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@@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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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="">2.1.1.9123</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9125</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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@@ -786,16 +786,16 @@ 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: 57 × 16</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></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;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-01-16 <span style="color: #949494;">11:00:46</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-01-16 <span style="color: #949494;">11:00:46</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-01-16 <span style="color: #949494;">11:00:53</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-01-16 <span style="color: #949494;">11:00:54</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-01-17 <span style="color: #949494;">11:16:11</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-01-17 <span style="color: #949494;">11:16:18</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-01-17 <span style="color: #949494;">11:16:18</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-01-17 <span style="color: #949494;">11:16:19</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-01-17 <span style="color: #949494;">11:16:19</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-01-17 <span style="color: #949494;">11:16:11</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-01-17 <span style="color: #949494;">11:16:18</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-01-17 <span style="color: #949494;">11:16:18</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-01-17 <span style="color: #949494;">11:16:19</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-01-17 <span style="color: #949494;">11:16:19</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
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@@ -835,7 +835,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></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 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">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</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 '19' truncated (38%) that were invalid</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 '20' truncated (38%) 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-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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<span class="r-in"><span><span class="va">sir_data</span> <span class="op"><-</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="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
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