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@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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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="">2.1.1.9251</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9252</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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@ -827,16 +827,16 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 65 × 17</span></span>
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<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</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;"><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;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-21 <span style="color: #949494;">14:09:00</span> 1 DISK ampicillin Strep pneu human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-21 <span style="color: #949494;">14:09:01</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-04-21 <span style="color: #949494;">14:09:01</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-25 <span style="color: #949494;">09:23:57</span> 1 DISK ampicillin Strep pneu human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-25 <span style="color: #949494;">09:23:58</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2025-04-25 <span style="color: #949494;">09:23:58</span> 1 DISK AMP Escherich… human 20 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-21 <span style="color: #949494;">14:09:01</span> 1 DISK GEN Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-21 <span style="color: #949494;">14:09:01</span> 1 DISK TOB Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-21 <span style="color: #949494;">14:09:02</span> 1 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-21 <span style="color: #949494;">14:09:02</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-21 <span style="color: #949494;">14:09:02</span> 2 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-21 <span style="color: #949494;">14:09:02</span> 3 MIC AMX B_STRPT_P… human 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-25 <span style="color: #949494;">09:23:58</span> 1 DISK GEN Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-25 <span style="color: #949494;">09:23:58</span> 1 DISK TOB Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-25 <span style="color: #949494;">09:23:59</span> 1 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-25 <span style="color: #949494;">09:23:59</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-25 <span style="color: #949494;">09:23:59</span> 2 MIC AMX B_STRPT_P… human 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-25 <span style="color: #949494;">09:23:59</span> 3 MIC AMX B_STRPT_P… human 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 55 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 10 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
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@ -875,7 +875,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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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></span>
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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 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 <span style="background-color: #EEEEEE;">as.sir()</span>: 3 results in index '20' truncated (38%) that were invalid</span>
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