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2025-04-07 16:49:19 +00:00
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reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9233</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9234</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -68,7 +68,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antimicrobials <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, digits <span class="op">=</span> <span class="fl">1</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fl">1</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>, <span class="fl">14</span><span class="op">)</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> sep <span class="op">=</span> <span class="st">" + "</span>, simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>,</span>
@ -590,9 +590,9 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 76.5% (60.8-88%) 95.3% (86.4-99.2%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 60.3% (42.1-80.7%) 90.6% (76.4-98.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 66.8% (38.4-91.3%) 89.7% (69.9-99.5%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 73.8% (53.8-89.1%) 93% (80.7-99.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 57.6% (31.5-85.2%) 85.5% (64-98.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 58.2% (18.1-94.1%) 77.6% (41.8-99.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
@ -617,9 +617,9 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Syndromic Group |Piperacillin/tazobactam |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |:---------------|:-----------------------|</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical |76% (60-88.6%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU |59.8% (40.7-79.7%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient |66.2% (37.9-91.3%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical |73% (53.9-89.6%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU |56.9% (30.3-84.6%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient |57.3% (19-94.4%) |</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>