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guess_ab_col, benchmarks

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dr. M.S. (Matthijs) Berends
2019-01-11 20:37:23 +01:00
parent 193a2d2863
commit 641d866db2
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docs/reference/key_antibiotics.html
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@ -151,6 +151,13 @@
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
@ -220,17 +227,20 @@
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"amox"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"amcl"</span>),
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfur"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"pita"</span>), <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cipr"</span>),
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"trsu"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"vanc"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"teic"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"tetr"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"eryt"</span>), <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"oxac"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"rifa"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"gent"</span>), <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"tobr"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"coli"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfot"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>,
<span class='st'>"cfta"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab.html'>guess_ab</a></span>(<span class='no'>tbl</span>, <span class='st'>"mero"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
<span class='st'>"amox"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"amcl"</span>),
<span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfur"</span>),
<span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"pita"</span>),
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cipr"</span>),
<span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"trsu"</span>),
<span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"vanc"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
<span class='st'>"teic"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"tetr"</span>),
<span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"eryt"</span>), <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
<span class='st'>"oxac"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"rifa"</span>),
<span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"gent"</span>), <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
<span class='st'>"tobr"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"coli"</span>),
<span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfot"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>,
<span class='st'>"cfta"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"mero"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
@ -248,15 +258,15 @@
</tr>
<tr>
<th>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th>
<td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive</p></td>
<td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
</tr>
<tr>
<th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
<td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive</p></td>
<td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
</tr>
<tr>
<th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
<td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive</p></td>
<td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
</tr>
<tr>
<th>warnings</th>
@ -290,7 +300,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it wouldn't.</p>
<p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it would not.</p>
<p>At default, the antibiotics that are used for <strong>Gram positive bacteria</strong> are (colum names): <br />
<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"vanc"</code>, <code>"teic"</code>, <code>"tetr"</code>, <code>"eryt"</code>, <code>"oxac"</code>, <code>"rifa"</code>.</p>
<p>At default, the antibiotics that are used for <strong>Gram negative bacteria</strong> are (colum names): <br />