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mirror of https://github.com/msberends/AMR.git synced 2025-07-09 10:21:49 +02:00

(v0.9.0.9009) antibiotics data set update

This commit is contained in:
2020-01-08 11:30:33 +01:00
parent ced1a7b7fa
commit 64f5ceef03
49 changed files with 134 additions and 59 deletions

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>
@ -356,7 +356,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<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></pre>
<span class='fu'>ab_name</span>(<span class='st'>"J01CF05"</span>) <span class='co'># "Flucloxacillin" (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>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>
@ -293,7 +293,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a> for the dataframe that is being used to determine ATCs.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># These examples all return "ERY", the ID of Erythromycin:</span>
<pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
<span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
<span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
<span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
@ -305,7 +305,13 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span>
<span class='fu'>as.ab</span>(<span class='st'>"Romycin"</span>) <span class='co'># trade name</span>
<span class='co'># Use ab_* functions to get a specific properties (see ?ab_property);</span>
<span class='co'># spelling from different languages and dyslexia are no problem</span>
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"ceftriaxon"</span>)
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephtriaxone"</span>)
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephthriaxone"</span>)
<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"seephthriaaksone"</span>)
<span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
<span class='co'># they use as.ab() internally:</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

View File

@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

View File

@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -86,7 +86,7 @@ This function requires an internet connection." />
</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">0.9.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>
@ -517,6 +517,12 @@
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
</td>
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
</tr><tr>
<td>
<p><code><a href="lifecycle.html">lifecycle</a></code> </p>
</td>
<td><p>Lifecycles of functions in the <code>AMR</code> package</p></td>
</tr>
</tbody><tbody>
<tr>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -87,7 +87,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
</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">0.9.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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">0.9.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>

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@ -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">0.9.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9009</span>
</span>
</div>