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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="">2.1.1.9273</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9274</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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@ -310,7 +310,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<p>The function <code>is.sir()</code> detects if the input contains class <code>sir</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> or <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, it iterates over all columns/items and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
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<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code> . <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
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<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or NI and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
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<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% potentially invalid antimicrobial interpretations, and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
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</div>
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<p><code>NA_sir_</code> is a missing value of the new <code>sir</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
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@ -414,10 +414,10 @@ 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: 4 × 18</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> 2025-05-05 <span style="color: #949494;">09:50:38</span> 1 MIC amoxicillin Escherich… human 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-05-05 <span style="color: #949494;">09:50:39</span> 1 MIC cipro Escherich… human 0.256 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-05-05 <span style="color: #949494;">09:50:39</span> 1 DISK tobra Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-05-05 <span style="color: #949494;">09:50:39</span> 1 DISK genta Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 MIC amoxicillin Escherich… human 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 MIC cipro Escherich… human 0.256 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-05-12 <span style="color: #949494;">10:40:00</span> 1 DISK tobra Escherich… human 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-05-12 <span style="color: #949494;">10:40:01</span> 1 DISK genta Escherich… human 18 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 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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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
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@ -616,7 +616,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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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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<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 SDD I R NI <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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<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-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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<span class="r-in"><span><span class="fu">is.sir</span><span class="op">(</span><span class="va">sir_data</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
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