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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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10
docs/reference/index.html
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</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">1.6.0.9047</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9048</span>
</span>
</div>
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<tr>
<th colspan="2">
<h2 id="section-analysing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-analysing-data-antimicrobial-resistance" class="anchor"></a>Analysing data: antimicrobial resistance</h2>
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/AMR-deprecated.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
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</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_betalactams()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_oxazolidinones()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> <code><a href="AMR-deprecated.html">filter_ab_class()</a></code> <code><a href="AMR-deprecated.html">filter_aminoglycosides()</a></code> <code><a href="AMR-deprecated.html">filter_betalactams()</a></code> <code><a href="AMR-deprecated.html">filter_carbapenems()</a></code> <code><a href="AMR-deprecated.html">filter_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_1st_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_2nd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_3rd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_4th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_5th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_fluoroquinolones()</a></code> <code><a href="AMR-deprecated.html">filter_glycopeptides()</a></code> <code><a href="AMR-deprecated.html">filter_macrolides()</a></code> <code><a href="AMR-deprecated.html">filter_oxazolidinones()</a></code> <code><a href="AMR-deprecated.html">filter_penicillins()</a></code> <code><a href="AMR-deprecated.html">filter_tetracyclines()</a></code> </p>
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<td><p>Filter Isolates on Result in Antimicrobial Class</p></td>
<td><p>Deprecated Functions</p></td>
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<tr>
<td>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> </p>
<p><code><a href="AMR-deprecated.html">p_symbol()</a></code> <code><a href="AMR-deprecated.html">filter_first_weighted_isolate()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics()</a></code> <code><a href="AMR-deprecated.html">key_antibiotics_equal()</a></code> <code><a href="AMR-deprecated.html">filter_ab_class()</a></code> <code><a href="AMR-deprecated.html">filter_aminoglycosides()</a></code> <code><a href="AMR-deprecated.html">filter_betalactams()</a></code> <code><a href="AMR-deprecated.html">filter_carbapenems()</a></code> <code><a href="AMR-deprecated.html">filter_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_1st_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_2nd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_3rd_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_4th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_5th_cephalosporins()</a></code> <code><a href="AMR-deprecated.html">filter_fluoroquinolones()</a></code> <code><a href="AMR-deprecated.html">filter_glycopeptides()</a></code> <code><a href="AMR-deprecated.html">filter_macrolides()</a></code> <code><a href="AMR-deprecated.html">filter_oxazolidinones()</a></code> <code><a href="AMR-deprecated.html">filter_penicillins()</a></code> <code><a href="AMR-deprecated.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Deprecated Functions</p></td>
</tr>