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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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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="">2.1.1.9267</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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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@ -63,16 +63,17 @@ Adhering to previously described approaches (see Source) and especially the Baye
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<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span>,</span>
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<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>
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<span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</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>,</span>
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<span> minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, wisca <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
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<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>
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<span> minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, sort_columns <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> wisca <span class="op">=</span> <span class="cn">FALSE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>,</span>
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<span> interval_side <span class="op">=</span> <span class="st">"two-tailed"</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>
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<span></span>
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<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>
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<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>
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<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>
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<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>
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<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>
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<span> interval_side <span class="op">=</span> <span class="st">"two-tailed"</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>
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<span> sep <span class="op">=</span> <span class="st">" + "</span>, sort_columns <span class="op">=</span> <span class="cn">TRUE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span>
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<span> conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
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<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>
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<span></span>
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<span><span class="fu">retrieve_wisca_parameters</span><span class="op">(</span><span class="va">wisca_model</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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@ -168,6 +169,10 @@ Adhering to previously described approaches (see Source) and especially the Baye
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<dd><p>A separating character for antimicrobial columns in combination antibiograms.</p></dd>
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<dt id="arg-sort-columns">sort_columns<a class="anchor" aria-label="anchor" href="#arg-sort-columns"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the antimicrobial columns must be sorted on name.</p></dd>
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<dt id="arg-wisca">wisca<a class="anchor" aria-label="anchor" href="#arg-wisca"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is <code>FALSE</code>). This will use a Bayesian decision model to estimate regimen coverage probabilities using <a href="https://en.wikipedia.org/wiki/Monte_Carlo_method" class="external-link">Monte Carlo simulations</a>. Set <code>simulations</code>, <code>conf_interval</code>, and <code>interval_side</code> to adjust.</p></dd>
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@ -572,9 +577,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 3 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
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<span class="r-out co"><span class="r-pr">#></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> Clinical 73.4% (68.3-78.6%) 92.4% (90.7-93.8%) </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 57.4% (49.7-65.4%) 85% (82.1-87.9%) </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 57% (47.4-66.7%) 74.4% (68.6-79.5%) </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 73.4% (68.3-78.6%) 92.3% (90.7-93.7%) </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 57.4% (49.7-65.4%) 84.9% (82.1-87.6%) </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 57% (47.4-66.7%) 74.6% (68.8-79.8%) </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ abbreviated name: ¹`Piperacillin/tazobactam + Gentamicin`</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` <chr></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
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