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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9281</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -91,7 +91,7 @@
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 20 May 2025.</p>
generated on 21 May 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-05-20</td>
<td align="center">2025-05-21</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">2025-05-20</td>
<td align="center">2025-05-21</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">2025-05-20</td>
<td align="center">2025-05-21</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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@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">20 May 2025</h4>
<h4 data-toc-skip class="date">21 May 2025</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>
articles/index.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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index.html
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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news/index.html
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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="">2.1.1.9281</small>
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@@ -49,11 +49,11 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9281" id="amr-2119281">AMR 2.1.1.9281<a class="anchor" aria-label="anchor" href="#amr-2119281"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9285" id="amr-2119285">AMR 2.1.1.9285<a class="anchor" aria-label="anchor" href="#amr-2119285"></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://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
<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 class="section level3">
<h3 id="tldr-2-1-1-9281">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9281"></a></h3>
<h3 id="tldr-2-1-1-9285">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9285"></a></h3>
<ul><li>Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).</li>
<li>Data Updates:
<ul><li>
@@ -103,15 +103,15 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="full-changelog-2-1-1-9281">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9281"></a></h3>
<h3 id="full-changelog-2-1-1-9285">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9285"></a></h3>
<div class="section level4">
<h4 id="breaking-2-1-1-9281">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9281"></a></h4>
<h4 id="breaking-2-1-1-9285">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9285"></a></h4>
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<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 two years ago.</li>
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> are now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
</ul></div>
<div class="section level4">
<h4 id="new-2-1-1-9281">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9281"></a></h4>
<h4 id="new-2-1-1-9285">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9285"></a></h4>
<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>
@@ -170,7 +170,7 @@
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="changed-2-1-1-9281">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9281"></a></h4>
<h4 id="changed-2-1-1-9285">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9285"></a></h4>
<ul><li>SIR interpretation
<ul><li>Support for parallel computing to greatly improve speed using the <code>parallel</code> package (part of base R). Use <code>as.sir(your_data, parallel = TRUE)</code> to run SIR interpretation using multiple cores.</li>
<li>It is now possible to use column names for arguments <code>guideline</code>, <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>
@@ -256,7 +256,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level4">
<h4 id="other-2-1-1-9281">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9281"></a></h4>
<h4 id="other-2-1-1-9285">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9285"></a></h4>
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain will remain to work.</li>
<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
@@ -267,7 +267,7 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9281">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9281"></a></h3>
<h3 id="older-versions-2-1-1-9285">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9285"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) 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>
pkgdown.yml
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PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2025-05-20T13:10Z
last_built: 2025-05-21T14:57Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles
reference/AMR-deprecated.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ab_from_text.html
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reference/add_custom_antimicrobials.html
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reference/add_custom_microorganisms.html
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reference/age.html
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@@ -112,16 +112,16 @@
<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 1999-06-30 25 25.88767 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.30411 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.45479 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.21918 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.54795 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.26027 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.24658 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.35616 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.72877 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.31233 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.89041 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.30685 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.45753 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.22192 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.55068 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.26301 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.24932 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.35890 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.73151 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.31507 21</span>
</code></pre></div>
</div>
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reference/age_groups.html
+1 -1
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9281</small>
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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+1 -1
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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+1 -1
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@@ -7,7 +7,7 @@
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+1 -1
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+1 -1
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@@ -7,7 +7,7 @@
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+1 -1
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@@ -7,7 +7,7 @@
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reference/as.mic.html
+1 -1
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@@ -7,7 +7,7 @@
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reference/as.mo.html
+1 -1
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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/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9281</small>
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@@ -414,10 +414,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-20 <span style="color: #949494;">13:10:50</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-20 <span style="color: #949494;">13:10:50</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-20 <span style="color: #949494;">13:10:51</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-20 <span style="color: #949494;">13:10:51</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-21 <span style="color: #949494;">14:58:11</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-21 <span style="color: #949494;">14:58:11</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-21 <span style="color: #949494;">14:58:11</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-21 <span style="color: #949494;">14:58:12</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
reference/atc_online.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="">2.1.1.9281</small>
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reference/availability.html
+1 -1
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@@ -7,7 +7,7 @@
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reference/bug_drug_combinations.html
+1 -1
View File
@@ -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 @@ 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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9281</small>
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reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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+1 -1
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+1 -1
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@@ -9,7 +9,7 @@
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+1 -1
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@@ -7,7 +7,7 @@
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+1 -1
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@@ -7,7 +7,7 @@
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+1 -1
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@@ -7,7 +7,7 @@
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reference/ggplot_sir.html
+1 -1
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@@ -7,7 +7,7 @@
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reference/guess_ab_col.html
+1 -1
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@@ -7,7 +7,7 @@
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reference/key_antimicrobials.html
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reference/microorganisms.html
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reference/mo_matching_score.html
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reference/mo_source.html
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reference/plot.html
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reference/proportion.html
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reference/resistance_predict.html
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reference/skewness.html
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reference/top_n_microorganisms.html
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reference/translate.html
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search.json
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[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] Line truncated
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