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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9100</small>
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<a class="navbar-brand me-2" href="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="">2.1.1.9099</small>
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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="">2.1.1.9099</small>
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@ -102,26 +102,26 @@ directly through Python code.</p>
</h2>
<ol style="list-style-type: decimal">
<li>
<p>First make sure you have R installed. There is <strong>no need to
<p>Since the Python package is available on the official <a href="https://pypi.org/project/AMR/" class="external-link">Python Package Index</a>, you can
just run:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">pip</span> install AMR</span></code></pre></div>
</li>
<li>
<p>Make sure you have R installed. There is <strong>no need to
install the <code>AMR</code> R package</strong>, as it will be installed
automatically.</p>
<p>For Linux:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="co"># Ubuntu / Debian</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">sudo</span> apt install r-base</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co"># Fedora:</span></span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="fu">sudo</span> dnf install R</span>
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="co"># CentOS/RHEL</span></span>
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="fu">sudo</span> yum install R</span></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># Ubuntu / Debian</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="fu">sudo</span> apt install r-base</span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="co"># Fedora:</span></span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="fu">sudo</span> dnf install R</span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a><span class="co"># CentOS/RHEL</span></span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a><span class="fu">sudo</span> yum install R</span></code></pre></div>
<p>For macOS (using <a href="https://brew.sh" class="external-link">Homebrew</a>):</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="ex">brew</span> install r</span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">brew</span> install r</span></code></pre></div>
<p>For Windows, visit the <a href="https://cran.r-project.org" class="external-link">CRAN
download page</a> to download and install R.</p>
</li>
<li>
<p>Since the Python package is available on the official <a href="https://pypi.org/project/AMR/" class="external-link">Python Package Index</a>, you can
just run:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">pip</span> install AMR</span></code></pre></div>
</li>
</ol>
</div>
<div class="section level2">

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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="">2.1.1.9099</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../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="">2.1.1.9099</small>
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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="">2.1.1.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9100</small>
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2
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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="">2.1.1.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9100</small>
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2
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="">2.1.1.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9100</small>
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16
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="">2.1.1.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9100</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="2.1.1.9099" id="amr-2119099">AMR 2.1.1.9099<a class="anchor" aria-label="anchor" href="#amr-2119099"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9100" id="amr-2119100">AMR 2.1.1.9100<a class="anchor" aria-label="anchor" href="#amr-2119100"></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-2-1-1-9099">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-2-1-1-9099"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9100">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-2-1-1-9100"></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-2-1-1-9099">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9099"></a></h3>
<h3 id="breaking-2-1-1-9100">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9100"></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-2-1-1-9099">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9099"></a></h3>
<h3 id="new-2-1-1-9100">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9100"></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>
@ -99,7 +99,7 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9099">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9099"></a></h3>
<h3 id="changed-2-1-1-9100">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9100"></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>
@ -152,14 +152,14 @@
<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-2-1-1-9099">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9099"></a></h3>
<h3 id="other-2-1-1-9100">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9100"></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-2-1-1-9099">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9099"></a></h3>
<h3 id="older-versions-2-1-1-9100">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9100"></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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@ -11,7 +11,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2024-10-17T09:59Z
last_built: 2024-10-17T13:25Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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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, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -7,7 +7,7 @@
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reference/age_groups.html
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@ -7,7 +7,7 @@
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reference/antibiogram.html
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@ -7,7 +7,7 @@
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reference/antibiotic_class_selectors.html
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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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reference/antibiotics.html
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@ -7,7 +7,7 @@
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reference/as.ab.html
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@ -7,7 +7,7 @@
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reference/as.av.html
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@ -7,7 +7,7 @@
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reference/as.disk.html
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@ -7,7 +7,7 @@
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reference/as.mic.html
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@ -7,7 +7,7 @@
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reference/as.mo.html
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@ -7,7 +7,7 @@
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reference/as.sir.html
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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> 2024-10-17 <span style="color: #949494;">10:00:40</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> 2024-10-17 <span style="color: #949494;">10:00:47</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> 2024-10-17 <span style="color: #949494;">10:00:47</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> 2024-10-17 <span style="color: #949494;">10:00:48</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> 2024-10-17 <span style="color: #949494;">10:00:48</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> 2024-10-17 <span style="color: #949494;">10:00:40</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> 2024-10-17 <span style="color: #949494;">10:00:47</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> 2024-10-17 <span style="color: #949494;">10:00:47</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> 2024-10-17 <span style="color: #949494;">10:00:48</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> 2024-10-17 <span style="color: #949494;">10:00:48</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;"> 1</span> 2024-10-17 <span style="color: #949494;">13:26:41</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> 2024-10-17 <span style="color: #949494;">13:26:48</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> 2024-10-17 <span style="color: #949494;">13:26:48</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> 2024-10-17 <span style="color: #949494;">13:26:49</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> 2024-10-17 <span style="color: #949494;">13:26:49</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> 2024-10-17 <span style="color: #949494;">13:26:41</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> 2024-10-17 <span style="color: #949494;">13:26:48</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> 2024-10-17 <span style="color: #949494;">13:26:48</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> 2024-10-17 <span style="color: #949494;">13:26:49</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> 2024-10-17 <span style="color: #949494;">13:26:49</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>

2
reference/atc_online.html
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@ -7,7 +7,7 @@
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reference/av_from_text.html
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@ -7,7 +7,7 @@
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reference/av_property.html
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@ -7,7 +7,7 @@
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reference/availability.html
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@ -7,7 +7,7 @@
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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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@ -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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reference/ggplot_sir.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="">2.1.1.9099</small>
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reference/index.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="">2.1.1.9099</small>
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9099</small>
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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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