mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 12:21:59 +02:00
(v0.9.0.9012) Support for LOINC codes
This commit is contained in:
@ -85,7 +85,7 @@
|
||||
</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">0.9.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -253,6 +253,8 @@
|
||||
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_loinc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_ddd</span>(<span class='no'>x</span>, <span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>ab_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
@ -332,18 +334,18 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"AMX"</span>) <span class='co'># "Amoxicillin"</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"AMX"</span>) <span class='co'># J01CA04 (ATC code from the WHO)</span>
|
||||
<span class='fu'>ab_cid</span>(<span class='st'>"AMX"</span>) <span class='co'># 33613 (Compound ID from PubChem)</span>
|
||||
|
||||
<span class='fu'>ab_synonyms</span>(<span class='st'>"AMX"</span>) <span class='co'># a list with brand names of amoxicillin</span>
|
||||
<span class='fu'>ab_tradenames</span>(<span class='st'>"AMX"</span>) <span class='co'># same</span>
|
||||
|
||||
<span class='fu'>ab_group</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactams/penicillins"</span>
|
||||
<span class='fu'>ab_atc_group1</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactam antibacterials, penicillins"</span>
|
||||
<span class='fu'>ab_atc_group2</span>(<span class='st'>"AMX"</span>) <span class='co'># "Penicillins with extended spectrum"</span>
|
||||
|
||||
<span class='co'># smart lowercase tranformation</span>
|
||||
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>)) <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>),
|
||||
<span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
|
||||
|
||||
<span class='co'># defined daily doses (DDD)</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>) <span class='co'># 1</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
|
||||
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>) <span class='co'># 1</span>
|
||||
@ -351,12 +353,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
|
||||
<span class='fu'>ab_info</span>(<span class='st'>"AMX"</span>) <span class='co'># all properties as a list</span>
|
||||
|
||||
<span class='co'># all ab_* functions use as.ab() internally:</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"Fluclox"</span>) <span class='co'># "Flucloxacillin"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"fluklox"</span>) <span class='co'># "Flucloxacillin"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"floxapen"</span>) <span class='co'># "Flucloxacillin"</span>
|
||||
<span class='fu'>ab_name</span>(<span class='fl'>21319</span>) <span class='co'># "Flucloxacillin" (using CID)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"J01CF05"</span>) <span class='co'># "Flucloxacillin" (using ATC)</span>
|
||||
<span class='co'># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"AMP"</span>) <span class='co'># ATC code of AMP (ampicillin)</span>
|
||||
<span class='fu'>ab_group</span>(<span class='st'>"J01CA01"</span>) <span class='co'># Drug group of ampicillins ATC code</span>
|
||||
<span class='fu'>ab_loinc</span>(<span class='st'>"ampicillin"</span>) <span class='co'># LOINC codes of ampicillin</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"21066-6"</span>) <span class='co'># "Ampicillin" (using LOINC)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='fl'>6249</span>) <span class='co'># "Ampicillin" (using CID)</span>
|
||||
<span class='fu'>ab_name</span>(<span class='st'>"J01CA01"</span>) <span class='co'># "Ampicillin" (using ATC)</span>
|
||||
|
||||
<span class='co'># spelling from different languages and dyslexia are no problem</span>
|
||||
<span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
|
||||
|
@ -85,7 +85,7 @@
|
||||
</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">0.9.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -244,7 +244,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 452 observations and 13 variables:</h3>
|
||||
<h3>For the antibiotics data set: a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 452 observations and 14 variables:</h3>
|
||||
|
||||
<ul>
|
||||
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
|
||||
@ -260,6 +260,7 @@
|
||||
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
|
||||
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
|
||||
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
|
||||
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the antimicrobial name of the drug. Use <code>ab_loic()</code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
|
||||
</ul>
|
||||
|
||||
|
||||
@ -322,7 +323,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N M Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
|
@ -6,7 +6,7 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>EUCAST rules — eucast_rules • AMR (for R)</title>
|
||||
<title>Apply EUCAST rules — eucast_rules • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
@ -50,7 +50,7 @@
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="EUCAST rules — eucast_rules" />
|
||||
<meta property="og:title" content="Apply EUCAST rules — eucast_rules" />
|
||||
<meta property="og:description" content="Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
|
||||
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</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">0.9.0.9009</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -229,7 +229,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>EUCAST rules</h1>
|
||||
<h1>Apply EUCAST rules</h1>
|
||||
|
||||
<div class="hidden name"><code>eucast_rules.Rd</code></div>
|
||||
</div>
|
||||
@ -305,10 +305,10 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
|
||||
<li><p>Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;</p></li>
|
||||
<li><p>Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;</p></li>
|
||||
<li><p>Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;</p></li>
|
||||
<li><p>Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
|
||||
To <em>not</em> use these rules, please use <code>eucast_rules(..., rules = c("breakpoints", "expert"))</code>.</p></li>
|
||||
<li><p>Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.</p></li>
|
||||
</ul>
|
||||
|
||||
<p>To <em>not</em> use these rules, please use <code>eucast_rules(..., rules = c("breakpoints", "expert"))</code>.</p>
|
||||
<p>The file containing all EUCAST rules is located here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
|
||||
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
|
||||
|
||||
|
@ -84,7 +84,7 @@
|
||||
</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">0.9.0.9011</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9012</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -280,7 +280,7 @@
|
||||
<td>
|
||||
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
|
||||
</td>
|
||||
<td><p>EUCAST rules</p></td>
|
||||
<td><p>Apply EUCAST rules</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
@ -316,7 +316,7 @@
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
|
||||
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of an antibiotic</p></td>
|
||||
</tr><tr>
|
||||
|
Reference in New Issue
Block a user