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2023-04-18 22:44:09 +00:00
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@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_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="">2.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9011</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">
@ -327,7 +327,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<h3 id="machine-readable-clinical-breakpoints">Machine-Readable Clinical Breakpoints<a class="anchor" aria-label="anchor" href="#machine-readable-clinical-breakpoints"></a></h3>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 17 918 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 18 271 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
</div>
<div class="section">
@ -508,10 +508,14 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu">as.sir</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> =&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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'CIP' (ciprofloxacin) 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-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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>
@ -527,23 +531,23 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Assigning class 'sir' 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>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli I I S S R</span>
<span class="r-in"><span></span></span>
<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">sir_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_input ab_guideline mo_input mo_guideline </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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-04-17 <span style="color: #949494;">09:34:07</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-04-17 <span style="color: #949494;">09:34:06</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-04-17 <span style="color: #949494;">09:34:06</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-04-17 <span style="color: #949494;">09:34:05</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-04-17 <span style="color: #949494;">09:33:59</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-04-17 <span style="color: #949494;">09:33:59</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-04-17 <span style="color: #949494;">09:33:59</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-04-17 <span style="color: #949494;">09:33:59</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-04-17 <span style="color: #949494;">09:33:59</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-04-17 <span style="color: #949494;">09:33:59</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guideline mo_input mo_guideline </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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-04-18 <span style="color: #949494;">22:40:53</span> 1 TOB TOB Escherich… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-04-18 <span style="color: #949494;">22:40:53</span> 1 GEN GEN Escherich… B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-04-18 <span style="color: #949494;">22:40:52</span> 1 CIP CIP Escherich… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-04-18 <span style="color: #949494;">22:40:52</span> 1 AMP AMP Escherich… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-04-18 <span style="color: #949494;">22:40:45</span> 1 CIP CIP B_ESCHR_C… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-04-18 <span style="color: #949494;">22:40:45</span> 2 CIP CIP B_ESCHR_C… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-04-18 <span style="color: #949494;">22:40:45</span> 3 CIP CIP B_ESCHR_C… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-04-18 <span style="color: #949494;">22:40:45</span> 4 CIP CIP B_ESCHR_C… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-04-18 <span style="color: #949494;">22:40:45</span> 5 CIP CIP B_ESCHR_C… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-04-18 <span style="color: #949494;">22:40:45</span> 6 CIP CIP B_ESCHR_C… UNKNOWN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: guideline &lt;chr&gt;, 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;sir&gt;, breakpoint_S_R &lt;chr&gt;</span></span>
@ -558,10 +562,12 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming an unspecified body site.</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] R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
@ -607,16 +613,24 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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>
@ -631,16 +645,24 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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>
@ -655,10 +677,14 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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>
@ -673,10 +699,14 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> isolates are from urine. See ?as.sir.</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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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>
@ -706,10 +736,14 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) 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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> prevent this</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> OK.</span>
@ -717,7 +751,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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> microorganism AMP CIP GEN TOB ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli I I S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
<span class="r-in"><span></span></span>