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88 changed files with 156 additions and 138 deletions
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@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9069</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9070</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">
@@ -58,7 +58,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, enforce_method <span class="op">=</span> <span class="st">"auto"</span><span class="op">)</span></span>
<span></span>
<span><span class="va">NA_sir_</span></span>
<span></span>
@@ -163,7 +163,11 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a>, e.g. <code>as.sir(df, penicillins())</code>.</p>
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a>, e.g. <code>as.sir(df, penicillins())</code>.</p></dd>
<dt id="arg-enforce-method">enforce_method<a class="anchor" aria-label="anchor" href="#arg-enforce-method"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> string to force interpretation as a specific method, useful when the S3 class of <code>x</code> is lost (e.g., when called from Python via rpy2). Must be one of <code>"auto"</code> (default), <code>"mic"</code>, or <code>"disk"</code>.</p>
<p>Otherwise: arguments passed on to methods.</p></dd>
@@ -458,10 +462,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-24 <span style="color: #949494;">18:34:31</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-24 <span style="color: #949494;">18:34:31</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-24 <span style="color: #949494;">18:34:32</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-24 <span style="color: #949494;">18:34:32</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-26 <span style="color: #949494;">07:32:01</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-26 <span style="color: #949494;">07:32:01</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-26 <span style="color: #949494;">07:32:01</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-26 <span style="color: #949494;">07:32:02</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -582,7 +586,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ..., enforce_method = "auto") ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span>
@@ -592,7 +596,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mics = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mics = (function (x, ..., enforce_method = "auto") ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span>
@@ -602,7 +606,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ...) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro = (function (x, ..., enforce_method = "auto") ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Some MICs were converted to the nearest higher log2 level, following the CLSI</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretation guideline.</span>