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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="">2.1.1.9048</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="">2.1.1.9048</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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@ -205,7 +205,7 @@
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 June 2024.</p>
generated on 14 June 2024.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2024-06-13</td>
<td align="center">2024-06-14</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">2024-06-13</td>
<td align="center">2024-06-14</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">2024-06-13</td>
<td align="center">2024-06-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -579,14 +579,14 @@ impression, as it comes with support for the new <code>mo</code> and
<span><span class="co">#&gt; Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #1 :B_ESCHR_COLI %I :16.1% (n=437) %I :12.0% (n=325) </span></span>
<span><span class="co">#&gt; #2 :B_STPHY_AURS %R :42.9% (n=1163) %R :36.1% (n=978) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %N : 0.0% (n=0) %N : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; CIP GEN first </span></span>
<span><span class="co">#&gt; Class:sir Class:sir Mode:logical </span></span>
<span><span class="co">#&gt; %S :51.5% (n=1396) %S :59.6% (n=1616) TRUE:2712 </span></span>
<span><span class="co">#&gt; %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
<span><span class="co">#&gt; %I : 6.6% (n=178) %I : 3.1% (n=85) </span></span>
<span><span class="co">#&gt; %R :42.0% (n=1138) %R :37.3% (n=1011) </span></span>
<span><span class="co">#&gt; %N : 0.0% (n=0) %N : 0.0% (n=0)</span></span></code></pre></div>
<span><span class="co">#&gt; %NI : 0.0% (n=0) %NI : 0.0% (n=0)</span></span></code></pre></div>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>

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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
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@ -372,7 +372,7 @@ Longest: 40</p>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; sir (numeric)<br>
Length: 500<br>
Levels: 5: S &lt; SDD &lt; I &lt; R &lt; N<br>
Levels: 5: S &lt; SDD &lt; I &lt; R &lt; NI<br>
Available: 481 (96.2%, NA: 19 = 3.8%)<br>
Unique: 3</p>
<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02)<br>

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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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@ -194,7 +194,7 @@
<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 June 2024</h4>
<h4 data-toc-skip class="date">14 June 2024</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -526,14 +526,14 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
<h2 id="antibiotics-antibiotic-antifungal-drugs">
<code>antibiotics</code>: Antibiotic (+Antifungal) Drugs<a class="anchor" aria-label="anchor" href="#antibiotics-antibiotic-antifungal-drugs"></a>
</h2>
<p>A data set with 484 rows and 14 columns, containing the following
<p>A data set with 485 rows and 14 columns, containing the following
column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
<em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
<em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 13 June 2024 18:55:17 UTC. Find more info
<p>It was last updated on 14 June 2024 20:39:01 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -905,47 +905,47 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 29 883 rows and 13 columns, containing the following
<p>A data set with 34 085 rows and 13 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</em>,
<em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>,
<em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>,
<em>breakpoint_R</em>, and <em>uti</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 24 February 2024 14:16:52 UTC. Find more info
<p>It was last updated on 14 June 2024 20:39:01 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (61 kB)<br>
R Data Structure (RDS) file</a> (71 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (2.5 MB)<br>
text file</a> (2.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.4 MB)<br>
Excel workbook</a> (1.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (1.3 MB)<br>
Feather file</a> (4.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (91 kB)<br>
Parquet file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
transport (XPT) file</a> (8.2 MB)<br>
transport (XPT) file</a> (9.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (4.9 MB)<br>
SPSS Statistics data file</a> (5.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (8.1 MB)</li>
DTA file</a> (9.2 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
</h3>
<p>This data set contains interpretation rules for MIC values and disk
diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
(2011-2023).</p>
diffusion diameters. Included guidelines are CLSI (2011-2024) and EUCAST
(2011-2024).</p>
<p>Clinical breakpoints in this package were validated through and
imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop
Windows application developed and supported by the WHO Collaborating
@ -1007,7 +1007,7 @@ use.</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -1024,7 +1024,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -1041,7 +1041,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -1058,7 +1058,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -1075,7 +1075,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">DISK</td>
@ -1092,7 +1092,7 @@ use.</p>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">EUCAST 2024</td>
<td align="center">human</td>
<td align="center">human</td>
<td align="center">MIC</td>
@ -2176,11 +2176,11 @@ which are used in the <code>clinical_breakpoints</code> data set.</p>
<h2 id="microorganisms-codes-common-laboratory-codes">
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
</h2>
<p>A data set with 4 958 rows and 2 columns, containing the following
<p>A data set with 4 972 rows and 2 columns, containing the following
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 13 June 2024 05:37:53 UTC. Find more info
<p>It was last updated on 14 June 2024 20:39:01 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>

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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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articles/other_pkg.html
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -39,7 +39,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
articles/welcome_to_AMR.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
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2
authors.html
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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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4
index.html
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@ -39,7 +39,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</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">
@ -779,7 +779,7 @@
<p>Manually, using:</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
</li>
<li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>

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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</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">
@ -159,18 +159,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9048" id="amr-2119048">AMR 2.1.1.9048<a class="anchor" aria-label="anchor" href="#amr-2119048"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9049" id="amr-2119049">AMR 2.1.1.9049<a class="anchor" aria-label="anchor" href="#amr-2119049"></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!)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9048">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9048"></a></h5>
<h5 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9049">A New Milestone: One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9049"></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</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-2-1-1-9048">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9048"></a></h3>
<h3 id="breaking-2-1-1-9049">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9049"></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-2-1-1-9048">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9048"></a></h3>
<h3 id="new-2-1-1-9049">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9049"></a></h3>
<ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal 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>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
@ -181,17 +181,22 @@
<code><a href="../reference/ab_property.html">ab_url()</a></code> now supports retrieving the WHOCC url of their ATCvet pages</li>
</ul></li>
<li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “N” for non-interpretable and “SDD” for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and N. Also, to get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (N will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain N and SDD.</li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “NI” for non-interpretable and “SDD” for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI. Also, to get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> or a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li>
<li>The function group <code>scale_*_mic()</code>, namely: <code><a href="../reference/plot.html">scale_x_mic()</a></code>, <code><a href="../reference/plot.html">scale_y_mic()</a></code>, <code><a href="../reference/plot.html">scale_colour_mic()</a></code> and <code><a href="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
<li>Function <code><a href="../reference/as.mic.html">rescale_mic()</a></code>, which allows to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that are in that group.</li>
<li>Clinical breakpoints and intrinsic resistance of EUCAST 2024 and CLSI 2024 have been added to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.</li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9048">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9048"></a></h3>
<h3 id="changed-2-1-1-9049">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9049"></a></h3>
<ul><li>For SIR interpretation, 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>Extended the antibiotic selectors with <code><a href="../reference/antibiotic_class_selectors.html">nitrofurans()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">rifamycins()</a></code>
</li>
<li>Added “clindamycin inducible screening” as <code>CLI1</code> to the <code>antibiotics</code> data set. Since clindamycin is a lincosamide, the antibiotic selector <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
<li>
<code>antibiotics</code> data set:
<ul><li>Added “clindamycin inducible screening” as <code>CLI1</code>. Since clindamycin is a lincosamide, the antibiotic selector <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
<li>Added Amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><a href="../reference/antibiotic_class_selectors.html">antifungals()</a></code> selector</li>
</ul></li>
<li>For MICs:
<ul><li>Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)</li>
<li>Added new argument <code>keep_operators</code> to <code><a href="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>. This argument is also available in the new <code><a href="../reference/as.mic.html">rescale_mic()</a></code> and <code>scale_*_mic()</code> functions.</li>
@ -210,12 +215,13 @@
</li>
<li>Fix for mapping ‘high level’ antibiotics in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li>
<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy</li>
<li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy. Specifically, more weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species.</li>
<li>When using antibiotic selectors such as <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using <code>only_treatable = FALSE</code>
</li>
<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9048">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9048"></a></h3>
<h3 id="other-2-1-1-9049">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9049"></a></h3>
<ul><li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div>
</div>

2
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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: 2024-06-13T18:58Z
last_built: 2024-06-14T20:46Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
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@ -173,7 +173,7 @@
<li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
<li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
<li><p><code>AMR_eucastrules</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default types of rules for <code><a href="eucast_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2023"</code>. Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).</p></li>
<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2024"</code>. Supported guideline are currently EUCAST (2011-2024) and CLSI (2011-2024).</p></li>
<li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to ignore (i.e., make <code>NA</code>) any match given in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
<li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>.</p></li>
<li><p><code>AMR_include_screening</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>.</p></li>

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@ -24,7 +24,7 @@ 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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@ -10,7 +10,7 @@
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reference/WHONET.html
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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
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reference/ab_from_text.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ab_property.html
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@ -10,7 +10,7 @@
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2
reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
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4
reference/add_custom_microorganisms.html
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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
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@ -207,7 +207,7 @@
<span class="r-in"><span><span class="co"># this will result in "Enterobacter cloacae cloacae",</span></span></span>
<span class="r-in"><span><span class="co"># since it resembles the input best:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacter cloacae cloacae"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacter asburiae"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.mo() and</span></span></span>
<span class="r-in"><span><span class="co"># all mo_*() functions</span></span></span>

22
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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
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@ -222,16 +222,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.52186 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.28415 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.61475 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.32787 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.31421 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.42350 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.79508 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.37978 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.98907 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.84153 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.52459 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.28689 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.61749 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.33060 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.31694 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.42623 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.79781 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.38251 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.99180 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.84426 13</span>
</code></pre></div>
</div>
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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
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@ -291,7 +291,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)</p></li>
<li><p><code>aminopenicillins()</code> can select: <br> amoxicillin (AMX) and ampicillin (AMP)</p></li>
<li><p><code>antifungals()</code> can select: <br> amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)</p></li>
<li><p><code>antifungals()</code> can select: <br> amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)</p></li>
<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)</p></li>
<li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)</p></li>
<li><p><code>carbapenems()</code> can select: <br> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)</p></li>

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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="">2.1.1.9048</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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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@ -243,8 +243,8 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
@ -254,18 +254,18 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'AMP' (ampicillin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'CIP' (ciprofloxacin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S &lt;NA&gt; S S</span>

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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</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">
@ -211,7 +211,7 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2023) and CLSI (2011-2023).</p>
<p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2024) and CLSI (2011-2024).</p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>x</span>
@ -290,8 +290,8 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Meningitis'.</span>
@ -306,8 +306,8 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMX' (amoxicillin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Meningitis'.</span>

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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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
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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"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, N.
<!-- 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"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • 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"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, N.
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><title>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • 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"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir"><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023;
For veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.
All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -174,10 +174,10 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
</div>
<div class="ref-description section level2">
<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>N</code>.</p>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023;</p></li>
<li><p>ECOFFs (Epidemiological cut-off values): EUCAST 2020-2023 and CLSI 2022-2023.</p></li>
<p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>NI</code>.</p>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024;</p></li>
<li><p>ECOFFs (Epidemiological cut-off values): EUCAST 2020-2024 and CLSI 2022-2024.</p></li>
</ul><p>All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
</div>
@ -197,7 +197,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<span> S <span class="op">=</span> <span class="st">"^(S|U)+$"</span>,</span>
<span> I <span class="op">=</span> <span class="st">"^(I)+$"</span>,</span>
<span> R <span class="op">=</span> <span class="st">"^(R)+$"</span>,</span>
<span> N <span class="op">=</span> <span class="st">"^(N|V)+$"</span>,</span>
<span> NI <span class="op">=</span> <span class="st">"^(N|NI|V)+$"</span>,</span>
<span> SDD <span class="op">=</span> <span class="st">"^(SDD|D|H)+$"</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
@ -256,10 +256,10 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01//" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01//</a>.</p></li>
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2023, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
<p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2024, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01//" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01//</a>.</p></li>
<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2024, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
</ul></div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@ -275,7 +275,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dd><p>maximum fraction of invalid antimicrobial interpretations of <code>x</code>, see <em>Examples</em></p></dd>
<dt>S, I, R, N, SDD</dt>
<dt>S, I, R, NI, SDD</dt>
<dd><p>a case-independent <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to translate input to this result. This regular expression will be run <em>after</em> all non-letters and whitespaces are removed from the input.</p></dd>
@ -288,7 +288,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt>guideline</dt>
<dd><p>defaults to EUCAST 2023 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2023) and CLSI (2011-2023), see <em>Details</em>.</p></dd>
<dd><p>defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see <em>Details</em>.</p></dd>
<dt>uti</dt>
@ -345,7 +345,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<h3 id="how-it-works">How it Works<a class="anchor" aria-label="anchor" href="#how-it-works"></a></h3>
<p>The <code>as.sir()</code> function can work in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain valid values, namely: <strong>S</strong> for susceptible, <strong>I</strong> for intermediate or 'susceptible, increased exposure', <strong>R</strong> for resistant, <strong>N</strong> for non-interpretable, and <strong>SDD</strong> for susceptible dose-dependent. Each of these can be set using a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a>. Furthermore, <code>as.sir()</code> will try its best to clean with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is invalid.</p></li>
<p>The <code>as.sir()</code> function can work in four ways:</p><ol><li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain valid values, namely: <strong>S</strong> for susceptible, <strong>I</strong> for intermediate or 'susceptible, increased exposure', <strong>R</strong> for resistant, <strong>NI</strong> for non-interpretable, and <strong>SDD</strong> for susceptible dose-dependent. Each of these can be set using a <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a>. Furthermore, <code>as.sir()</code> will try its best to clean with some intelligence. For example, mixed values with SIR interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is invalid.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href="as.mic.html">as.mic()</a></code>, that also gives your columns the new data class <code><a href="as.mic.html">mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, SIR interpretation can be done very easily with either:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">your_data</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/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span>
<span><span class="va">your_data</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/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span>
@ -373,8 +373,8 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2023 and CLSI 2011-2023, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2023 and CLSI 2019-2023.</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2023"</code> or <code>"CLSI 2023"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024.</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2024"</code> or <code>"CLSI 2024"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>You can set the default guideline with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span>
@ -397,7 +397,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<h3 id="machine-readable-clinical-breakpoints">Machine-Readable Clinical Breakpoints<a class="anchor" aria-label="anchor" href="#machine-readable-clinical-breakpoints"></a></h3>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 29 883 rows and 13 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 34 085 rows and 13 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
</div>
<div class="section">
@ -406,7 +406,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<p>The function <code>is.sir()</code> detects if the input contains class <code>sir</code>. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
<p>The base R function <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> can be used to retrieve quantitative values from a <code>sir</code> object: <code>"S"</code> = 1, <code>"I"</code>/<code>"SDD"</code> = 2, <code>"R"</code> = 3. All other values are rendered <code>NA</code> . <strong>Note:</strong> Do not use <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code>, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.</p>
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or N and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
<p>The function <code>is_sir_eligible()</code> returns <code>TRUE</code> when a column contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R and/or NI and/or SDD), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> argument. If the input is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, it iterates over all columns and returns a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector.</p>
</div>
<p><code>NA_sir_</code> is a missing value of the new <code>sir</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
@ -472,98 +472,98 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> Mode :character Unique:90 %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #1 :B_ESCHR_COLI %I : 0.7% (n=11) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #2 :B_STPHY_CONS %R :73.7% (n=1201) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #3 :B_STPHY_AURS %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> #3 :B_STPHY_AURS %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :68.8% (n=251) %S :70.5% (n=665) %S :40.2% (n=543) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AMC AMP TZP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :71.4% (n=1342) %S :40.2% (n=543) %S :86.1% (n=862) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 4.8% (n=91) %I : 0.2% (n=3) %I : 1.3% (n=13) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CZO FEP CXM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :54.9% (n=245) %S :85.6% (n=620) %S :72.5% (n=1297) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.4% (n=2) %I : 0.1% (n=1) %I : 1.2% (n=22) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FOX CTX CAZ </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :71.6% (n=586) %S :84.4% (n=796) %S :33.5% (n=607) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 1.0% (n=8) %I : 0.1% (n=1) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CRO GEN TOB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :84.4% (n=796) %S :74.0% (n=1372) %S :65.1% (n=879) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.1% (n=1) %I : 1.5% (n=27) %I : 0.5% (n=7) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AMK KAN TMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :36.3% (n=251) %S : 0.0% (n=0) %S :61.2% (n=918) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.7% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SXT NIT FOS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :79.1% (n=1392) %S :76.0% (n=565) %S :57.8% (n=203) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.3% (n=6) %I : 6.9% (n=51) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> LNZ CIP MFX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :30.7% (n=314) %S :78.9% (n=1112) %S :64.5% (n=136) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 4.9% (n=69) %I : 1.9% (n=4) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> VAN TEC TCY </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :61.7% (n=1149) %S :24.3% (n=237) %S :68.3% (n=820) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 1.9% (n=23) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TGC DOX ERY </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :87.3% (n=697) %S :71.7% (n=814) %S :42.3% (n=801) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.6% (n=7) %I : 0.5% (n=9) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CLI AZM IPM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :38.6% (n=586) %S :42.3% (n=801) %S :92.7% (n=824) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.3% (n=4) %I : 0.5% (n=9) %I : 1.1% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> MEM MTR CHL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :94.1% (n=780) %S :85.3% (n=29) %S :78.6% (n=121) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> COL MUP RIF </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :18.8% (n=309) %S :93.0% (n=251) %S :30.2% (n=303) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 1.1% (n=3) %I : 0.2% (n=2) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %N : 0.0% (n=0) %N : 0.0% (n=0) %N : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
<span class="r-in"><span></span></span>
@ -580,18 +580,18 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'CIP' (ciprofloxacin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'GEN' (gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'TOB' (tobramycin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
@ -603,19 +603,19 @@ 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: 13 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo input</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-13 <span style="color: #949494;">18:59:07</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-13 <span style="color: #949494;">18:59:02</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-06-13 <span style="color: #949494;">18:59:01</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-06-14 <span style="color: #949494;">20:46:45</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-06-14 <span style="color: #949494;">20:46:40</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-06-14 <span style="color: #949494;">20:46:39</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-06-14 <span style="color: #949494;">20:46:39</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 7 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, host &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
<span class="r-in"><span></span></span>
@ -629,8 +629,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Non-meningitis'.</span>
@ -646,8 +646,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'ampicillin' (AMP), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R</span>
@ -685,104 +685,104 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2024...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
@ -793,8 +793,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'NIT' (nitrofurantoin), EUCAST 2024...</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
@ -802,25 +802,25 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'AMP' (ampicillin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'CIP' (ciprofloxacin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'GEN' (gentamicin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'TOB' (tobramycin), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism AMP CIP GEN TOB ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S &lt;NA&gt; S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For CLEANING existing SIR values ------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): 3 results in column '24' truncated (38%) that were invalid</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B", and "C"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R N &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S SDD I R NI &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="st">"&lt;= 0.002; S"</span><span class="op">)</span> <span class="co"># will return "S"</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S</span>
@ -833,10 +833,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-plt img"><img src="as.sir-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</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://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 3 4 5 NA</span>
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"N"</span>, <span class="cn">NA</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://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 2 3 NA NA</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># the dplyr way</span></span></span>

2
reference/atc_online.html
View File

@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_from_text.html
View File

@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_property.html
View File

@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/availability.html
View File

@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</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">

72
reference/bug_drug_combinations.html
View File

@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</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">
@ -275,15 +275,15 @@
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R N total</span>
<span class="r-out co"><span class="r-pr">#&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;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> (unknown species) AMC 15 0 0 0 0 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> (unknown species) AMK 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> (unknown species) AMP 15 0 0 1 0 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 0 1 0 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AZM 3 0 0 3 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI total N </span>
<span class="r-out co"><span class="r-pr">#&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;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> (unknown species) AMC 15 0 0 0 0 15 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> (unknown species) AMK 0 0 0 0 0 0 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> (unknown species) AMP 15 0 0 1 0 16 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 0 1 0 16 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AZM 3 0 0 3 0 6 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0 <span style="color: #BB0000;">NA</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
@ -307,19 +307,19 @@
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_gramstain</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R N total</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative AMC 463 0 89 174 0 726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative AMK 251 0 0 5 0 256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative AMP 226 0 0 405 0 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 0 405 0 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AZM 1 0 2 696 0 699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative CAZ 607 0 0 27 0 634</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative CHL 1 0 0 30 0 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP 610 0 11 63 0 684</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 0 1 709 0 728</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 0 78 0 387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI total N </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative AMC 463 0 89 174 0 726 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative AMK 251 0 0 5 0 256 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative AMP 226 0 0 405 0 631 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 0 405 0 631 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AZM 1 0 2 696 0 699 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative CAZ 607 0 0 27 0 634 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative CHL 1 0 0 30 0 31 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP 610 0 11 63 0 684 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 0 1 709 0 728 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 0 78 0 387 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span></span></span>
@ -331,19 +331,19 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">}</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R N total</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E. coli AMC 332 0 74 61 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli AMK 171 0 0 0 0 171</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. coli AMP 196 0 0 196 0 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 0 196 0 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E. coli AZM 0 0 0 467 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E. coli CAZ 449 0 0 11 0 460</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E. coli CHL 0 0 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E. coli CIP 398 0 1 57 0 456</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 0 467 0 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 0 0 240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S SDD I R NI total N </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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E. coli AMC 332 0 74 61 0 467 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli AMK 171 0 0 0 0 171 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. coli AMP 196 0 0 196 0 392 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 0 196 0 392 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E. coli AZM 0 0 0 467 0 467 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E. coli CAZ 449 0 0 11 0 460 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E. coli CHL 0 0 0 0 0 0 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E. coli CIP 398 0 1 57 0 456 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 0 467 0 467 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 0 0 240 <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span><span class="co"># }</span></span></span>

40
reference/clinical_breakpoints.html
View File

@ -1,10 +1,10 @@
<!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"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2024 and CLSI 2011-2024.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2024 and CLSI 2019-2024.
Use as.sir() to transform MICs or disks measurements to SIR values."><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • 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"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2024 and CLSI 2011-2024.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2024 and CLSI 2019-2024.
Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@ -16,7 +16,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<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="">2.1.1.9048</small>
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@ -167,8 +167,8 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="ref-description section level2">
<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.</p>
<p>Currently available breakpoint guidelines for <strong>clinical microbiology</strong> are EUCAST 2011-2023 and CLSI 2011-2023.</p>
<p>Currently available breakpoint guidelines for <strong>veterinary microbiology</strong> are EUCAST 2021-2023 and CLSI 2019-2023.</p>
<p>Currently available breakpoint guidelines for <strong>clinical microbiology</strong> are EUCAST 2011-2024 and CLSI 2011-2024.</p>
<p>Currently available breakpoint guidelines for <strong>veterinary microbiology</strong> are EUCAST 2021-2024 and CLSI 2019-2024.</p>
<p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
</div>
@ -179,7 +179,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 29 883 observations and 13 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 34 085 observations and 13 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
<li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"</p></li>
<li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
@ -235,20 +235,20 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 29,883 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 34,085 × 13</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> guideline type host method site mo rank_index ab ref_tbl </span>
<span class="r-out co"><span class="r-pr">#&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 style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&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> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2023 human human DISK <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2023 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2023 human human MIC <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2023 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 29,873 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2024 human human DISK <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2024 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2024 human human MIC <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2024 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 34,075 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4 more variables: disk_dose &lt;chr&gt;, breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># uti &lt;lgl&gt;</span></span>
</code></pre></div>

2
reference/count.html
View File

@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 30 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li>
<li><p>antifungals<br>(amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>carbapenems<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)</p></li>

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<code><a href="microorganisms.codes.html">microorganisms.codes</a></code>
</dt>
<dd>Data Set with 4 958 Common Microorganism Codes</dd>
<dd>Data Set with 4 972 Common Microorganism Codes</dd>
</dl><dl><dt>
<code><a href="microorganisms.groups.html">microorganisms.groups</a></code>
@ -450,7 +450,7 @@
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code>
</dt>
<dd>Data Sets with 604 Antimicrobial Drugs</dd>
<dd>Data Sets with 605 Antimicrobial Drugs</dd>
</dl><dl><dt>
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@ -154,7 +154,7 @@
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 958 Common Microorganism Codes</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 972 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>microorganisms.codes.Rd</code></div>
</div>
@ -170,7 +170,7 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 4 958 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em>This is a unique identifier.</em></p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 4 972 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em>This is a unique identifier.</em></p></li>
<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
</ul></div>
<div class="section level2">
@ -185,7 +185,7 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms.codes</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,958 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,972 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> code mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&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> 1011 B_GRAMP </span>
@ -198,7 +198,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100 B_STRPT </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101 B_STRPT_VIRI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102 B_STRPT_HAEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,948 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,962 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
<span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span>

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@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -12,7 +12,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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@ -349,7 +349,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<div class="section level2">
<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 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 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>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>
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -203,7 +203,7 @@
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The base <span style="R">R</span> function <code><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample()</a></code> is used for generating values.</p>
<p>Generated values are based on the EUCAST 2023 guideline as implemented in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
<p>Generated values are based on the EUCAST 2024 guideline as implemented in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/translate.html
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@ -10,7 +10,7 @@
<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="">2.1.1.9048</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9049</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
search.json
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