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@@ -33,7 +33,7 @@
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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="">3.0.0.9004</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</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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@@ -99,10 +99,10 @@
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</blockquote>
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<div style="display: flex; font-size: 0.8em;">
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<p style="text-align:left; width: 50%;">
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<small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small>
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<small><a href="https://amr-for-r.org/">amr-for-r.org</a></small>
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</p>
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<p style="text-align:right; width: 50%;">
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<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">https://doi.org/10.18637/jss.v104.i03</a></small>
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<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">doi.org/10.18637/jss.v104.i03</a></small>
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</p>
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</div>
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<p><a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120"></a></p>
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@@ -407,9 +407,9 @@
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<span><span class="co">#> # A tibble: 3 × 5</span></span>
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<span><span class="co">#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
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<span><span class="co">#> <chr> <dbl> <chr> <dbl> <chr> </span></span>
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<span><span class="co">#> 1 Clinical 0.2289362 0.205-0.254 0.3147503 0.284-0.347 </span></span>
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<span><span class="co">#> 2 ICU 0.2902655 0.253-0.33 0.4004739 0.353-0.449 </span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.131-0.285 0.3676471 0.254-0.493</span></span></code></pre></div>
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<span><span class="co">#> 1 Clinical 0.229 0.205-0.254 0.315 0.284-0.347 </span></span>
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<span><span class="co">#> 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449 </span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493</span></span></code></pre></div>
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<p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
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<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
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@@ -432,29 +432,29 @@
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<span><span class="co">#> "Outpatient" (minimum = 30).</span></span>
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<span><span class="va">out</span></span>
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<span><span class="co">#> # A tibble: 3 × 6</span></span>
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<span><span class="co">#> ward GEN TOB AMK KAN COL</span></span>
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<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
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<span><span class="co">#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
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<span><span class="co">#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
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<span><span class="co">#> ward GEN TOB AMK KAN COL</span></span>
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<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
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<span><span class="co">#> 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
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<span><span class="co">#> 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
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<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span>
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<span><span class="co">#> # A tibble: 3 × 6</span></span>
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<span><span class="co">#> ward gentamicin tobramycin amikacin kanamycin colistin</span></span>
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<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
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<span><span class="co">#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
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<span><span class="co">#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
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<span><span class="co">#> ward gentamicin tobramycin amikacin kanamycin colistin</span></span>
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<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
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<span><span class="co">#> 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
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<span><span class="co">#> 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
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<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
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<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span>
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<span><span class="co">#> # A tibble: 3 × 6</span></span>
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<span><span class="co">#> ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01</span></span>
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<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
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<span><span class="co">#> 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
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<span><span class="co">#> 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
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<span><span class="co">#> ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01</span></span>
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<span><span class="co">#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl></span></span>
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<span><span class="co">#> 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
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<span><span class="co">#> 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
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<span><span class="co">#> 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
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</div>
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</div>
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<div class="section level2">
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