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<h1>Deprecated Functions</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/deprecated.R'><code>R/deprecated.R</code></a></small>
<div class="hidden name"><code>AMR-deprecated.Rd</code></div>
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<div class="ref-description">
<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 Using the functions will give a warning with the name of the function it has been replaced by (if there is one).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>
<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>key_antibiotics</span><span class='op'>(</span>
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
universal_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>,
universal_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span><span class='op'>)</span>,
universal_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefuroxime"</span><span class='op'>)</span>,
universal_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"piperacillin/tazobactam"</span><span class='op'>)</span>,
universal_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ciprofloxacin"</span><span class='op'>)</span>,
universal_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"trimethoprim/sulfamethoxazole"</span><span class='op'>)</span>,
GramPos_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"vancomycin"</span><span class='op'>)</span>,
GramPos_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"teicoplanin"</span><span class='op'>)</span>,
GramPos_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tetracycline"</span><span class='op'>)</span>,
GramPos_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"erythromycin"</span><span class='op'>)</span>,
GramPos_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"oxacillin"</span><span class='op'>)</span>,
GramPos_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"rifampin"</span><span class='op'>)</span>,
GramNeg_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"gentamicin"</span><span class='op'>)</span>,
GramNeg_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"tobramycin"</span><span class='op'>)</span>,
GramNeg_3 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"colistin"</span><span class='op'>)</span>,
GramNeg_4 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"cefotaxime"</span><span class='op'>)</span>,
GramNeg_5 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"ceftazidime"</span><span class='op'>)</span>,
GramNeg_6 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"meropenem"</span><span class='op'>)</span>,
warnings <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>key_antibiotics_equal</span><span class='op'>(</span>
<span class='va'>y</span>,
<span class='va'>z</span>,
type <span class='op'>=</span> <span class='st'>"keyantimicrobials"</span>,
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
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>
<p><img src='figures/lifecycle_retired.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</strong>. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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