P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:47:54 +02:00
Code Releases Activity

Built site for AMR: 2.0.0.9024@f065945

Browse Source
This commit is contained in:
github-actions
2023-06-22 13:20:36 +00:00
parent a061a2a482
commit 9fabe8ad02
117 changed files with 476 additions and 407 deletions
Download Patch File Download Diff File Expand all files Collapse all files

176
reference/as.sir.html
View File

@ -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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@ -188,6 +188,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
<span> include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> ecoff <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_ecoff"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
@ -202,6 +203,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<span> reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
<span> include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> ecoff <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_ecoff"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
@ -216,7 +218,8 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<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="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
<span> include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
<span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span></span>
<span> include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> ecoff <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_ecoff"</span>, <span class="cn">FALSE</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
@ -228,9 +231,9 @@ All breakpoints used for interpretation are publicly available in the clinical_b
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2013-2022, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>M100 Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2013-2022, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2013-2022, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>M100 Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2023, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@ -255,7 +258,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<dt>guideline</dt>
<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2013-2022) and CLSI (2013-2022), see <em>Details</em>.</p></dd>
<dd><p>defaults to EUCAST 2023 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2023) and CLSI (2011-2023), see <em>Details</em>.</p></dd>
<dt>uti</dt>
@ -282,6 +285,10 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
<dt>ecoff</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that ECOFF (Epidemiological Cut-Off) values must be used <strong>instead</strong> of other clinical breakpoints - the default is <code>FALSE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_ecoff</a></code>.</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
@ -323,8 +330,8 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
<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>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2023"</code> or <code>"CLSI 2023"</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 <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code> (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>
@ -344,7 +351,7 @@ 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 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>
<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 42 599 rows and 12 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">
@ -524,19 +531,24 @@ 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-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> 2023...</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 ampicillin (AMP) 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.sir.</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> EUCAST 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> to EUCAST 2023...</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.sir.</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> to EUCAST 2023...</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>
@ -551,16 +563,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 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> 2023-05-27 <span style="color: #949494;">08:50:58</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> 2023-05-27 <span style="color: #949494;">08:50:58</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> 2023-05-27 <span style="color: #949494;">08:50:57</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> 2023-05-27 <span style="color: #949494;">08:50:57</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> 2023-05-27 <span style="color: #949494;">08:50:52</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> 2023-05-27 <span style="color: #949494;">08:50:52</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> 2023-05-27 <span style="color: #949494;">08:50:52</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> 2023-05-27 <span style="color: #949494;">08:50:52</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> 2023-05-27 <span style="color: #949494;">08:50:52</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> 2023-05-27 <span style="color: #949494;">08:50:52</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-06-22 <span style="color: #949494;">13:16:45</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> 2023-06-22 <span style="color: #949494;">13:16:45</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> 2023-06-22 <span style="color: #949494;">13:16:44</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> 2023-06-22 <span style="color: #949494;">13:16:43</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> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-06-22 <span style="color: #949494;">13:16:36</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</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>
@ -573,7 +585,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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 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> 2023...</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>
@ -587,7 +599,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<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) 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> EUCAST 2023...</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 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
@ -623,91 +635,121 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</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 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> 'microorganism' according to EUCAST 2023...</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 ampicillin (AMP) 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.sir.</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> 'microorganism' according to EUCAST 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> 'microorganism' according to EUCAST 2023...</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 ampicillin (AMP) 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.sir.</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> 'microorganism' according to EUCAST 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> 'microorganism' according to EUCAST 2023...</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.sir.</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> 'microorganism' according to EUCAST 2023...</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.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> 'microorganism' according to EUCAST 2023...</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 ampicillin (AMP) 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.sir.</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> 'microorganism' according to EUCAST 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> 'microorganism' according to EUCAST 2023...</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 ampicillin (AMP) 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.sir.</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> 'microorganism' according to EUCAST 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> 'microorganism' according to EUCAST 2023...</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.sir.</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> 'microorganism' according to EUCAST 2023...</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.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> 'microorganism' according to EUCAST 2023...</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 ampicillin (AMP) 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.sir.</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> 'microorganism' according to EUCAST 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> 'microorganism' according to EUCAST 2023...</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.sir.</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> 'microorganism' according to EUCAST 2023...</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.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> 2023...</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 ampicillin (AMP) 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.sir.</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> 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> EUCAST 2023...</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.sir.</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> EUCAST 2023...</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.sir.</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-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): 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.sir.</span>
@ -716,22 +758,24 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use as.sir(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-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): 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.sir.</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> 2023...</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> =&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> 2023...</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 ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</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> EUCAST 2023...</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> =&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> EUCAST 2023...</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>