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@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -238,7 +238,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
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<dt>guideline</dt>
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<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 option <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>
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<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>
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<dt>uti</dt>
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@ -258,15 +258,15 @@ All breakpoints used for interpretation are publicly available in the clinical_b
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<dt>include_screening</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed, defaults to <code>FALSE</code>. Can also be set with the option <code><a href="AMR-options.html">AMR_include_screening</a></code>.</p></dd>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed - 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_include_screening</a></code>.</p></dd>
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<dt>include_PKPD</dt>
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<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, defaults to <code>TRUE</code>. Can also be set with the option <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
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<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>
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<dt>col_mo</dt>
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<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to 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>
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<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>
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<dt>clean</dt>
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@ -308,7 +308,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
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<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022).</p>
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<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>
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<p>You can set the default guideline with the option <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
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<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>
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<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>
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<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>
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<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>
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@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-02-18 <span style="color: #949494;">14:03:27</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-02-18 <span style="color: #949494;">14:03:26</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-02-18 <span style="color: #949494;">14:03:26</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-02-18 <span style="color: #949494;">14:03:25</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-02-18 <span style="color: #949494;">14:03:20</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-02-22 <span style="color: #949494;">13:45:00</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-02-22 <span style="color: #949494;">13:44:59</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-02-22 <span style="color: #949494;">13:44:59</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-02-22 <span style="color: #949494;">13:44:58</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-02-22 <span style="color: #949494;">13:44:54</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table <chr>, method <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># input <dbl>, outcome <sir>, breakpoint_S_R <chr>, ab_considered <lgl>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># mo_considered <lgl>, breakpoint_S <lgl>, breakpoint_R <lgl>,</span></span>
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@ -725,7 +725,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"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>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '24' truncated (50%) that were invalid</span>
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<span class="r-wrn co"><span class="r-pr">#></span> antimicrobial interpretations: "A", "B" and "C"</span>
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<span class="r-wrn co"><span class="r-pr">#></span> antimicrobial interpretations: "A", "B", and "C"</span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S I R <NA> <NA> <NA></span>
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<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"<= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
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