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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="">2.0.0.9020</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9021</small>
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@ -551,16 +551,16 @@ 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 × 12</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_input ab_guideline mo_input mo_guideline </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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-05-26 <span style="color: #949494;">14:15:02</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-05-26 <span style="color: #949494;">14:15:02</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-05-26 <span style="color: #949494;">14:15:01</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-05-26 <span style="color: #949494;">14:15:01</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-05-26 <span style="color: #949494;">14:14:52</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-05-26 <span style="color: #949494;">17:28:00</span> 1 TOB TOB Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-05-26 <span style="color: #949494;">17:27:59</span> 1 GEN GEN Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-05-26 <span style="color: #949494;">17:27:58</span> 1 CIP CIP Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-05-26 <span style="color: #949494;">17:27:58</span> 1 AMP AMP Escherichia… B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-05-26 <span style="color: #949494;">17:27:51</span> 1 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-05-26 <span style="color: #949494;">17:27:51</span> 2 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-05-26 <span style="color: #949494;">17:27:51</span> 3 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-05-26 <span style="color: #949494;">17:27:51</span> 4 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-05-26 <span style="color: #949494;">17:27:51</span> 5 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-05-26 <span style="color: #949494;">17:27:51</span> 6 CIP CIP B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 6 more variables: guideline <chr>, 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></span></span>
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@ -575,10 +575,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
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<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
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<span class="r-msg co"><span class="r-pr">#></span> Note:</span>
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<span class="r-msg co"><span class="r-pr">#></span> • (Some) PK/PD breakpoints were applied - use include_PKPD = FALSE to</span>
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<span class="r-msg co"><span class="r-pr">#></span> prevent this</span>
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<span class="r-msg co"><span class="r-pr">#></span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
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<span class="r-msg co"><span class="r-pr">#></span> pneumoniae - assuming body site 'Non-meningitis'.</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</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
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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></span>
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<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>
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