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404.html
@@ -31,7 +31,7 @@
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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
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||||||
|
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9053</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
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||||||
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||||||
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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">
|
<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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@@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<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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||||||
@@ -230,9 +230,10 @@ _pkgdown.yml # pkgdown website configuration</code></pre>
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|||||||
<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
|
<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
|
||||||
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
|
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
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||||||
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
|
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
|
||||||
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..<span class="va">${defaultbranch})</span></span>
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<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="fu">git</span> fetch origin <span class="va">${defaultbranch}</span> <span class="at">--quiet</span></span>
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||||||
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
|
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..origin/<span class="va">${defaultbranch})</span></span>
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||||||
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
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<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
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||||||
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<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
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<p>The <code>+ 1</code> accounts for the fact that this PR’s squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p>
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<p>The <code>+ 1</code> accounts for the fact that this PR’s squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p>
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<ol style="list-style-type: decimal"><li><p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</p></li>
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<ol style="list-style-type: decimal"><li><p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</p></li>
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<li>
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<li>
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@@ -191,7 +191,8 @@ string to use:
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currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
|
currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
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||||||
currenttagfull=$(git describe --tags --abbrev=0)
|
currenttagfull=$(git describe --tags --abbrev=0)
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||||||
defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
|
defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
|
||||||
currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
|
git fetch origin ${defaultbranch} --quiet
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||||||
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currentcommit=$(git rev-list --count ${currenttagfull}..origin/${defaultbranch})
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||||||
currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
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currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
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||||||
echo "$currentversion"
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echo "$currentversion"
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```
|
```
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@@ -7,7 +7,7 @@
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|||||||
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||||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
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||||||
|
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||||||
|
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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">
|
<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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||||||
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@@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
|
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
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||||||
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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">
|
<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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@@ -1177,77 +1177,447 @@ function on a grouped <code>tibble</code>, i.e., using
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<span> <span class="va">gender</span></span>
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<span> <span class="va">gender</span></span>
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<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
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<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
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||||||
<span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span>antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
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<span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span>antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
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<table class="table">
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<table style="width:100%;" class="table">
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<colgroup>
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<colgroup>
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<col width="8%">
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<col width="1%">
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<col width="6%">
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<col width="0%">
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<col width="20%">
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<col width="2%">
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<col width="32%">
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<col width="2%">
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<col width="32%">
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<col width="3%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="2%">
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<col width="3%">
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<col width="2%">
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</colgroup>
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</colgroup>
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<thead><tr class="header">
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<thead><tr class="header">
|
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<th align="left">age_group</th>
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<th align="left">age_group</th>
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<th align="left">gender</th>
|
<th align="left">gender</th>
|
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|
<th align="left">Amikacin</th>
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|
<th align="left">Amoxicillin</th>
|
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|
<th align="left">Amoxicillin/clavulanic acid</th>
|
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<th align="left">Ampicillin</th>
|
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|
<th align="left">Azithromycin</th>
|
||||||
|
<th align="left">Benzylpenicillin</th>
|
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|
<th align="left">Cefazolin</th>
|
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|
<th align="left">Cefepime</th>
|
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|
<th align="left">Cefotaxime</th>
|
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|
<th align="left">Cefoxitin</th>
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|
<th align="left">Ceftazidime</th>
|
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|
<th align="left">Ceftriaxone</th>
|
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|
<th align="left">Cefuroxime</th>
|
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|
<th align="left">Chloramphenicol</th>
|
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|
<th align="left">Ciprofloxacin</th>
|
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|
<th align="left">Clindamycin</th>
|
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|
<th align="left">Colistin</th>
|
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|
<th align="left">Doxycycline</th>
|
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<th align="left">Erythromycin</th>
|
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<th align="left">Flucloxacillin</th>
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<th align="left">Fosfomycin</th>
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<th align="left">Gentamicin</th>
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<th align="left">Imipenem</th>
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<th align="left">Kanamycin</th>
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<th align="left">Linezolid</th>
|
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<th align="left">Meropenem</th>
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<th align="left">Metronidazole</th>
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<th align="left">Moxifloxacin</th>
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<th align="left">Mupirocin</th>
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<th align="left">Nitrofurantoin</th>
|
||||||
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<th align="left">Oxacillin</th>
|
||||||
<th align="left">Piperacillin/tazobactam</th>
|
<th align="left">Piperacillin/tazobactam</th>
|
||||||
<th align="left">Piperacillin/tazobactam + Gentamicin</th>
|
<th align="left">Rifampicin</th>
|
||||||
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
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<th align="left">Teicoplanin</th>
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||||||
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<th align="left">Tetracycline</th>
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||||||
|
<th align="left">Tigecycline</th>
|
||||||
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<th align="left">Tobramycin</th>
|
||||||
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<th align="left">Trimethoprim</th>
|
||||||
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<th align="left">Trimethoprim/sulfamethoxazole</th>
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<th align="left">Vancomycin</th>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">0-24</td>
|
<td align="left">0-24</td>
|
||||||
<td align="left">F</td>
|
<td align="left">F</td>
|
||||||
<td align="left">56.6% (25.2-83.9%)</td>
|
<td align="left">45.4% (15.4-79%)</td>
|
||||||
<td align="left">73.6% (48-91.6%)</td>
|
<td align="left">50.1% (20.5-77.6%)</td>
|
||||||
<td align="left">68.6% (42.9-89.5%)</td>
|
<td align="left">69% (44.5-88.5%)</td>
|
||||||
|
<td align="left">50.4% (20.6-77.3%)</td>
|
||||||
|
<td align="left">41.9% (18.1-65.6%)</td>
|
||||||
|
<td align="left">36.1% (12.3-64.3%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">63.9% (34.6-87.6%)</td>
|
||||||
|
<td align="left">56.7% (25.9-85.8%)</td>
|
||||||
|
<td align="left">51.5% (25.6-74.4%)</td>
|
||||||
|
<td align="left">63.4% (32-88.1%)</td>
|
||||||
|
<td align="left">70.4% (45.4-89.1%)</td>
|
||||||
|
<td align="left">54% (22.3-85.3%)</td>
|
||||||
|
<td align="left">69.8% (45.9-88.9%)</td>
|
||||||
|
<td align="left">39.3% (17.7-64.6%)</td>
|
||||||
|
<td align="left">45.3% (18.1-75.9%)</td>
|
||||||
|
<td align="left">50.1% (21.5-80.5%)</td>
|
||||||
|
<td align="left">41.7% (19.1-67.6%)</td>
|
||||||
|
<td align="left">55.8% (23.7-83.3%)</td>
|
||||||
|
<td align="left">63.5% (32.6-89.4%)</td>
|
||||||
|
<td align="left">69.3% (44.6-88.3%)</td>
|
||||||
|
<td align="left">63.6% (36.1-88.2%)</td>
|
||||||
|
<td align="left">45.5% (15.7-77.7%)</td>
|
||||||
|
<td align="left">43.3% (17.8-71.2%)</td>
|
||||||
|
<td align="left">55.9% (24.3-82.2%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">56.5% (24.3-85%)</td>
|
||||||
|
<td align="left">56.8% (30.9-82.3%)</td>
|
||||||
|
<td align="left">50.5% (19.4-80.8%)</td>
|
||||||
|
<td align="left">56.9% (26.7-85%)</td>
|
||||||
|
<td align="left">42.3% (18.3-68.8%)</td>
|
||||||
|
<td align="left">40.2% (17.6-67.7%)</td>
|
||||||
|
<td align="left">49.8% (20-79.3%)</td>
|
||||||
|
<td align="left">56.1% (22-85.4%)</td>
|
||||||
|
<td align="left">64.5% (39.6-85.5%)</td>
|
||||||
|
<td align="left">69.7% (42.3-90.4%)</td>
|
||||||
|
<td align="left">75.4% (52.1-91.7%)</td>
|
||||||
|
<td align="left">48.5% (24.3-72.6%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">0-24</td>
|
<td align="left">0-24</td>
|
||||||
<td align="left">M</td>
|
<td align="left">M</td>
|
||||||
<td align="left">60.3% (28.4-87.1%)</td>
|
<td align="left">41.9% (15.2-72.5%)</td>
|
||||||
<td align="left">79.7% (57.6-94.2%)</td>
|
<td align="left">49.4% (23.3-75.5%)</td>
|
||||||
<td align="left">60.1% (29.5-87.7%)</td>
|
<td align="left">73.8% (51.8-90.1%)</td>
|
||||||
|
<td align="left">49.3% (22.7-76%)</td>
|
||||||
|
<td align="left">63.4% (40.7-83.5%)</td>
|
||||||
|
<td align="left">41.8% (20.4-64.8%)</td>
|
||||||
|
<td align="left">56.8% (25.2-83.5%)</td>
|
||||||
|
<td align="left">58.2% (29.1-85.8%)</td>
|
||||||
|
<td align="left">59.7% (29.1-87.4%)</td>
|
||||||
|
<td align="left">59.3% (29.1-86.6%)</td>
|
||||||
|
<td align="left">24.9% (8.9-47.3%)</td>
|
||||||
|
<td align="left">58.5% (28-86.5%)</td>
|
||||||
|
<td align="left">72.1% (47.9-90.5%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">77.2% (53-93.2%)</td>
|
||||||
|
<td align="left">61.6% (36.2-83.6%)</td>
|
||||||
|
<td align="left">25.5% (8.7-46.1%)</td>
|
||||||
|
<td align="left">69.4% (44.6-89.4%)</td>
|
||||||
|
<td align="left">63.4% (41.8-82.7%)</td>
|
||||||
|
<td align="left">64% (37.6-85.6%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">63.5% (40.9-83.1%)</td>
|
||||||
|
<td align="left">58.7% (27.6-86.5%)</td>
|
||||||
|
<td align="left">41.8% (13.6-71.2%)</td>
|
||||||
|
<td align="left">48.3% (17.9-78%)</td>
|
||||||
|
<td align="left">59.2% (27.4-86.4%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">53% (21.3-83.7%)</td>
|
||||||
|
<td align="left">57.2% (24.6-84.6%)</td>
|
||||||
|
<td align="left">59.9% (29.7-85.6%)</td>
|
||||||
|
<td align="left">48.2% (16.1-80.4%)</td>
|
||||||
|
<td align="left">48.4% (17.4-79.8%)</td>
|
||||||
|
<td align="left">68% (43.5-87.3%)</td>
|
||||||
|
<td align="left">65.7% (36-89.2%)</td>
|
||||||
|
<td align="left">44.3% (17.2-73.4%)</td>
|
||||||
|
<td align="left">69.4% (46.9-87.8%)</td>
|
||||||
|
<td align="left">74% (50.8-90.9%)</td>
|
||||||
|
<td align="left">75.3% (52.4-92.2%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">25-49</td>
|
<td align="left">25-49</td>
|
||||||
<td align="left">F</td>
|
<td align="left">F</td>
|
||||||
<td align="left">66.6% (45.6-85.5%)</td>
|
<td align="left">46.8% (26.7-65.6%)</td>
|
||||||
<td align="left">91.7% (84.6-96.7%)</td>
|
<td align="left">39% (26.3-52.9%)</td>
|
||||||
<td align="left">83% (67.9-94%)</td>
|
<td align="left">73.8% (63.5-82.6%)</td>
|
||||||
|
<td align="left">39.3% (27.2-54.4%)</td>
|
||||||
|
<td align="left">54.8% (44.9-64.8%)</td>
|
||||||
|
<td align="left">36.5% (26.3-47.1%)</td>
|
||||||
|
<td align="left">66.4% (46.1-85%)</td>
|
||||||
|
<td align="left">69.2% (49.1-86.2%)</td>
|
||||||
|
<td align="left">70.2% (50.5-86.2%)</td>
|
||||||
|
<td align="left">68.1% (48.6-85.4%)</td>
|
||||||
|
<td align="left">27.9% (19.2-37.9%)</td>
|
||||||
|
<td align="left">70.1% (50.5-87.1%)</td>
|
||||||
|
<td align="left">71.4% (61.7-80.4%)</td>
|
||||||
|
<td align="left">58.2% (35.3-79.9%)</td>
|
||||||
|
<td align="left">85.5% (74.1-94.2%)</td>
|
||||||
|
<td align="left">67.1% (55.8-77.4%)</td>
|
||||||
|
<td align="left">25.8% (17-36%)</td>
|
||||||
|
<td align="left">75.5% (61.2-88.2%)</td>
|
||||||
|
<td align="left">54.9% (44.8-65.6%)</td>
|
||||||
|
<td align="left">55.2% (37.8-72.5%)</td>
|
||||||
|
<td align="left">60.9% (38.3-81.8%)</td>
|
||||||
|
<td align="left">75.2% (65.7-83.5%)</td>
|
||||||
|
<td align="left">69.9% (50.1-86.6%)</td>
|
||||||
|
<td align="left">37.5% (17.7-57.9%)</td>
|
||||||
|
<td align="left">50.7% (30.8-68.7%)</td>
|
||||||
|
<td align="left">69.4% (48.6-86.7%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">56.9% (36.2-77.7%)</td>
|
||||||
|
<td align="left">53.3% (30.9-75.6%)</td>
|
||||||
|
<td align="left">60.1% (38.1-81.8%)</td>
|
||||||
|
<td align="left">64.3% (43.2-83.6%)</td>
|
||||||
|
<td align="left">66% (45.7-85.2%)</td>
|
||||||
|
<td align="left">50.1% (30-69.6%)</td>
|
||||||
|
<td align="left">38.8% (19.6-58.9%)</td>
|
||||||
|
<td align="left">75.8% (61.6-88.1%)</td>
|
||||||
|
<td align="left">73.3% (56.6-89.5%)</td>
|
||||||
|
<td align="left">62.7% (47.6-77.1%)</td>
|
||||||
|
<td align="left">70.4% (58.7-80.2%)</td>
|
||||||
|
<td align="left">90% (82.9-95.4%)</td>
|
||||||
|
<td align="left">71.6% (61.7-80.4%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">25-49</td>
|
<td align="left">25-49</td>
|
||||||
<td align="left">M</td>
|
<td align="left">M</td>
|
||||||
<td align="left">56.4% (29.1-81.7%)</td>
|
<td align="left">49.8% (24.2-75.8%)</td>
|
||||||
<td align="left">89.2% (80.3-95.7%)</td>
|
<td align="left">16.5% (8.1-27.4%)</td>
|
||||||
<td align="left">72.4% (49.7-90%)</td>
|
<td align="left">72.4% (60.5-83.5%)</td>
|
||||||
|
<td align="left">16.6% (7.7-28.2%)</td>
|
||||||
|
<td align="left">55.9% (43.6-67.9%)</td>
|
||||||
|
<td align="left">24.9% (14.7-37.6%)</td>
|
||||||
|
<td align="left">60.3% (33.2-82.4%)</td>
|
||||||
|
<td align="left">55.3% (27.6-81.8%)</td>
|
||||||
|
<td align="left">55.9% (29.7-81.1%)</td>
|
||||||
|
<td align="left">56.2% (27.7-82.1%)</td>
|
||||||
|
<td align="left">22.2% (12.7-33.9%)</td>
|
||||||
|
<td align="left">55.6% (29.1-81.8%)</td>
|
||||||
|
<td align="left">73.7% (62.6-83.8%)</td>
|
||||||
|
<td align="left">52.9% (25.2-79.6%)</td>
|
||||||
|
<td align="left">67.1% (53-79.8%)</td>
|
||||||
|
<td align="left">57.8% (43.5-71.8%)</td>
|
||||||
|
<td align="left">22.3% (12.6-33.6%)</td>
|
||||||
|
<td align="left">73% (57.8-85.5%)</td>
|
||||||
|
<td align="left">55.8% (43-68.2%)</td>
|
||||||
|
<td align="left">66.5% (51.6-79.4%)</td>
|
||||||
|
<td align="left">63.1% (40.3-84.5%)</td>
|
||||||
|
<td align="left">83.9% (74.5-91.7%)</td>
|
||||||
|
<td align="left">56.4% (28.4-84%)</td>
|
||||||
|
<td align="left">45.4% (18.9-73.8%)</td>
|
||||||
|
<td align="left">59.4% (37.6-77.9%)</td>
|
||||||
|
<td align="left">56.3% (28.8-81.1%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">52.8% (24.7-78.7%)</td>
|
||||||
|
<td align="left">64.2% (40.2-84.5%)</td>
|
||||||
|
<td align="left">62.9% (37.7-85.1%)</td>
|
||||||
|
<td align="left">60.5% (37.1-80.7%)</td>
|
||||||
|
<td align="left">55.8% (29.4-82.9%)</td>
|
||||||
|
<td align="left">65.4% (48.7-80.8%)</td>
|
||||||
|
<td align="left">54.5% (31.7-73.7%)</td>
|
||||||
|
<td align="left">72.8% (58.7-84.8%)</td>
|
||||||
|
<td align="left">84.8% (72.4-93.6%)</td>
|
||||||
|
<td align="left">66.7% (44.5-84.1%)</td>
|
||||||
|
<td align="left">71.4% (58.9-82.6%)</td>
|
||||||
|
<td align="left">86.6% (77.9-93.7%)</td>
|
||||||
|
<td align="left">77.1% (65.5-87.1%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">50-74</td>
|
<td align="left">50-74</td>
|
||||||
<td align="left">F</td>
|
<td align="left">F</td>
|
||||||
<td align="left">67.8% (55.8-80.1%)</td>
|
<td align="left">44.8% (35.8-54.1%)</td>
|
||||||
<td align="left">95.6% (93.2-97.5%)</td>
|
<td align="left">30.1% (24.9-35.3%)</td>
|
||||||
<td align="left">88.1% (80.4-94.6%)</td>
|
<td align="left">74.1% (69.2-78.7%)</td>
|
||||||
|
<td align="left">30% (24.6-35.4%)</td>
|
||||||
|
<td align="left">41.9% (36.5-47.3%)</td>
|
||||||
|
<td align="left">23.5% (18.6-29%)</td>
|
||||||
|
<td align="left">73.1% (62-82.9%)</td>
|
||||||
|
<td align="left">76.6% (66.1-86%)</td>
|
||||||
|
<td align="left">74.8% (64.9-84.5%)</td>
|
||||||
|
<td align="left">74.6% (64.2-83.3%)</td>
|
||||||
|
<td align="left">37.5% (32.3-43.4%)</td>
|
||||||
|
<td align="left">74.8% (64.4-83.8%)</td>
|
||||||
|
<td align="left">74.5% (69.7-78.9%)</td>
|
||||||
|
<td align="left">61.2% (40.3-82.4%)</td>
|
||||||
|
<td align="left">79.4% (73-85%)</td>
|
||||||
|
<td align="left">44.9% (38.7-51%)</td>
|
||||||
|
<td align="left">37.8% (32.7-43.3%)</td>
|
||||||
|
<td align="left">63.8% (47.6-80.1%)</td>
|
||||||
|
<td align="left">41.7% (36.6-46.9%)</td>
|
||||||
|
<td align="left">58.1% (40-75.1%)</td>
|
||||||
|
<td align="left">65.2% (53.5-76.6%)</td>
|
||||||
|
<td align="left">78.7% (73.8-83.2%)</td>
|
||||||
|
<td align="left">80.6% (70.3-90%)</td>
|
||||||
|
<td align="left">28.1% (10.1-46.6%)</td>
|
||||||
|
<td align="left">53.2% (42.9-62.4%)</td>
|
||||||
|
<td align="left">79.3% (68.7-88.6%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">49.5% (37.5-61.8%)</td>
|
||||||
|
<td align="left">67.8% (48.5-86%)</td>
|
||||||
|
<td align="left">75.1% (63.3-86.3%)</td>
|
||||||
|
<td align="left">56.6% (37.8-74.2%)</td>
|
||||||
|
<td align="left">67.7% (56.4-79.6%)</td>
|
||||||
|
<td align="left">50.6% (40.9-59.1%)</td>
|
||||||
|
<td align="left">41.3% (31.5-50.4%)</td>
|
||||||
|
<td align="left">59% (48.3-74.5%)</td>
|
||||||
|
<td align="left">87.7% (80.4-94.1%)</td>
|
||||||
|
<td align="left">62.2% (55.4-68.4%)</td>
|
||||||
|
<td align="left">55.5% (49.8-61.1%)</td>
|
||||||
|
<td align="left">68% (62.7-73.3%)</td>
|
||||||
|
<td align="left">60.9% (55.8-66.1%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">50-74</td>
|
<td align="left">50-74</td>
|
||||||
<td align="left">M</td>
|
<td align="left">M</td>
|
||||||
<td align="left">66.2% (54.8-75.8%)</td>
|
<td align="left">38.8% (30.6-48.6%)</td>
|
||||||
<td align="left">95.2% (92.4-97.4%)</td>
|
<td align="left">34.6% (29.1-40.3%)</td>
|
||||||
<td align="left">84.4% (74.4-92.5%)</td>
|
<td align="left">75% (70-79.5%)</td>
|
||||||
|
<td align="left">34.7% (29.2-40.5%)</td>
|
||||||
|
<td align="left">43.4% (37.8-48.5%)</td>
|
||||||
|
<td align="left">21% (16.5-26.4%)</td>
|
||||||
|
<td align="left">64.3% (54.1-74.1%)</td>
|
||||||
|
<td align="left">65.9% (56.5-75.4%)</td>
|
||||||
|
<td align="left">67.3% (58.3-77%)</td>
|
||||||
|
<td align="left">65.9% (56.1-75.9%)</td>
|
||||||
|
<td align="left">32.9% (27.6-38%)</td>
|
||||||
|
<td align="left">67.3% (57.4-76.8%)</td>
|
||||||
|
<td align="left">74.1% (69.2-78.8%)</td>
|
||||||
|
<td align="left">63.5% (42.4-83%)</td>
|
||||||
|
<td align="left">76.9% (71.6-81.9%)</td>
|
||||||
|
<td align="left">47.3% (40.9-53.8%)</td>
|
||||||
|
<td align="left">30.8% (26.1-36.1%)</td>
|
||||||
|
<td align="left">68.5% (53.5-81.9%)</td>
|
||||||
|
<td align="left">43.4% (37.7-48.8%)</td>
|
||||||
|
<td align="left">58.1% (42.4-73.2%)</td>
|
||||||
|
<td align="left">68.1% (53.5-82.2%)</td>
|
||||||
|
<td align="left">79.1% (74.4-83.1%)</td>
|
||||||
|
<td align="left">69% (59.7-78.3%)</td>
|
||||||
|
<td align="left">24.8% (9.5-40.5%)</td>
|
||||||
|
<td align="left">49.7% (35-63.2%)</td>
|
||||||
|
<td align="left">68.1% (58.1-77.6%)</td>
|
||||||
|
<td align="left">53.8% (32-75%)</td>
|
||||||
|
<td align="left">51.7% (36.1-67.3%)</td>
|
||||||
|
<td align="left">68.8% (51.1-85.7%)</td>
|
||||||
|
<td align="left">70.2% (54.7-85.3%)</td>
|
||||||
|
<td align="left">53.2% (37.5-68.7%)</td>
|
||||||
|
<td align="left">66.5% (55-76.8%)</td>
|
||||||
|
<td align="left">56.2% (45.8-65.4%)</td>
|
||||||
|
<td align="left">44% (30.3-57.5%)</td>
|
||||||
|
<td align="left">71.9% (58.2-82.2%)</td>
|
||||||
|
<td align="left">86.8% (77.3-93.6%)</td>
|
||||||
|
<td align="left">54.1% (46.9-61.4%)</td>
|
||||||
|
<td align="left">67.1% (61.5-72.5%)</td>
|
||||||
|
<td align="left">81% (76.4-85.2%)</td>
|
||||||
|
<td align="left">66.3% (61-71.2%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="odd">
|
<tr class="odd">
|
||||||
<td align="left">75+</td>
|
<td align="left">75+</td>
|
||||||
<td align="left">F</td>
|
<td align="left">F</td>
|
||||||
<td align="left">71.7% (61-81.7%)</td>
|
<td align="left">51.4% (41.7-62%)</td>
|
||||||
<td align="left">96.6% (94.4-98.2%)</td>
|
<td align="left">30.9% (26.2-36.5%)</td>
|
||||||
<td align="left">90.6% (84.6-95.3%)</td>
|
<td align="left">74.4% (70.3-78.6%)</td>
|
||||||
|
<td align="left">30.9% (25.7-36.1%)</td>
|
||||||
|
<td align="left">36.6% (32-41.6%)</td>
|
||||||
|
<td align="left">20.7% (16.2-25.4%)</td>
|
||||||
|
<td align="left">73.6% (63.6-82.5%)</td>
|
||||||
|
<td align="left">79.1% (70.6-86.8%)</td>
|
||||||
|
<td align="left">78.6% (69.9-86.3%)</td>
|
||||||
|
<td align="left">76% (67.5-83.7%)</td>
|
||||||
|
<td align="left">43.1% (38.6-48%)</td>
|
||||||
|
<td align="left">78.9% (70.5-86.4%)</td>
|
||||||
|
<td align="left">77% (72.6-81.3%)</td>
|
||||||
|
<td align="left">63.2% (43.2-84.1%)</td>
|
||||||
|
<td align="left">77.7% (72.1-83.2%)</td>
|
||||||
|
<td align="left">41.2% (36-46.4%)</td>
|
||||||
|
<td align="left">39.1% (34.2-44.4%)</td>
|
||||||
|
<td align="left">63.7% (46.3-80.6%)</td>
|
||||||
|
<td align="left">36.5% (31.9-41.2%)</td>
|
||||||
|
<td align="left">57.1% (39.8-76%)</td>
|
||||||
|
<td align="left">65.8% (57.2-73.5%)</td>
|
||||||
|
<td align="left">84.6% (80.6-88%)</td>
|
||||||
|
<td align="left">81.9% (73.7-89.5%)</td>
|
||||||
|
<td align="left">33.3% (13.7-53%)</td>
|
||||||
|
<td align="left">49.6% (42.3-56.1%)</td>
|
||||||
|
<td align="left">81.3% (73.2-88.9%)</td>
|
||||||
|
<td align="left">55.9% (33.5-76.5%)</td>
|
||||||
|
<td align="left">41% (31.4-51.8%)</td>
|
||||||
|
<td align="left">63.7% (43.8-82.3%)</td>
|
||||||
|
<td align="left">77.8% (66-87.4%)</td>
|
||||||
|
<td align="left">56.3% (37.3-75.1%)</td>
|
||||||
|
<td align="left">71.8% (62-82.2%)</td>
|
||||||
|
<td align="left">48.3% (41.5-54.9%)</td>
|
||||||
|
<td align="left">43.3% (36.2-50.7%)</td>
|
||||||
|
<td align="left">63% (45.3-80.3%)</td>
|
||||||
|
<td align="left">85.9% (79.9-90.9%)</td>
|
||||||
|
<td align="left">70.4% (64.1-76.8%)</td>
|
||||||
|
<td align="left">60.4% (55.1-65.8%)</td>
|
||||||
|
<td align="left">77.6% (73.4-82.1%)</td>
|
||||||
|
<td align="left">55.3% (50.4-60.1%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
<tr class="even">
|
<tr class="even">
|
||||||
<td align="left">75+</td>
|
<td align="left">75+</td>
|
||||||
<td align="left">M</td>
|
<td align="left">M</td>
|
||||||
<td align="left">72.9% (63.8-82%)</td>
|
<td align="left">52.6% (43.3-62.6%)</td>
|
||||||
<td align="left">96.6% (94.6-98.1%)</td>
|
<td align="left">33% (28.1-38%)</td>
|
||||||
<td align="left">92.8% (87.8-96.5%)</td>
|
<td align="left">77.4% (73.3-81.5%)</td>
|
||||||
|
<td align="left">33% (28.2-38.2%)</td>
|
||||||
|
<td align="left">36.8% (32.3-41.8%)</td>
|
||||||
|
<td align="left">17.9% (12.6-23.2%)</td>
|
||||||
|
<td align="left">64.4% (55.4-73.3%)</td>
|
||||||
|
<td align="left">71.2% (63.1-79.1%)</td>
|
||||||
|
<td align="left">67.9% (59.5-75.8%)</td>
|
||||||
|
<td align="left">65.3% (56.3-73.6%)</td>
|
||||||
|
<td align="left">42.6% (37.8-47.4%)</td>
|
||||||
|
<td align="left">68.2% (59.7-76.4%)</td>
|
||||||
|
<td align="left">75.1% (70.9-79.2%)</td>
|
||||||
|
<td align="left">64.1% (45.8-81.8%)</td>
|
||||||
|
<td align="left">77.6% (72-82.6%)</td>
|
||||||
|
<td align="left">41% (36-46.4%)</td>
|
||||||
|
<td align="left">39.9% (35.1-44.5%)</td>
|
||||||
|
<td align="left">62.1% (46-78.8%)</td>
|
||||||
|
<td align="left">36.9% (32.4-41.4%)</td>
|
||||||
|
<td align="left">59.7% (43.4-76.6%)</td>
|
||||||
|
<td align="left">64.7% (56.6-73.6%)</td>
|
||||||
|
<td align="left">83% (79.4-86.7%)</td>
|
||||||
|
<td align="left">75.7% (66.6-83%)</td>
|
||||||
|
<td align="left">31.6% (12.1-51.7%)</td>
|
||||||
|
<td align="left">51.8% (44.9-58%)</td>
|
||||||
|
<td align="left">74.2% (65.8-82.7%)</td>
|
||||||
|
<td align="left">NA</td>
|
||||||
|
<td align="left">52.2% (41.5-60.8%)</td>
|
||||||
|
<td align="left">69.3% (50.5-86.4%)</td>
|
||||||
|
<td align="left">72.2% (58.7-83.4%)</td>
|
||||||
|
<td align="left">59.3% (41.6-76.7%)</td>
|
||||||
|
<td align="left">73.1% (64.3-81.4%)</td>
|
||||||
|
<td align="left">49.9% (42.4-56.9%)</td>
|
||||||
|
<td align="left">46.3% (38.2-53.1%)</td>
|
||||||
|
<td align="left">59.7% (44.2-75.7%)</td>
|
||||||
|
<td align="left">86.8% (81.4-91.3%)</td>
|
||||||
|
<td align="left">72% (66.3-77.6%)</td>
|
||||||
|
<td align="left">55.8% (50.3-61.1%)</td>
|
||||||
|
<td align="left">73.3% (68.9-77.6%)</td>
|
||||||
|
<td align="left">57% (52.2-61.6%)</td>
|
||||||
</tr>
|
</tr>
|
||||||
</tbody>
|
</tbody>
|
||||||
</table>
|
</table>
|
||||||
|
|||||||
@@ -805,16 +805,16 @@ example_isolates %>%
|
|||||||
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
|
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
|
||||||
```
|
```
|
||||||
|
|
||||||
| age_group | gender | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|
| age_group | gender | Amikacin | Amoxicillin | Amoxicillin/clavulanic acid | Ampicillin | Azithromycin | Benzylpenicillin | Cefazolin | Cefepime | Cefotaxime | Cefoxitin | Ceftazidime | Ceftriaxone | Cefuroxime | Chloramphenicol | Ciprofloxacin | Clindamycin | Colistin | Doxycycline | Erythromycin | Flucloxacillin | Fosfomycin | Gentamicin | Imipenem | Kanamycin | Linezolid | Meropenem | Metronidazole | Moxifloxacin | Mupirocin | Nitrofurantoin | Oxacillin | Piperacillin/tazobactam | Rifampicin | Teicoplanin | Tetracycline | Tigecycline | Tobramycin | Trimethoprim | Trimethoprim/sulfamethoxazole | Vancomycin |
|
||||||
|:---|:---|:---|:---|:---|
|
|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|:---|
|
||||||
| 0-24 | F | 56.6% (25.2-83.9%) | 73.6% (48-91.6%) | 68.6% (42.9-89.5%) |
|
| 0-24 | F | 45.4% (15.4-79%) | 50.1% (20.5-77.6%) | 69% (44.5-88.5%) | 50.4% (20.6-77.3%) | 41.9% (18.1-65.6%) | 36.1% (12.3-64.3%) | NA | NA | 63.9% (34.6-87.6%) | 56.7% (25.9-85.8%) | 51.5% (25.6-74.4%) | 63.4% (32-88.1%) | 70.4% (45.4-89.1%) | 54% (22.3-85.3%) | 69.8% (45.9-88.9%) | 39.3% (17.7-64.6%) | 45.3% (18.1-75.9%) | 50.1% (21.5-80.5%) | 41.7% (19.1-67.6%) | 55.8% (23.7-83.3%) | 63.5% (32.6-89.4%) | 69.3% (44.6-88.3%) | 63.6% (36.1-88.2%) | 45.5% (15.7-77.7%) | 43.3% (17.8-71.2%) | 55.9% (24.3-82.2%) | NA | NA | 56.5% (24.3-85%) | 56.8% (30.9-82.3%) | 50.5% (19.4-80.8%) | 56.9% (26.7-85%) | 42.3% (18.3-68.8%) | 40.2% (17.6-67.7%) | 49.8% (20-79.3%) | 56.1% (22-85.4%) | 64.5% (39.6-85.5%) | 69.7% (42.3-90.4%) | 75.4% (52.1-91.7%) | 48.5% (24.3-72.6%) |
|
||||||
| 0-24 | M | 60.3% (28.4-87.1%) | 79.7% (57.6-94.2%) | 60.1% (29.5-87.7%) |
|
| 0-24 | M | 41.9% (15.2-72.5%) | 49.4% (23.3-75.5%) | 73.8% (51.8-90.1%) | 49.3% (22.7-76%) | 63.4% (40.7-83.5%) | 41.8% (20.4-64.8%) | 56.8% (25.2-83.5%) | 58.2% (29.1-85.8%) | 59.7% (29.1-87.4%) | 59.3% (29.1-86.6%) | 24.9% (8.9-47.3%) | 58.5% (28-86.5%) | 72.1% (47.9-90.5%) | NA | 77.2% (53-93.2%) | 61.6% (36.2-83.6%) | 25.5% (8.7-46.1%) | 69.4% (44.6-89.4%) | 63.4% (41.8-82.7%) | 64% (37.6-85.6%) | NA | 63.5% (40.9-83.1%) | 58.7% (27.6-86.5%) | 41.8% (13.6-71.2%) | 48.3% (17.9-78%) | 59.2% (27.4-86.4%) | NA | NA | NA | 53% (21.3-83.7%) | 57.2% (24.6-84.6%) | 59.9% (29.7-85.6%) | 48.2% (16.1-80.4%) | 48.4% (17.4-79.8%) | 68% (43.5-87.3%) | 65.7% (36-89.2%) | 44.3% (17.2-73.4%) | 69.4% (46.9-87.8%) | 74% (50.8-90.9%) | 75.3% (52.4-92.2%) |
|
||||||
| 25-49 | F | 66.6% (45.6-85.5%) | 91.7% (84.6-96.7%) | 83% (67.9-94%) |
|
| 25-49 | F | 46.8% (26.7-65.6%) | 39% (26.3-52.9%) | 73.8% (63.5-82.6%) | 39.3% (27.2-54.4%) | 54.8% (44.9-64.8%) | 36.5% (26.3-47.1%) | 66.4% (46.1-85%) | 69.2% (49.1-86.2%) | 70.2% (50.5-86.2%) | 68.1% (48.6-85.4%) | 27.9% (19.2-37.9%) | 70.1% (50.5-87.1%) | 71.4% (61.7-80.4%) | 58.2% (35.3-79.9%) | 85.5% (74.1-94.2%) | 67.1% (55.8-77.4%) | 25.8% (17-36%) | 75.5% (61.2-88.2%) | 54.9% (44.8-65.6%) | 55.2% (37.8-72.5%) | 60.9% (38.3-81.8%) | 75.2% (65.7-83.5%) | 69.9% (50.1-86.6%) | 37.5% (17.7-57.9%) | 50.7% (30.8-68.7%) | 69.4% (48.6-86.7%) | NA | 56.9% (36.2-77.7%) | 53.3% (30.9-75.6%) | 60.1% (38.1-81.8%) | 64.3% (43.2-83.6%) | 66% (45.7-85.2%) | 50.1% (30-69.6%) | 38.8% (19.6-58.9%) | 75.8% (61.6-88.1%) | 73.3% (56.6-89.5%) | 62.7% (47.6-77.1%) | 70.4% (58.7-80.2%) | 90% (82.9-95.4%) | 71.6% (61.7-80.4%) |
|
||||||
| 25-49 | M | 56.4% (29.1-81.7%) | 89.2% (80.3-95.7%) | 72.4% (49.7-90%) |
|
| 25-49 | M | 49.8% (24.2-75.8%) | 16.5% (8.1-27.4%) | 72.4% (60.5-83.5%) | 16.6% (7.7-28.2%) | 55.9% (43.6-67.9%) | 24.9% (14.7-37.6%) | 60.3% (33.2-82.4%) | 55.3% (27.6-81.8%) | 55.9% (29.7-81.1%) | 56.2% (27.7-82.1%) | 22.2% (12.7-33.9%) | 55.6% (29.1-81.8%) | 73.7% (62.6-83.8%) | 52.9% (25.2-79.6%) | 67.1% (53-79.8%) | 57.8% (43.5-71.8%) | 22.3% (12.6-33.6%) | 73% (57.8-85.5%) | 55.8% (43-68.2%) | 66.5% (51.6-79.4%) | 63.1% (40.3-84.5%) | 83.9% (74.5-91.7%) | 56.4% (28.4-84%) | 45.4% (18.9-73.8%) | 59.4% (37.6-77.9%) | 56.3% (28.8-81.1%) | NA | 52.8% (24.7-78.7%) | 64.2% (40.2-84.5%) | 62.9% (37.7-85.1%) | 60.5% (37.1-80.7%) | 55.8% (29.4-82.9%) | 65.4% (48.7-80.8%) | 54.5% (31.7-73.7%) | 72.8% (58.7-84.8%) | 84.8% (72.4-93.6%) | 66.7% (44.5-84.1%) | 71.4% (58.9-82.6%) | 86.6% (77.9-93.7%) | 77.1% (65.5-87.1%) |
|
||||||
| 50-74 | F | 67.8% (55.8-80.1%) | 95.6% (93.2-97.5%) | 88.1% (80.4-94.6%) |
|
| 50-74 | F | 44.8% (35.8-54.1%) | 30.1% (24.9-35.3%) | 74.1% (69.2-78.7%) | 30% (24.6-35.4%) | 41.9% (36.5-47.3%) | 23.5% (18.6-29%) | 73.1% (62-82.9%) | 76.6% (66.1-86%) | 74.8% (64.9-84.5%) | 74.6% (64.2-83.3%) | 37.5% (32.3-43.4%) | 74.8% (64.4-83.8%) | 74.5% (69.7-78.9%) | 61.2% (40.3-82.4%) | 79.4% (73-85%) | 44.9% (38.7-51%) | 37.8% (32.7-43.3%) | 63.8% (47.6-80.1%) | 41.7% (36.6-46.9%) | 58.1% (40-75.1%) | 65.2% (53.5-76.6%) | 78.7% (73.8-83.2%) | 80.6% (70.3-90%) | 28.1% (10.1-46.6%) | 53.2% (42.9-62.4%) | 79.3% (68.7-88.6%) | NA | 49.5% (37.5-61.8%) | 67.8% (48.5-86%) | 75.1% (63.3-86.3%) | 56.6% (37.8-74.2%) | 67.7% (56.4-79.6%) | 50.6% (40.9-59.1%) | 41.3% (31.5-50.4%) | 59% (48.3-74.5%) | 87.7% (80.4-94.1%) | 62.2% (55.4-68.4%) | 55.5% (49.8-61.1%) | 68% (62.7-73.3%) | 60.9% (55.8-66.1%) |
|
||||||
| 50-74 | M | 66.2% (54.8-75.8%) | 95.2% (92.4-97.4%) | 84.4% (74.4-92.5%) |
|
| 50-74 | M | 38.8% (30.6-48.6%) | 34.6% (29.1-40.3%) | 75% (70-79.5%) | 34.7% (29.2-40.5%) | 43.4% (37.8-48.5%) | 21% (16.5-26.4%) | 64.3% (54.1-74.1%) | 65.9% (56.5-75.4%) | 67.3% (58.3-77%) | 65.9% (56.1-75.9%) | 32.9% (27.6-38%) | 67.3% (57.4-76.8%) | 74.1% (69.2-78.8%) | 63.5% (42.4-83%) | 76.9% (71.6-81.9%) | 47.3% (40.9-53.8%) | 30.8% (26.1-36.1%) | 68.5% (53.5-81.9%) | 43.4% (37.7-48.8%) | 58.1% (42.4-73.2%) | 68.1% (53.5-82.2%) | 79.1% (74.4-83.1%) | 69% (59.7-78.3%) | 24.8% (9.5-40.5%) | 49.7% (35-63.2%) | 68.1% (58.1-77.6%) | 53.8% (32-75%) | 51.7% (36.1-67.3%) | 68.8% (51.1-85.7%) | 70.2% (54.7-85.3%) | 53.2% (37.5-68.7%) | 66.5% (55-76.8%) | 56.2% (45.8-65.4%) | 44% (30.3-57.5%) | 71.9% (58.2-82.2%) | 86.8% (77.3-93.6%) | 54.1% (46.9-61.4%) | 67.1% (61.5-72.5%) | 81% (76.4-85.2%) | 66.3% (61-71.2%) |
|
||||||
| 75+ | F | 71.7% (61-81.7%) | 96.6% (94.4-98.2%) | 90.6% (84.6-95.3%) |
|
| 75+ | F | 51.4% (41.7-62%) | 30.9% (26.2-36.5%) | 74.4% (70.3-78.6%) | 30.9% (25.7-36.1%) | 36.6% (32-41.6%) | 20.7% (16.2-25.4%) | 73.6% (63.6-82.5%) | 79.1% (70.6-86.8%) | 78.6% (69.9-86.3%) | 76% (67.5-83.7%) | 43.1% (38.6-48%) | 78.9% (70.5-86.4%) | 77% (72.6-81.3%) | 63.2% (43.2-84.1%) | 77.7% (72.1-83.2%) | 41.2% (36-46.4%) | 39.1% (34.2-44.4%) | 63.7% (46.3-80.6%) | 36.5% (31.9-41.2%) | 57.1% (39.8-76%) | 65.8% (57.2-73.5%) | 84.6% (80.6-88%) | 81.9% (73.7-89.5%) | 33.3% (13.7-53%) | 49.6% (42.3-56.1%) | 81.3% (73.2-88.9%) | 55.9% (33.5-76.5%) | 41% (31.4-51.8%) | 63.7% (43.8-82.3%) | 77.8% (66-87.4%) | 56.3% (37.3-75.1%) | 71.8% (62-82.2%) | 48.3% (41.5-54.9%) | 43.3% (36.2-50.7%) | 63% (45.3-80.3%) | 85.9% (79.9-90.9%) | 70.4% (64.1-76.8%) | 60.4% (55.1-65.8%) | 77.6% (73.4-82.1%) | 55.3% (50.4-60.1%) |
|
||||||
| 75+ | M | 72.9% (63.8-82%) | 96.6% (94.6-98.1%) | 92.8% (87.8-96.5%) |
|
| 75+ | M | 52.6% (43.3-62.6%) | 33% (28.1-38%) | 77.4% (73.3-81.5%) | 33% (28.2-38.2%) | 36.8% (32.3-41.8%) | 17.9% (12.6-23.2%) | 64.4% (55.4-73.3%) | 71.2% (63.1-79.1%) | 67.9% (59.5-75.8%) | 65.3% (56.3-73.6%) | 42.6% (37.8-47.4%) | 68.2% (59.7-76.4%) | 75.1% (70.9-79.2%) | 64.1% (45.8-81.8%) | 77.6% (72-82.6%) | 41% (36-46.4%) | 39.9% (35.1-44.5%) | 62.1% (46-78.8%) | 36.9% (32.4-41.4%) | 59.7% (43.4-76.6%) | 64.7% (56.6-73.6%) | 83% (79.4-86.7%) | 75.7% (66.6-83%) | 31.6% (12.1-51.7%) | 51.8% (44.9-58%) | 74.2% (65.8-82.7%) | NA | 52.2% (41.5-60.8%) | 69.3% (50.5-86.4%) | 72.2% (58.7-83.4%) | 59.3% (41.6-76.7%) | 73.1% (64.3-81.4%) | 49.9% (42.4-56.9%) | 46.3% (38.2-53.1%) | 59.7% (44.2-75.7%) | 86.8% (81.4-91.3%) | 72% (66.3-77.6%) | 55.8% (50.3-61.1%) | 73.3% (68.9-77.6%) | 57% (52.2-61.6%) |
|
||||||
|
|
||||||
#### Plotting antibiograms
|
#### Plotting antibiograms
|
||||||
|
|
||||||
|
|||||||
@@ -30,7 +30,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
||||||
|
|
||||||
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</div>
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<div class="section level2">
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<div class="section level2">
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||||||
<h2 class="pkg-version" data-toc-text="3.0.1.9053" id="amr-3019053">AMR 3.0.1.9053<a class="anchor" aria-label="anchor" href="#amr-3019053"></a></h2>
|
<h2 class="pkg-version" data-toc-text="3.0.1.9055" id="amr-3019055">AMR 3.0.1.9055<a class="anchor" aria-label="anchor" href="#amr-3019055"></a></h2>
|
||||||
<p>This will become release v3.1.0, intended for launch end of May.</p>
|
<p>This will become release v3.1.0, intended for launch end of May.</p>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="new-3-0-1-9053">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9053"></a></h4>
|
<h4 id="new-3-0-1-9055">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9055"></a></h4>
|
||||||
<ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
|
<ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
|
||||||
<li>Support for the <a href="https://future.futureverse.org" class="external-link"><code>future</code></a> package and its framework, as the previous implementation of parallel computing was slow
|
<li>Support for the <a href="https://future.futureverse.org" class="external-link"><code>future</code></a> package and its framework, as the previous implementation of parallel computing was slow
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<strong>Breaking change</strong>: <code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>parallel = TRUE</code> now requires a non-sequential <code><a href="https://future.futureverse.org/reference/plan.html" class="external-link">future::plan()</a></code> to be active before the call — e.g., <code>future::plan(future::multisession)</code> — and throws an informative error if none is set.</li>
|
<strong>Breaking change</strong>: <code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>parallel = TRUE</code> now requires a non-sequential <code><a href="https://future.futureverse.org/reference/plan.html" class="external-link">future::plan()</a></code> to be active before the call — e.g., <code>future::plan(future::multisession)</code> — and throws an informative error if none is set.</li>
|
||||||
<li>New all-core usage setup: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure and processing time)</li>
|
<li>New all-core usage setup: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure and processing time)</li>
|
||||||
|
<li>
|
||||||
|
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code> gained a <code>parallel</code> argument using the same <code>future</code>/<code>future.apply</code> pattern: for WISCA, Monte Carlo simulations are split into <code>(group, chunk)</code> job pairs distributed across workers; for grouped antibiograms, each group is processed by a separate worker (<a href="https://github.com/msberends/AMR/issues/281" class="external-link">#281</a>)</li>
|
||||||
</ul></li>
|
</ul></li>
|
||||||
<li>Integration with the <em>tidymodels</em> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
|
<li>Integration with the <em>tidymodels</em> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
|
||||||
<ul><li>
|
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|
||||||
@@ -92,7 +94,7 @@
|
|||||||
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
|
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
|
||||||
</ul></div>
|
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|
||||||
<div class="section level4">
|
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|
||||||
<h4 id="fixes-3-0-1-9053">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9053"></a></h4>
|
<h4 id="fixes-3-0-1-9055">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9055"></a></h4>
|
||||||
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
|
<ul><li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
|
||||||
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
|
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
|
||||||
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
|
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
|
||||||
@@ -112,7 +114,7 @@
|
|||||||
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> ignoring <code>info = FALSE</code> for columns with no breakpoints (e.g. cefoxitin against <em>E. coli</em>)</li>
|
<li>Fixed <code><a href="../reference/as.sir.html">as.sir()</a></code> ignoring <code>info = FALSE</code> for columns with no breakpoints (e.g. cefoxitin against <em>E. coli</em>)</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level4">
|
<div class="section level4">
|
||||||
<h4 id="updates-3-0-1-9053">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9053"></a></h4>
|
<h4 id="updates-3-0-1-9055">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9055"></a></h4>
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>reference_data</code>: custom guideline names now correctly classify values as R using EUCAST convention (<code>> breakpoint_R</code> for MIC, <code>< breakpoint_R</code> for disk); custom breakpoints with <code>host = NA</code> now serve as a host-agnostic fallback when no host-specific row matches (<a href="https://github.com/msberends/AMR/issues/239" class="external-link">#239</a>)</li>
|
<code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>reference_data</code>: custom guideline names now correctly classify values as R using EUCAST convention (<code>> breakpoint_R</code> for MIC, <code>< breakpoint_R</code> for disk); custom breakpoints with <code>host = NA</code> now serve as a host-agnostic fallback when no host-specific row matches (<a href="https://github.com/msberends/AMR/issues/239" class="external-link">#239</a>)</li>
|
||||||
<li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
|
<li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
|
||||||
|
|||||||
@@ -1,6 +1,6 @@
|
|||||||
# Changelog
|
# Changelog
|
||||||
|
|
||||||
## AMR 3.0.1.9053
|
## AMR 3.0.1.9055
|
||||||
|
|
||||||
This will become release v3.1.0, intended for launch end of May.
|
This will become release v3.1.0, intended for launch end of May.
|
||||||
|
|
||||||
@@ -28,6 +28,13 @@ This will become release v3.1.0, intended for launch end of May.
|
|||||||
dataset on a 16-core machine would only use 6 cores; now all 16 are
|
dataset on a 16-core machine would only use 6 cores; now all 16 are
|
||||||
used, with each worker processing a smaller row slice (lower
|
used, with each worker processing a smaller row slice (lower
|
||||||
per-worker memory pressure and processing time)
|
per-worker memory pressure and processing time)
|
||||||
|
- [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md)
|
||||||
|
and [`wisca()`](https://amr-for-r.org/reference/antibiogram.md)
|
||||||
|
gained a `parallel` argument using the same `future`/`future.apply`
|
||||||
|
pattern: for WISCA, Monte Carlo simulations are split into
|
||||||
|
`(group, chunk)` job pairs distributed across workers; for grouped
|
||||||
|
antibiograms, each group is processed by a separate worker
|
||||||
|
([\#281](https://github.com/msberends/AMR/issues/281))
|
||||||
- Integration with the *tidymodels* framework to allow seamless use of
|
- Integration with the *tidymodels* framework to allow seamless use of
|
||||||
SIR, MIC and disk data in modelling pipelines via `recipes`
|
SIR, MIC and disk data in modelling pipelines via `recipes`
|
||||||
- [`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md)
|
- [`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md)
|
||||||
|
|||||||
@@ -10,7 +10,7 @@ articles:
|
|||||||
PCA: PCA.html
|
PCA: PCA.html
|
||||||
WHONET: WHONET.html
|
WHONET: WHONET.html
|
||||||
WISCA: WISCA.html
|
WISCA: WISCA.html
|
||||||
last_built: 2026-04-30T08:02Z
|
last_built: 2026-04-30T17:47Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://amr-for-r.org/reference
|
reference: https://amr-for-r.org/reference
|
||||||
article: https://amr-for-r.org/articles
|
article: https://amr-for-r.org/articles
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
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|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
|
||||||
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|
||||||
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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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -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>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -65,7 +65,8 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
|||||||
<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>
|
<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>
|
||||||
<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>
|
<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>
|
||||||
<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>
|
<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>
|
||||||
<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>
|
<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>, parallel <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||||||
|
<span> <span class="va">...</span><span class="op">)</span></span>
|
||||||
<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><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>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</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>
|
||||||
@@ -73,7 +74,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
|||||||
<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> 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>, sort_columns <span class="op">=</span> <span class="cn">TRUE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span>
|
<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>
|
||||||
<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>
|
<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>
|
||||||
<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> 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>, parallel <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
|
||||||
<span></span>
|
<span></span>
|
||||||
<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>
|
<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>
|
||||||
<span></span>
|
<span></span>
|
||||||
@@ -147,7 +148,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
|||||||
|
|
||||||
|
|
||||||
<dt id="arg-formatting-type">formatting_type<a class="anchor" aria-label="anchor" href="#arg-formatting-type"></a></dt>
|
<dt id="arg-formatting-type">formatting_type<a class="anchor" aria-label="anchor" href="#arg-formatting-type"></a></dt>
|
||||||
<dd><p>Numeric value (1–22 for WISCA, 1-12 for non-WISCA) indicating how the 'cells' of the antibiogram table should be formatted. See <em>Details</em> > <em>Formatting Type</em> for a list of options.</p></dd>
|
<dd><p>Numeric value (1-22 for WISCA, 1-12 for non-WISCA) indicating how the 'cells' of the antibiogram table should be formatted. See <em>Details</em> > <em>Formatting Type</em> for a list of options.</p></dd>
|
||||||
|
|
||||||
|
|
||||||
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
|
<dt id="arg-col-mo">col_mo<a class="anchor" aria-label="anchor" href="#arg-col-mo"></a></dt>
|
||||||
@@ -194,6 +195,10 @@ Adhering to previously described approaches (see Source) and especially the Baye
|
|||||||
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
|
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode.</p></dd>
|
||||||
|
|
||||||
|
|
||||||
|
<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
|
||||||
|
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. Requires the <code><a href="https://future.apply.futureverse.org/reference/future_lapply.html" class="external-link">future.apply</a></code> package. For WISCA, Monte Carlo simulations are distributed across workers; for grouped antibiograms, each group is processed by a separate worker. <strong>A non-sequential <code><a href="https://future.futureverse.org/reference/plan.html" class="external-link">future::plan()</a></code> must already be active before setting <code>parallel = TRUE</code></strong> – for example, <code>future::plan(future::multisession)</code>. An error is thrown if <code>parallel = TRUE</code> is used without a plan set by the user.</p></dd>
|
||||||
|
|
||||||
|
|
||||||
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
||||||
<dd><p>When used in <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">R Markdown or Quarto</a>: arguments passed on to <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> (otherwise, has no use).</p></dd>
|
<dd><p>When used in <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">R Markdown or Quarto</a>: arguments passed on to <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> (otherwise, has no use).</p></dd>
|
||||||
|
|
||||||
|
|||||||
@@ -19,7 +19,8 @@ antibiogram(x, antimicrobials = where(is.sir), mo_transform = "shortname",
|
|||||||
ifelse(wisca, 14, 18)), col_mo = NULL, language = get_AMR_locale(),
|
ifelse(wisca, 14, 18)), col_mo = NULL, language = get_AMR_locale(),
|
||||||
minimum = 30, combine_SI = TRUE, sep = " + ", sort_columns = TRUE,
|
minimum = 30, combine_SI = TRUE, sep = " + ", sort_columns = TRUE,
|
||||||
wisca = FALSE, simulations = 1000, conf_interval = 0.95,
|
wisca = FALSE, simulations = 1000, conf_interval = 0.95,
|
||||||
interval_side = "two-tailed", info = interactive(), ...)
|
interval_side = "two-tailed", info = interactive(), parallel = FALSE,
|
||||||
|
...)
|
||||||
|
|
||||||
wisca(x, antimicrobials = where(is.sir), ab_transform = "name",
|
wisca(x, antimicrobials = where(is.sir), ab_transform = "name",
|
||||||
syndromic_group = NULL, only_all_tested = FALSE, digits = 1,
|
syndromic_group = NULL, only_all_tested = FALSE, digits = 1,
|
||||||
@@ -27,7 +28,7 @@ wisca(x, antimicrobials = where(is.sir), ab_transform = "name",
|
|||||||
col_mo = NULL, language = get_AMR_locale(), combine_SI = TRUE,
|
col_mo = NULL, language = get_AMR_locale(), combine_SI = TRUE,
|
||||||
sep = " + ", sort_columns = TRUE, simulations = 1000,
|
sep = " + ", sort_columns = TRUE, simulations = 1000,
|
||||||
conf_interval = 0.95, interval_side = "two-tailed",
|
conf_interval = 0.95, interval_side = "two-tailed",
|
||||||
info = interactive(), ...)
|
info = interactive(), parallel = FALSE, ...)
|
||||||
|
|
||||||
retrieve_wisca_parameters(wisca_model, ...)
|
retrieve_wisca_parameters(wisca_model, ...)
|
||||||
|
|
||||||
@@ -183,7 +184,7 @@ knit_print(x, italicise = TRUE,
|
|||||||
|
|
||||||
- formatting_type:
|
- formatting_type:
|
||||||
|
|
||||||
Numeric value (1–22 for WISCA, 1-12 for non-WISCA) indicating how the
|
Numeric value (1-22 for WISCA, 1-12 for non-WISCA) indicating how the
|
||||||
'cells' of the antibiogram table should be formatted. See *Details* \>
|
'cells' of the antibiogram table should be formatted. See *Details* \>
|
||||||
*Formatting Type* for a list of options.
|
*Formatting Type* for a list of options.
|
||||||
|
|
||||||
@@ -251,6 +252,19 @@ knit_print(x, italicise = TRUE,
|
|||||||
A [logical](https://rdrr.io/r/base/logical.html) to indicate info
|
A [logical](https://rdrr.io/r/base/logical.html) to indicate info
|
||||||
should be printed - the default is `TRUE` only in interactive mode.
|
should be printed - the default is `TRUE` only in interactive mode.
|
||||||
|
|
||||||
|
- parallel:
|
||||||
|
|
||||||
|
A [logical](https://rdrr.io/r/base/logical.html) to indicate if
|
||||||
|
parallel computing must be used, defaults to `FALSE`. Requires the
|
||||||
|
[`future.apply`](https://future.apply.futureverse.org/reference/future_lapply.html)
|
||||||
|
package. For WISCA, Monte Carlo simulations are distributed across
|
||||||
|
workers; for grouped antibiograms, each group is processed by a
|
||||||
|
separate worker. **A non-sequential
|
||||||
|
[`future::plan()`](https://future.futureverse.org/reference/plan.html)
|
||||||
|
must already be active before setting `parallel = TRUE`** – for
|
||||||
|
example, `future::plan(future::multisession)`. An error is thrown if
|
||||||
|
`parallel = TRUE` is used without a plan set by the user.
|
||||||
|
|
||||||
- ...:
|
- ...:
|
||||||
|
|
||||||
When used in [R Markdown or
|
When used in [R Markdown or
|
||||||
|
|||||||
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&gt;%
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@@ -420,10 +420,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||||
<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>
|
<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>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-04-30 <span style="color: #949494;">08:03:38</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2026-04-30 <span style="color: #949494;">17:47:55</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-04-30 <span style="color: #949494;">08:03:38</span> 1 MIC cipro Escherich… human 0.256 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2026-04-30 <span style="color: #949494;">17:47:55</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-04-30 <span style="color: #949494;">08:03:38</span> 1 DISK tobra Escherich… human 16 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2026-04-30 <span style="color: #949494;">17:47:55</span> 1 DISK tobra Escherich… human 16 </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-04-30 <span style="color: #949494;">08:03:39</span> 1 DISK genta Escherich… human 18 </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2026-04-30 <span style="color: #949494;">17:47:55</span> 1 DISK genta Escherich… human 18 </span>
|
||||||
<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>
|
<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>
|
||||||
<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>
|
<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>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||||
|
|||||||
@@ -667,10 +667,10 @@ sir_interpretation_history()
|
|||||||
#> # A tibble: 4 × 18
|
#> # A tibble: 4 × 18
|
||||||
#> datetime index method ab_given mo_given host_given input_given
|
#> datetime index method ab_given mo_given host_given input_given
|
||||||
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
|
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
|
||||||
#> 1 2026-04-30 08:03:38 1 MIC amoxicillin Escherich… human 8
|
#> 1 2026-04-30 17:47:55 1 MIC amoxicillin Escherich… human 8
|
||||||
#> 2 2026-04-30 08:03:38 1 MIC cipro Escherich… human 0.256
|
#> 2 2026-04-30 17:47:55 1 MIC cipro Escherich… human 0.256
|
||||||
#> 3 2026-04-30 08:03:38 1 DISK tobra Escherich… human 16
|
#> 3 2026-04-30 17:47:55 1 DISK tobra Escherich… human 16
|
||||||
#> 4 2026-04-30 08:03:39 1 DISK genta Escherich… human 18
|
#> 4 2026-04-30 17:47:55 1 DISK genta Escherich… human 18
|
||||||
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
|
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
|
||||||
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
|
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
|
||||||
#> # breakpoint_S_R <chr>, site <chr>
|
#> # breakpoint_S_R <chr>, site <chr>
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
|||||||
@@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">3.0.1.9053</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9055</small>
|
||||||
|
|
||||||
|
|
||||||
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<dt>stdres</dt>
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standard deviations are less than or equal to <code>tol</code> times the
|
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standard deviation of the first component.) With the default null
|
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setting, no components are omitted (unless <code>rank.</code> is specified
|
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less than <code>min(dim(x))</code>.). Other settings for <code>tol</code> could be
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|
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component.) With the default null setting, no components are omitted
|
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|
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(unless `rank.` is specified less than `min(dim(x))`.). Other settings
|
(unless `rank.` is specified less than `min(dim(x))`.). Other settings
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|
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Reference in New Issue
Block a user