P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 20:21:58 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9039@9444ed6

Browse Source
This commit is contained in:
github-actions
2022-10-30 20:14:42 +00:00
parent ec6f7db383
commit 05ea686a1e
94 changed files with 561 additions and 557 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
reference/add_custom_antimicrobials.html
View File

@ -10,7 +10,7 @@
<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="">1.8.2.9038</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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">
@ -153,7 +153,7 @@
<span><span class="co"># Add custom antibiotic codes:</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials</a></span><span class="op">(</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"TEST"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span>
<span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span>
<span> group <span class="op">=</span> <span class="st">"Test Group"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre><p></p></div>
@ -166,16 +166,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># returns NA and throws a warning (which is now suppressed):</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/warning.html" class="external-link">suppressWarnings</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FUS</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;NA&gt;</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.ab() and</span></span></span>
<span class="r-in"><span><span class="co"># all ab_*() functions</span></span></span>
<span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"TEST"</span>,</span></span>
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span></span>
<span class="r-in"><span> <span class="co"># you can add any property present in the</span></span></span>
<span class="r-in"><span> <span class="co"># 'antibiotics' data set, such as 'group':</span></span></span>
@ -184,18 +184,18 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added one record to the internal `antibiotics` data set.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># "test" is now a new antibiotic:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TEST</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TESTAB</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Test Antibiotic"</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_group</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_group</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Test Group"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_info</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_info</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $ab</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "TEST"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "TESTAB"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $cid</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
@ -259,13 +259,13 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># even antibiotic selectors work</span></span></span>
<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> random_column <span class="op">=</span> <span class="st">"test"</span>,</span></span>
<span class="r-in"><span> random_column <span class="op">=</span> <span class="st">"some value"</span>,</span></span>
<span class="r-in"><span> coflu <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ampicillin <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> random_column coflu ampicillin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 test S R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 some value S R</span>
<span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `betalactams()` using columns 'coflu' (co-fluampicil) and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'ampicillin'</span>