<span><span class="va">data_time</span></span>
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<span><span class="co">#> <span style="color: #949494;"># A tibble: 32 × 5</span></span></span>
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