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(v1.6.0.9021) join functions update

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dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
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12
docs/reference/key_antimicrobials.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9021</span>
</span>
</div>
@ -297,7 +297,7 @@
</tr>
<tr>
<th>only_rsi_columns</th>
<td><p>a logical to indicate whether only columns must be included that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether only columns must be included that were transformed to class <code>&lt;rsi&gt;</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
</tr>
<tr>
<th>...</th>
@ -305,7 +305,7 @@
</tr>
<tr>
<th>y, z</th>
<td><p>character vectors to compare</p></td>
<td><p><a href='https://rdrr.io/r/base/character.html'>character</a> vectors to compare</p></td>
</tr>
<tr>
<th>type</th>
@ -313,7 +313,7 @@
</tr>
<tr>
<th>ignore_I</th>
<td><p>logical to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></td>
<td><p><a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>points_threshold</th>
@ -324,7 +324,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>key_antimicrobials()</code> and <code>all_antimicrobials()</code> functions are context-aware. This means that then the <code>x</code> argument can be left blank, see <em>Examples</em>.</p>
<p>The function <code>key_antimicrobials()</code> returns a character vector with 12 antimicrobial results for every isolate. The function <code>all_antimicrobials()</code> returns a character vector with all antimicrobial results for every isolate. These vectors can then be compared using <code>antimicrobials_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antimicrobials()</code> and ignored by <code>antimicrobials_equal()</code>.</p>
<p>The function <code>key_antimicrobials()</code> returns a <a href='https://rdrr.io/r/base/character.html'>character</a> vector with 12 antimicrobial results for every isolate. The function <code>all_antimicrobials()</code> returns a <a href='https://rdrr.io/r/base/character.html'>character</a> vector with all antimicrobial results for every isolate. These vectors can then be compared using <code>antimicrobials_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antimicrobials()</code> and ignored by <code>antimicrobials_equal()</code>.</p>
<p>Please see the <code><a href='first_isolate.html'>first_isolate()</a></code> function how these important functions enable the 'phenotype-based' method for determination of first isolates.</p>
<p>The default antimicrobial agents used for <strong>all rows</strong> (set in <code>universal</code>) are:</p><ul>
<li><p>Ampicillin</p></li>
@ -391,7 +391,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># TRUE, because I is ignored (as well as missing values)</span>
<span class='fu'>antimicrobials_equal</span><span class='op'>(</span><span class='va'>strainA</span>, <span class='va'>strainB</span>, type <span class='op'>=</span> <span class='st'>"keyantimicrobials"</span>, ignore_I <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># FALSE, because I is not ignored and so the 4th character differs</span>
<span class='co'># FALSE, because I is not ignored and so the 4th [character] differs</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>