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404.html
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@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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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>
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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 13 December 2024.</p>
generated on 15 December 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">2024-12-13</td>
<td align="center">2024-12-15</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">2024-12-13</td>
<td align="center">2024-12-15</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">2024-12-13</td>
<td align="center">2024-12-15</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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articles/MDR.html
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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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@ -216,7 +216,7 @@ on this data set, we get:</p>
Length: 2,000<br>
Levels: 4: Negative &lt; Multi-drug-resistant (MDR) &lt; Extensively
drug-resistant …<br>
Available: 1,729 (86.45%, NA: 271 = 13.55%)<br>
Available: 1,745 (87.25%, NA: 255 = 12.75%)<br>
Unique: 2</p>
<table style="width:100%;" class="table">
<colgroup>
@ -239,18 +239,18 @@ Unique: 2</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Negative</td>
<td align="right">1601</td>
<td align="right">92.6%</td>
<td align="right">1601</td>
<td align="right">92.6%</td>
<td align="right">1617</td>
<td align="right">92.66%</td>
<td align="right">1617</td>
<td align="right">92.66%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Multi-drug-resistant (MDR)</td>
<td align="right">128</td>
<td align="right">7.4%</td>
<td align="right">1729</td>
<td align="right">100.0%</td>
<td align="right">7.34%</td>
<td align="right">1745</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>

2
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@ -29,7 +29,7 @@
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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">13 December 2024</h4>
<h4 data-toc-skip class="date">15 December 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>

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@ -29,7 +29,7 @@
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@ -7,7 +7,7 @@
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5
extra.css
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@ -213,6 +213,11 @@ pre .co, .co {
color: var(--amr-green-dark) !important;
font-style: italic !important;
}
div.sourceCode  pre .co,
div.sourceCode .co {
/* comments in example sections, since functions are already green too */
color: var(--bs-gray-600) !important;
}
pre code .r-out,
pre code .r-msg {
/* output of functions */

2
index.html
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@ -32,7 +32,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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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="">2.1.1.9117</small>
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@ -47,18 +47,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9117" id="amr-2119117">AMR 2.1.1.9117<a class="anchor" aria-label="anchor" href="#amr-2119117"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9118" id="amr-2119118">AMR 2.1.1.9118<a class="anchor" aria-label="anchor" href="#amr-2119118"></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-2-1-1-9117">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-2-1-1-9117"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9118">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-2-1-1-9118"></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-2-1-1-9117">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9117"></a></h3>
<h3 id="breaking-2-1-1-9118">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9118"></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-2-1-1-9117">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9117"></a></h3>
<h3 id="new-2-1-1-9118">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9118"></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-2-1-1-9117">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9117"></a></h3>
<h3 id="changed-2-1-1-9118">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9118"></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>
@ -152,17 +152,17 @@
<li>Updated the prevalence calculation to include genera from the World Health Organization’s (WHO) Priority Pathogen List</li>
<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>
<li>
<code><a href="../reference/ggplot_sir.html">scale_y_percent()</a></code> can now cope with ranges outside the 0-100% range</li>
<code><a href="../reference/plot.html">scale_y_percent()</a></code> can now cope with ranges outside the 0-100% range</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9117">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9117"></a></h3>
<h3 id="other-2-1-1-9118">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9118"></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-2-1-1-9117">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9117"></a></h3>
<h3 id="older-versions-2-1-1-9118">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9118"></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: 2024-12-13T09:39Z
last_built: 2024-12-15T19:20Z
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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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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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>
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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 59 59.02186 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.78415 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.11475 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.82787 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.81421 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.92350 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.29508 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.87978 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.48907 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.34153 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.02732 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.78962 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.12022 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.83333 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.81967 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.92896 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.30055 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.88525 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.49454 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.34699 13</span>
</code></pre></div>
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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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@ -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> 2024-12-13 <span style="color: #949494;">09:40:07</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> 2024-12-13 <span style="color: #949494;">09:40:15</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> 2024-12-13 <span style="color: #949494;">09:40:15</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> 2024-12-13 <span style="color: #949494;">09:40:16</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> 2024-12-13 <span style="color: #949494;">09:40:16</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> 2024-12-13 <span style="color: #949494;">09:40:07</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> 2024-12-13 <span style="color: #949494;">09:40:15</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> 2024-12-13 <span style="color: #949494;">09:40:15</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> 2024-12-13 <span style="color: #949494;">09:40:16</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> 2024-12-13 <span style="color: #949494;">09:40:16</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> 2024-12-15 <span style="color: #949494;">19:21:00</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> 2024-12-15 <span style="color: #949494;">19:21:07</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> 2024-12-15 <span style="color: #949494;">19:21:08</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> 2024-12-15 <span style="color: #949494;">19:21:09</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> 2024-12-15 <span style="color: #949494;">19:21:09</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> 2024-12-15 <span style="color: #949494;">19:21:00</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> 2024-12-15 <span style="color: #949494;">19:21:07</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> 2024-12-15 <span style="color: #949494;">19:21:08</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> 2024-12-15 <span style="color: #949494;">19:21:08</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> 2024-12-15 <span style="color: #949494;">19:21:09</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
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@ -7,7 +7,7 @@
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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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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</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">

4
reference/facet_sir.html
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@ -1,8 +1,8 @@
<html>
<head>
<meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/ggplot_sir.html" />
<meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/plot.html" />
<meta name="robots" content="noindex">
<link rel="canonical" href="https://msberends.github.io/AMR/reference/ggplot_sir.html">
<link rel="canonical" href="https://msberends.github.io/AMR/reference/plot.html">
</head>
</html>

2
reference/first_isolate.html
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@ -9,7 +9,7 @@
<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="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</small>
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2
reference/g.test.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="">2.1.1.9117</small>
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2
reference/get_episode.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="">2.1.1.9117</small>
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2
reference/ggplot_pca.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="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</small>
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57
reference/ggplot_sir.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="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</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">
@ -88,28 +88,6 @@
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">facet_sir</span><span class="op">(</span>facet <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"interpretation"</span>, <span class="st">"antibiotic"</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_y_percent</span><span class="op">(</span></span>
<span> breaks <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
<span> limits <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_sir_colours</span><span class="op">(</span><span class="va">...</span>, aesthetics <span class="op">=</span> <span class="st">"fill"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">theme_sir</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">labels_sir_count</span><span class="op">(</span></span>
<span> position <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> x <span class="op">=</span> <span class="st">"antibiotic"</span>,</span>
<span> translate_ab <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> datalabels.size <span class="op">=</span> <span class="fl">3</span>,</span>
<span> datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
@ -170,7 +148,7 @@
<dt id="arg-datalabels">datalabels<a class="anchor" aria-label="anchor" href="#arg-datalabels"></a></dt>
<dd><p>show datalabels using <code>labels_sir_count()</code></p></dd>
<dd><p>show datalabels using <code><a href="plot.html">labels_sir_count()</a></code></p></dd>
<dt id="arg-datalabels-size">datalabels.size<a class="anchor" aria-label="anchor" href="#arg-datalabels-size"></a></dt>
@ -202,7 +180,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>other arguments passed on to <code>geom_sir()</code> or, in case of <code>scale_sir_colours()</code>, named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See <em>Examples</em>.</p></dd>
<dd><p>other arguments passed on to <code>geom_sir()</code> or, in case of <code><a href="plot.html">scale_sir_colours()</a></code>, named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See <em>Examples</em>.</p></dd>
<dt id="arg-aesthetics">aesthetics<a class="anchor" aria-label="anchor" href="#arg-aesthetics"></a></dt>
@ -211,19 +189,14 @@
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href="ab_property.html">ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href="count.html">count_df()</a></code>.</p><div class="section">
<h3 id="the-functions">The Functions<a class="anchor" aria-label="anchor" href="#the-functions"></a></h3>
<p>At default, the names of antibiotics will be shown on the plots using <code><a href="ab_property.html">ab_name()</a></code>. This can be set with the <code>translate_ab</code> argument. See <code><a href="count.html">count_df()</a></code>.</p>
<p><code>geom_sir()</code> will take any variable from the data that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) using <code><a href="proportion.html">sir_df()</a></code> and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_sir()</code> creates 2d plots (at default based on S/I/R) using <code><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html" class="external-link">ggplot2::facet_wrap()</a></code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">ggplot2::scale_y_continuous()</a></code>.</p>
<p><code>scale_sir_colours()</code> sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p>
<p><code>theme_sir()</code> is a [ggplot2 theme][<code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> with minimal distraction.</p>
<p><code>labels_sir_count()</code> print datalabels on the bars with percentage and amount of isolates using <code><a href="https://ggplot2.tidyverse.org/reference/geom_text.html" class="external-link">ggplot2::geom_text()</a></code>.</p>
<p><code>ggplot_sir()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See <em>Examples</em>.</p>
</div>
<p>Additional functions include:</p><ul><li><p><code><a href="plot.html">facet_sir()</a></code> creates 2d plots (at default based on S/I/R) using <code><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html" class="external-link">ggplot2::facet_wrap()</a></code>.</p></li>
<li><p><code><a href="plot.html">scale_y_percent()</a></code> transforms the y axis to a 0 to 100% range using <code><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">ggplot2::scale_y_continuous()</a></code>.</p></li>
<li><p><code><a href="plot.html">scale_sir_colours()</a></code> sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p></li>
<li><p><code><a href="plot.html">theme_sir()</a></code> is a [ggplot2 theme][<code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> with minimal distraction.</p></li>
<li><p><code><a href="plot.html">labels_sir_count()</a></code> print datalabels on the bars with percentage and amount of isolates using <code><a href="https://ggplot2.tidyverse.org/reference/geom_text.html" class="external-link">ggplot2::geom_text()</a></code>.</p></li>
</ul><p><code>ggplot_sir()</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See <em>Examples</em>.</p>
</div>
<div class="section level2">
@ -240,10 +213,10 @@
<span class="r-in"><span> <span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">geom_sir</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_y_percent</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_sir_colours</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">labels_sir_count</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">theme_sir</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="plot.html">scale_y_percent</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="plot.html">scale_sir_colours</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="plot.html">labels_sir_count</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="plot.html">theme_sir</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="ggplot_sir-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -290,7 +263,7 @@
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">x</span>, y <span class="op">=</span> <span class="va">y</span>, fill <span class="op">=</span> <span class="va">z</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_sir_colours</span><span class="op">(</span>Value4 <span class="op">=</span> <span class="st">"S"</span>, Value5 <span class="op">=</span> <span class="st">"I"</span>, Value6 <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="plot.html">scale_sir_colours</a></span><span class="op">(</span>Value4 <span class="op">=</span> <span class="st">"S"</span>, Value5 <span class="op">=</span> <span class="st">"I"</span>, Value6 <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="ggplot_sir-7.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>

2
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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="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</small>
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reference/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="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</small>
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@ -275,13 +275,13 @@
<dl><dt>
<code><a href="plot.html">scale_x_mic()</a></code> <code><a href="plot.html">scale_y_mic()</a></code> <code><a href="plot.html">scale_colour_mic()</a></code> <code><a href="plot.html">scale_fill_mic()</a></code> <code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;sir&gt;</i>)</a></code>
<code><a href="plot.html">scale_x_mic()</a></code> <code><a href="plot.html">scale_y_mic()</a></code> <code><a href="plot.html">scale_colour_mic()</a></code> <code><a href="plot.html">scale_fill_mic()</a></code> <code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">facet_sir()</a></code> <code><a href="plot.html">scale_y_percent()</a></code> <code><a href="plot.html">scale_sir_colours()</a></code> <code><a href="plot.html">theme_sir()</a></code> <code><a href="plot.html">labels_sir_count()</a></code>
</dt>
<dd>Plotting for Classes <code>sir</code>, <code>mic</code> and <code>disk</code></dd>
<dd>Plotting Helpers for AMR Data Analysis</dd>
</dl><dl><dt>
<code><a href="ggplot_sir.html">ggplot_sir()</a></code> <code><a href="ggplot_sir.html">geom_sir()</a></code> <code><a href="ggplot_sir.html">facet_sir()</a></code> <code><a href="ggplot_sir.html">scale_y_percent()</a></code> <code><a href="ggplot_sir.html">scale_sir_colours()</a></code> <code><a href="ggplot_sir.html">theme_sir()</a></code> <code><a href="ggplot_sir.html">labels_sir_count()</a></code>
<code><a href="ggplot_sir.html">ggplot_sir()</a></code> <code><a href="ggplot_sir.html">geom_sir()</a></code>
</dt>
<dd>AMR Plots with <code>ggplot2</code></dd>

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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="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</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">

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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="">2.1.1.9117</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9118</small>
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@ -7,7 +7,7 @@
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@ -48,7 +48,7 @@
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<div class="ref-description section level2">
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.</p>
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.</p>
</div>
<div class="section level2">
@ -163,8 +163,11 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<li><p><code>guideline = "MRGN"</code></p>
<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; <a href="https://doi.org/10.1186/s13756-015-0047-6" class="external-link">doi:10.1186/s13756-015-0047-6</a></p></li>
<li><p><code>guideline = "BRMO"</code></p>
<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p></li>
</ul><p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link">https://github.com/msberends/AMR/issues/new</a>.</p>
<p>The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" (<a href="https://www.sri-richtlijnen.nl/brmo" class="external-link">link</a>)</p>
<p>Also:</p><ul><li><p><code>guideline = "BRMO 2017"</code></p>
<p>The former Dutch national guideline - Werkgroep Infectiepreventie (WIP), RIVM, last revision as of 2017: "Bijzonder Resistente Micro-Organismen (BRMO)"</p></li>
</ul></li>
</ul><p>Please suggest to implement guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link">https://github.com/msberends/AMR/issues/new</a>.</p>
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<div class="section level2">
<h2 id="using-custom-guidelines">Using Custom Guidelines<a class="anchor" aria-label="anchor" href="#using-custom-guidelines"></a></h2>
@ -229,7 +232,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> out</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Positive, unconfirmed Positive </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1978 0 6 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1994 0 6 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu">custom_mdro_guideline</span><span class="op">(</span></span></span>
@ -263,7 +266,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with pct_required_classes)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> .</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Multi-drug-resistant (MDR) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1601 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1617 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Extensively drug-resistant (XDR) Pandrug-resistant (PDR) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 </span>
<span class="r-in"><span><span class="co"># }</span></span></span>

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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Plotting for Classes sir, mic and disk — plot • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Plotting for Classes sir, mic and disk — plot"><meta name="description" content="Functions to plot classes sir, mic and disk, with support for base R and ggplot2.
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Especially the scale_*_mic() functions are relevant wrappers to plot MIC values for ggplot2. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values."><meta property="og:description" content="Functions to plot classes sir, mic and disk, with support for base R and ggplot2.
Especially the scale_*_mic() functions are relevant wrappers to plot MIC values for ggplot2. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@ -44,7 +44,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Plotting for Classes <code>sir</code>, <code>mic</code> and <code>disk</code></h1>
<img src="../logo.svg" class="logo" alt=""><h1>Plotting Helpers for AMR Data Analysis</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/plotting.R" class="external-link"><code>R/plotting.R</code></a></small>
<div class="d-none name"><code>plot.Rd</code></div>
</div>
@ -160,7 +160,33 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for class 'sir'</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">facet_sir</span><span class="op">(</span>facet <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"interpretation"</span>, <span class="st">"antibiotic"</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_y_percent</span><span class="op">(</span></span>
<span> breaks <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
<span> limits <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_sir_colours</span><span class="op">(</span></span>
<span> <span class="va">...</span>,</span>
<span> aesthetics <span class="op">=</span> <span class="st">"fill"</span>,</span>
<span> colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">theme_sir</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">labels_sir_count</span><span class="op">(</span></span>
<span> position <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> x <span class="op">=</span> <span class="st">"antibiotic"</span>,</span>
<span> translate_ab <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> datalabels.size <span class="op">=</span> <span class="fl">3</span>,</span>
<span> datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
@ -236,7 +262,17 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2024", "EUCAST 2023", "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2024", "CLSI 2023", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", and "CLSI 2011".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p><div class="section">
<h3 id="additional-ggplot-functions">Additional <code>ggplot2</code> Functions<a class="anchor" aria-label="anchor" href="#additional-ggplot-functions"></a></h3>
<p>This package contains several functions that extend the <code>ggplot2</code> package, to help in visualising AMR data results. All these functions are internally used by <code><a href="ggplot_sir.html">ggplot_sir()</a></code> too.</p><ul><li><p><code>facet_sir()</code> creates 2d plots (at default based on S/I/R) using <code><a href="https://ggplot2.tidyverse.org/reference/facet_wrap.html" class="external-link">ggplot2::facet_wrap()</a></code>.</p></li>
<li><p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code><a href="https://ggplot2.tidyverse.org/reference/scale_continuous.html" class="external-link">ggplot2::scale_y_continuous()</a></code>.</p></li>
<li><p><code>scale_sir_colours()</code> sets colours to the bars (green for S, yellow for I, and red for R). Has multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.</p></li>
<li><p><code>theme_sir()</code> is a [ggplot2 theme][<code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> with minimal distraction.</p></li>
<li><p><code>labels_sir_count()</code> print datalabels on the bars with percentage and number of isolates, using <code><a href="https://ggplot2.tidyverse.org/reference/geom_text.html" class="external-link">ggplot2::geom_text()</a></code>.</p></li>
</ul></div>
</div>
<div class="section level2">

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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -7,7 +7,7 @@
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@ -1,8 +1,8 @@
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<meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/plot.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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@ -1,8 +1,8 @@
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