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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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articles/AMR.html
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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@ -87,7 +87,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 06 October 2024.</p>
generated on 10 October 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-10-06</td>
<td align="center">2024-10-10</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2024-10-06</td>
<td align="center">2024-10-10</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2024-10-06</td>
<td align="center">2024-10-10</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/datasets.html
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
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@ -76,7 +76,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">06 October 2024</h4>
<h4 data-toc-skip class="date">10 October 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -444,18 +444,18 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 October 2024 20:30:52 UTC. Find more info
<p>It was last updated on 10 October 2024 14:38:20 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original
R Data Structure (RDS) file</a> (49 kB)<br>
R Data Structure (RDS) file</a> (44 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft
Excel workbook</a> (82 kB)<br>
Excel workbook</a> (75 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache
Feather file</a> (0.1 MB)<br>
@ -505,7 +505,7 @@ Names and Codes)</a></li>
<col width="12%">
<col width="17%">
<col width="6%">
<col width="14%">
<col width="13%">
<col width="2%">
<col width="3%">
<col width="2%">
@ -538,7 +538,7 @@ Names and Codes)</a></li>
<td align="center">Aminoglycoside antibacterials</td>
<td align="center">Other aminoglycosides</td>
<td align="center">ak, ami, amik, …</td>
<td align="center">ambutyrosin a, ambutyrosin b, ambuyrosin a, …</td>
<td align="center">amicacin, amikacillin, amikacin, …</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
@ -554,7 +554,7 @@ Names and Codes)</a></li>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
<td align="center">ac, amox, amx</td>
<td align="center">actimoxi, acuotricina, agram, …</td>
<td align="center">actimoxi, amoclen, amolin, …</td>
<td align="center">1.5</td>
<td align="center">g</td>
<td align="center">3.0</td>
@ -619,7 +619,7 @@ inhibitors</td>
<td align="center">Combinations of antibacterials</td>
<td align="center">Combinations of antibacterials</td>
<td align="center">bepe, pen, peni, …</td>
<td align="center">abbocillin, amcap, amcill, …</td>
<td align="center">abbocillin, ayercillin, bencilpenicilina, …</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">3.6</td>

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articles/index.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -29,7 +29,7 @@
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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authors.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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extra.js
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@ -59,8 +59,9 @@ $(document).ready(function() {
// make Python part more fancy - prepare for CSS
if (window.location.href.includes('AMR_for_Python')) {
$('body').addClass('amr-for-python');
$('img[src="../logo.svg"]').attr('src', '../logo_python.svg');
$('body').addClass('amr-for-python'); /* to set colours in CSS */
$('img[src="../logo.svg"]').attr('src', '../logo_python.svg'); /* replace base logo */
$('img[src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"]').attr('src', 'https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT_python.svg'); /* replace GPT logo */
}
// add doctoral titles to authors

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index.html
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@ -32,7 +32,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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news/index.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -47,18 +47,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9093" id="amr-2119093">AMR 2.1.1.9093<a class="anchor" aria-label="anchor" href="#amr-2119093"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9094" id="amr-2119094">AMR 2.1.1.9094<a class="anchor" aria-label="anchor" href="#amr-2119094"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9093">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9093"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9094">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9094"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9093">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9093"></a></h3>
<h3 id="breaking-2-1-1-9094">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9094"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9093">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9093"></a></h3>
<h3 id="new-2-1-1-9094">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9094"></a></h3>
<ul><li>
<strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -95,7 +95,7 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9093">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9093"></a></h3>
<h3 id="changed-2-1-1-9094">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9094"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -147,14 +147,14 @@
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9093">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9093"></a></h3>
<h3 id="other-2-1-1-9094">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9094"></a></h3>
<ul><li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
<li>Greatly updated and expanded documentation</li>
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9093">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9093"></a></h3>
<h3 id="older-versions-2-1-1-9094">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9094"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

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pkgdown.yml
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@ -12,7 +12,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2024-10-06T20:50Z
last_built: 2024-10-10T14:41Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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reference/AMR-options.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/AMR.html
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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/WHOCC.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -71,17 +71,10 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Meropenem"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_tradenames</a></span><span class="op">(</span><span class="st">"flucloxacillin"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "ankerbin" "austrastaph" "bactopen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "cloxacap" "cloxacillinanhydrous" "cloxacillinhydrate" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "cloxacillinsalt" "cloxapen" "cloxypen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "culpen" "dariclox" "ekvacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "floxacillin" "floxapen" "floxapen sodium salt"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "fluclox" "flucloxacilina" "flucloxacilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "flucloxacillinum" "fluorochloroxacillin" "gelstaph" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "latocillin" "orbenin" "orbeninhydrate" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "prevencilina p" "prostaphilin a" "prostaphlin a" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "staphybiotic" "staphylex" "syntarpensalt" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "tegopen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "culpen" "floxacillin" "floxacillin sodium" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "floxapen" "floxapen sodium salt" "fluclox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "flucloxacilina" "flucloxacillin" "flucloxacilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "flucloxacillinum" "fluorochloroxacillin" "staphylex" </span>
</code></pre></div>
</div>
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2
reference/WHONET.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ab_from_text.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

167
reference/ab_property.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9094</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -177,79 +177,45 @@
<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 33613</span>
<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "acuotricina" "agram" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "alfamox" "alfida" "alfoxil enjektabl" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amitron" "amoclen" "amodex" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoksicillin" "amoksicillin forte" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amopen" "amopenixin" "amophar" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoran" "amoxibiotic" "amoxicaps" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "amoxicilina" "amoxicillin pulsys" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "amoxicillinsalt" "amoxicillinum" "amoxidal" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "amoxiden" "amoxil" "amoxil trihydrate" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "amoxillat" "amoxina" "amoxine" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "amoxipen" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "amoxycillin" "amoxyke" "anemolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "aspenil" "atoksilin" "biomox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "bristamox" "cemoxin" "ciblor" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "clamoxyl" "damoxy" "danoxillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "delacillin" "demoksil" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "dura" "efpenix" "eupen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "flemoxin" "flemoxine" "galenamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "gramidil" "hiconcil" "himinomax" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [58] "histocillin" "hydroxyampicillin" "ibiamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "imacillin" "izoltil" "kentrocyllin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [64] "lamoxy" "largopen" "larotid" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [67] "matasedrin" "metafarma capsules" "metifarma" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [70] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] "moxaline" "moxatag" "neotetranase" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] "novabritine" "ospamox" "pacetocin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [79] "pamocil" "pamoxicillin" "paradroxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [82] "pasetocin" "penamox" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] "promoxil" "quimiopen" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [88] "riotapen" "robamox" "sawacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [91] "sawamox" "siganopen" "simplamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [94] "sintopen" "tolodina" "topramoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] "trifamox" "trimox" "unicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [100] "utimox" "velamox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [103] "wymox" "zamocillin" "zamocilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [106] "zimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxiden" "amoxil" "amoxivet" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "anemolin" "aspenil" "atoksilin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "clamoxyl" "damoxy" "delacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "demoksil" "dispermox" "efpenix" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "flemoxin" "hiconcil" "histocillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "piramox" "promoxil" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "topramoxin" "unicillin" "utimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "vetramox" </span>
<span class="r-in"><span><span class="fu">ab_tradenames</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "acuotricina" "agram" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "alfamox" "alfida" "alfoxil enjektabl" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amitron" "amoclen" "amodex" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoksicillin" "amoksicillin forte" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amopen" "amopenixin" "amophar" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoran" "amoxibiotic" "amoxicaps" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "amoxicilina" "amoxicillin pulsys" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "amoxicillinsalt" "amoxicillinum" "amoxidal" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "amoxiden" "amoxil" "amoxil trihydrate" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "amoxillat" "amoxina" "amoxine" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "amoxipen" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "amoxycillin" "amoxyke" "anemolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "aspenil" "atoksilin" "biomox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "bristamox" "cemoxin" "ciblor" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "clamoxyl" "damoxy" "danoxillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "delacillin" "demoksil" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "dura" "efpenix" "eupen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "flemoxin" "flemoxine" "galenamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "gramidil" "hiconcil" "himinomax" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [58] "histocillin" "hydroxyampicillin" "ibiamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "imacillin" "izoltil" "kentrocyllin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [64] "lamoxy" "largopen" "larotid" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [67] "matasedrin" "metafarma capsules" "metifarma" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [70] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] "moxaline" "moxatag" "neotetranase" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] "novabritine" "ospamox" "pacetocin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [79] "pamocil" "pamoxicillin" "paradroxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [82] "pasetocin" "penamox" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] "promoxil" "quimiopen" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [88] "riotapen" "robamox" "sawacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [91] "sawamox" "siganopen" "simplamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [94] "sintopen" "tolodina" "topramoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] "trifamox" "trimox" "unicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [100] "utimox" "velamox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [103] "wymox" "zamocillin" "zamocilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [106] "zimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxiden" "amoxil" "amoxivet" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "anemolin" "aspenil" "atoksilin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "clamoxyl" "damoxy" "delacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "demoksil" "dispermox" "efpenix" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "flemoxin" "hiconcil" "histocillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "piramox" "promoxil" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "topramoxin" "unicillin" "utimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "vetramox" </span>
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactams/penicillins"</span>
<span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
@ -299,42 +265,25 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Penicillins with extended spectrum"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $tradenames</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "acuotricina" "agram" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "alfamox" "alfida" "alfoxil enjektabl" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amitron" "amoclen" "amodex" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoksicillin" "amoksicillin forte" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amopen" "amopenixin" "amophar" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoran" "amoxibiotic" "amoxicaps" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "amoxicilina" "amoxicillin pulsys" "amoxicilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "amoxicillinsalt" "amoxicillinum" "amoxidal" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "amoxiden" "amoxil" "amoxil trihydrate" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "amoxillat" "amoxina" "amoxine" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "amoxipen" "amoxivet" "amoxy" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "amoxycillin" "amoxyke" "anemolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "aspenil" "atoksilin" "biomox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "bristamox" "cemoxin" "ciblor" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "clamoxyl" "damoxy" "danoxillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "delacillin" "demoksil" "dispermox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "dura" "efpenix" "eupen" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "flemoxin" "flemoxine" "galenamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "gramidil" "hiconcil" "himinomax" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [58] "histocillin" "hydroxyampicillin" "ibiamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "imacillin" "izoltil" "kentrocyllin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [64] "lamoxy" "largopen" "larotid" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [67] "matasedrin" "metafarma capsules" "metifarma" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [70] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] "moxaline" "moxatag" "neotetranase" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] "novabritine" "ospamox" "pacetocin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [79] "pamocil" "pamoxicillin" "paradroxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [82] "pasetocin" "penamox" "piramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] "promoxil" "quimiopen" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [88] "riotapen" "robamox" "sawacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [91] "sawamox" "siganopen" "simplamox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [94] "sintopen" "tolodina" "topramoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] "trifamox" "trimox" "unicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [100] "utimox" "velamox" "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [103] "wymox" "zamocillin" "zamocilline" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [106] "zimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "actimoxi" "amoclen" "amolin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "amoxiden" "amoxil" "amoxivet" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "anemolin" "aspenil" "atoksilin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [22] "biomox" "bristamox" "cemoxin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "clamoxyl" "damoxy" "delacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [28] "demoksil" "dispermox" "efpenix" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "flemoxin" "hiconcil" "histocillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "piramox" "promoxil" "remoxil" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "robamox" "sawamox pm" "tolodina" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [52] "topramoxin" "unicillin" "utimox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [55] "vetramox" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $loinc</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "101498-4" "15-8" "16-6" "16365-9" "17-4" "18-2" </span>

2
reference/add_custom_antimicrobials.html
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@ -7,7 +7,7 @@
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reference/add_custom_microorganisms.html
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@ -7,7 +7,7 @@
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reference/age.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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@ -110,16 +110,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.83607 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.59836 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.92896 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.64208 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.62842 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.73770 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.10929 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.69399 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.30328 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.15574 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.84699 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.60929 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.93989 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.65301 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.63934 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.74863 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.12022 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.70492 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.31421 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.16667 13</span>
</code></pre></div>
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
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@ -7,7 +7,7 @@
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4
reference/as.ab.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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@ -152,7 +152,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythrocin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] CLR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>
<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Romycin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'ab'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ERY</span>

2
reference/as.av.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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@ -785,16 +785,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-10-06 <span style="color: #949494;">20:51:09</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-10-06 <span style="color: #949494;">20:51:16</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-10-06 <span style="color: #949494;">20:51:16</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-10-06 <span style="color: #949494;">20:51:17</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-10-06 <span style="color: #949494;">20:51:17</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-10-06 <span style="color: #949494;">20:51:09</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-10-06 <span style="color: #949494;">20:51:16</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-10-06 <span style="color: #949494;">20:51:16</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-10-06 <span style="color: #949494;">20:51:17</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-10-06 <span style="color: #949494;">20:51:17</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-10-10 <span style="color: #949494;">14:42:40</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-10-10 <span style="color: #949494;">14:42:40</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-10-10 <span style="color: #949494;">14:42:47</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-10-10 <span style="color: #949494;">14:42:48</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

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reference/av_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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reference/availability.html
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@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9093</small>
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reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
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reference/clinical_breakpoints.html
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@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
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reference/dosage.html
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@ -7,7 +7,7 @@
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reference/eucast_rules.html
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates.html
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@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
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reference/first_isolate.html
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@ -9,7 +9,7 @@
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reference/g.test.html
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@ -7,7 +7,7 @@
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reference/get_episode.html
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@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@ -7,7 +7,7 @@
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reference/index.html
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@ -7,7 +7,7 @@
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reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
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reference/italicise_taxonomy.html
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@ -7,7 +7,7 @@
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reference/join.html
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@ -7,7 +7,7 @@
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reference/key_antimicrobials.html
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@ -7,7 +7,7 @@
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reference/kurtosis.html
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@ -7,7 +7,7 @@
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reference/like.html
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@ -7,7 +7,7 @@
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reference/mdro.html
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@ -7,7 +7,7 @@
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reference/mean_amr_distance.html
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@ -7,7 +7,7 @@
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reference/microorganisms.codes.html
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@ -7,7 +7,7 @@
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reference/microorganisms.groups.html
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@ -7,7 +7,7 @@
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reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/mo_matching_score.html
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@ -7,7 +7,7 @@
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reference/mo_property.html
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@ -7,7 +7,7 @@
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reference/mo_source.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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@ -7,7 +7,7 @@
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reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@ -7,7 +7,7 @@
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reference/resistance_predict.html
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@ -7,7 +7,7 @@
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reference/skewness.html
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@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/translate.html
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search.json
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