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@ -10,7 +10,7 @@
<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="">1.8.2.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</small>
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@ -151,7 +151,7 @@
<span> <span class="va">x</span>,</span>
<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
@ -164,7 +164,7 @@
<span> <span class="va">x</span>,</span>
<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> ab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="rsi_translation.html">rsi_translation</a></span>,</span>
@ -176,7 +176,7 @@
<span> <span class="va">x</span>,</span>
<span> <span class="va">...</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> uti <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> conserve_capped_values <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
@ -219,7 +219,7 @@
<dt>guideline</dt>
<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="rsi_translation.html">rsi_translation</a> data set), supports EUCAST (2013-2022) and CLSI (2013-2022), see <em>Details</em></p></dd>
<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="rsi_translation.html">rsi_translation</a> data set), but can be set with the <a href="https://rdrr.io/r/base/options.html" class="external-link">option</a> <code>AMR_guideline</code>. Supports EUCAST (2013-2022) and CLSI (2013-2022), see <em>Details</em>.</p></dd>
<dt>uti</dt>
@ -263,13 +263,13 @@
<p>The <code>as.rsi()</code> function works in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><a href="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.mic, as.rsi) <span class="co"># until dplyr 1.0.0</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.mic), as.rsi)) <span class="co"># since dplyr 1.0.0</span></span></code></pre><p></p></div></li>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.mic, as.rsi)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.mic), as.rsi))</span></code></pre><p></p></div></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.disk, as.rsi) <span class="co"># until dplyr 1.0.0</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.disk), as.rsi)) <span class="co"># since dplyr 1.0.0</span></span></code></pre><p></p></div></li>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate_if</span>(is.disk, as.rsi)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>your_data <span class="sc">%&gt;%</span> <span class="fu">mutate</span>(<span class="fu">across</span>(<span class="fu">where</span>(is.disk), as.rsi))</span></code></pre><p></p></div></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(your_data)</code>.</p></li>
</ol><p>For points 2, 3 and 4: Use <code>rsi_interpretation_history()</code> to retrieve a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> (or <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> if the <code>tibble</code> package is installed) with all results of the last <code>as.rsi()</code> call.</p>
@ -281,6 +281,12 @@
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2022"</code> or <code>"CLSI 2022"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>You can set the default guideline with the <code>AMR_guideline</code> <a href="https://rdrr.io/r/base/options.html" class="external-link">option</a> (e.g. in your <code>.Rprofile</code> file), such as:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"EUCAST 2020"</span>)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="co"># or to reset:</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="cn">NULL</span>)</span></code></pre><p></p></div>
</div>
<div class="section">
@ -472,7 +478,6 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Using column 'microorganism' as input for `col_mo`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -481,16 +486,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Assigning class 'rsi' to already clean column 'ERY' (erythromycin)...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
@ -499,21 +504,21 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
<span class="r-in"><span><span class="fu">rsi_interpretation_history</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: 50 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_userinput ab_actual mo_us…¹ mo_actual guide…²</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;ab&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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-11-17 <span style="color: #949494;">14:29:45</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-11-17 <span style="color: #949494;">14:29:45</span> 1 AMP AMP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-11-17 <span style="color: #949494;">14:29:46</span> 1 CIP CIP Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-11-17 <span style="color: #949494;">14:29:46</span> 1 GEN GEN Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-11-17 <span style="color: #949494;">14:29:46</span> 1 TOB TOB Escher… B_ESCHR_COLI EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-11-17 <span style="color: #949494;">14:29:47</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-11-17 <span style="color: #949494;">14:29:47</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-11-17 <span style="color: #949494;">14:29:48</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-11-17 <span style="color: #949494;">14:29:48</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-11-17 <span style="color: #949494;">14:29:48</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_gu…¹ mo_in…² mo_guideline guide…³</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;ab&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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-11-24 <span style="color: #949494;">19:34:50</span> 1 ampicillin AMP Strep … B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-11-24 <span style="color: #949494;">19:34:51</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-11-24 <span style="color: #949494;">19:34:51</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-11-24 <span style="color: #949494;">19:34:51</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-11-24 <span style="color: #949494;">19:34:52</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-11-24 <span style="color: #949494;">19:34:52</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-11-24 <span style="color: #949494;">19:34:53</span> 1 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-11-24 <span style="color: #949494;">19:34:53</span> 2 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-11-24 <span style="color: #949494;">19:34:53</span> 3 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-11-24 <span style="color: #949494;">19:34:53</span> 4 AMX AMX B_STRP… B_STRPT_PNMN EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​mo_userinput, ²guideline</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># names ¹​ab_guideline, ²mo_input, ³guideline</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># for single values</span></span></span>
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span></span></span>
@ -524,9 +529,9 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints available for S. pneumoniae / ampicillin - assuming body site</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'Non-meningitis'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Non-meningitis'.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
<span class="r-in"><span></span></span>
@ -536,8 +541,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'ampicillin' (AMP, ampicillin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'ampicillin' (AMP) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
@ -586,16 +591,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -610,16 +615,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -628,16 +633,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism' according to EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -646,33 +651,31 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / gentamicin (GEN) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for E. coli / tobramycin (TOB) -</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> assuming non-UTI. Use argument `uti` to set which isolates are from urine.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Using column 'mo' as input for `col_mo`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * NOTE *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.rsi(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming `uti = TRUE`. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * WARNING *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use `as.rsi(uti = FALSE)` to prevent this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Using column 'mo' as input for `col_mo`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use as.rsi(uti = FALSE) to prevent this.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2022...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.rsi(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming `uti = TRUE`. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> WARNING.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.rsi.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> * WARNING *</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2022...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK.</span>
@ -691,7 +694,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
<span class="r-in"><span><span class="co"># For CLEANING existing R/SI values ------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.rsi</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">"I"</span>, <span class="st">"R"</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 `as.rsi()`: 3 results in column '24' truncated (50%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.rsi(): 3 results in column '24' truncated (50%) 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 'rsi'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I R &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>