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(v1.6.0.9048) ab selectors overhaul

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dr. M.S. (Matthijs) Berends
2021-05-19 22:55:42 +02:00
parent 6920c0be41
commit 2413efd5c1
32 changed files with 1182 additions and 939 deletions
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136
docs/reference/AMR-deprecated.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">1.6.0.9048</span>
</span>
</div>
@ -239,7 +239,7 @@
</div>
<div class="ref-description">
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
<p>These functions are so-called '<a href='https://rdrr.io/r/base/Deprecated.html'>Deprecated</a>'. <strong>They will be removed in a future release.</strong> Using the functions will give a warning with the name of the function it has been replaced by (if there is one).</p>
</div>
<pre class="usage"><span class='fu'>p_symbol</span><span class='op'>(</span><span class='va'>p</span>, emptychar <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span>
@ -286,9 +286,141 @@
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_ab_class</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>ab_class</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_aminoglycosides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_betalactams</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_carbapenems</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_1st_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_2nd_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_3rd_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_4th_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_5th_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_glycopeptides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_macrolides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_oxazolidinones</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_penicillins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_tetracyclines</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All antibiotic class selectors (such as <code><a href='antibiotic_class_selectors.html'>carbapenems()</a></code>, <code><a href='antibiotic_class_selectors.html'>aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code>filter_carbapenems()</code>, <code>filter_aminoglycosides()</code>).</p>
<h2 class="hasAnchor" id="retired-lifecycle"><a class="anchor" href="#retired-lifecycle"></a>Retired Lifecycle</h2>