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@ -401,19 +401,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 S I R I S I</span></span>
<span><span class="co">#&gt; 2 S R I S S R</span></span>
<span><span class="co">#&gt; 3 S I S R I S</span></span>
<span><span class="co">#&gt; 4 I S R R S S</span></span>
<span><span class="co">#&gt; 5 S R R S S I</span></span>
<span><span class="co">#&gt; 6 R S S I R S</span></span>
<span><span class="co">#&gt; 1 R I S I I I</span></span>
<span><span class="co">#&gt; 2 S R S I I I</span></span>
<span><span class="co">#&gt; 3 R R I R I R</span></span>
<span><span class="co">#&gt; 4 R S S S R S</span></span>
<span><span class="co">#&gt; 5 I I R I S I</span></span>
<span><span class="co">#&gt; 6 R R I I S R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -454,40 +454,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3243</td>
<td align="right">64.86%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">946</td>
<td align="right">18.92%</td>
<td align="right">4189</td>
<td align="right">83.78%</td>
<td align="right">989</td>
<td align="right">19.78%</td>
<td align="right">4182</td>
<td align="right">83.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">439</td>
<td align="right">8.78%</td>
<td align="right">4628</td>
<td align="right">92.56%</td>
<td align="right">451</td>
<td align="right">9.02%</td>
<td align="right">4633</td>
<td align="right">92.66%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">272</td>
<td align="right">5.44%</td>
<td align="right">4900</td>
<td align="right">98.00%</td>
<td align="right">270</td>
<td align="right">5.40%</td>
<td align="right">4903</td>
<td align="right">98.06%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">100</td>
<td align="right">2.00%</td>
<td align="right">97</td>
<td align="right">1.94%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

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@ -270,8 +270,8 @@ and the Global Biodiversity Information Facility (GBIF):</p>
with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong>
International Journal of Systematic and Evolutionary Microbiology, 70,
5607-5612; . Accessed from <a href="https://lpsn.dsmz.de" class="external-link uri">https://lpsn.dsmz.de</a> on December 11th, 2022.</li>
<li>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset .
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on December 11th, 2022.</li>
<li>GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset .
Accessed from <a href="https://www.gbif.org" class="external-link uri">https://www.gbif.org</a> on January 8th, 2024.</li>
<li>Public Health Information Network Vocabulary Access and Distribution
System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value
Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link uri">https://phinvads.cdc.gov</a>

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index.html
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@ -42,7 +42,7 @@
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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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@ -159,23 +159,23 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9008" id="amr-2119008">AMR 2.1.1.9008<a class="anchor" aria-label="anchor" href="#amr-2119008"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9009" id="amr-2119009">AMR 2.1.1.9009<a class="anchor" aria-label="anchor" href="#amr-2119009"></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 level3">
<h3 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9008">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-2-1-1-9008"></a></h3>
<h3 id="a-new-milestone-one-health-support--human--veterinary--environmental-2-1-1-9009">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-2-1-1-9009"></a></h3>
<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. * <code><a href="../reference/as.sir.html">as.sir()</a></code> now supports 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. * 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>. * The <code>antibiotics</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well. * <code><a href="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antibiotics (that all start with “Q”) * <code><a href="../reference/ab_property.html">ab_url()</a></code> now supports retrieving the WHOCC url of their ATCvet pages</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9008">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9008"></a></h3>
<h3 id="breaking-2-1-1-9009">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9009"></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-functions-2-1-1-9008">New functions<a class="anchor" aria-label="anchor" href="#new-functions-2-1-1-9008"></a></h3>
<h3 id="new-functions-2-1-1-9009">New functions<a class="anchor" aria-label="anchor" href="#new-functions-2-1-1-9009"></a></h3>
<ul><li>The 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>
<code><a href="../reference/as.mic.html">limit_mic_range()</a></code>, which allows to limit 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>
</ul><div class="section level4">
<h4 id="changed-2-1-1-9008">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9008"></a></h4>
<h4 id="changed-2-1-1-9009">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9009"></a></h4>
<ul><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">limit_mic_range()</a></code> and <code>scale_*_mic()</code> functions.</li>

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pkgdown.yml
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@ -11,7 +11,7 @@ articles:
other_pkg: other_pkg.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2024-02-24T17:55Z
last_built: 2024-02-24T18:29Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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@ -10,7 +10,7 @@
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@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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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="">2.1.1.9008</small>
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2
reference/age.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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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2
reference/age_groups.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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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2
reference/antibiogram.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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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2
reference/antibiotic_class_selectors.html
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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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2
reference/antibiotics.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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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2
reference/as.ab.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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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2
reference/as.av.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="">2.1.1.9008</small>
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2
reference/as.disk.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="">2.1.1.9008</small>
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2
reference/as.mic.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="">2.1.1.9008</small>
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2
reference/as.mo.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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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28
reference/as.sir.html
View File

@ -24,7 +24,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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@ -592,19 +592,19 @@ 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> 2024-02-24 <span style="color: #949494;">17:56:35</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> 2024-02-24 <span style="color: #949494;">17:56:35</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> 2024-02-24 <span style="color: #949494;">17:56:35</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> 2024-02-24 <span style="color: #949494;">17:56:34</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> 2024-02-24 <span style="color: #949494;">17:56:30</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> 2024-02-24 <span style="color: #949494;">17:56:30</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> 2024-02-24 <span style="color: #949494;">17:56:30</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> 2024-02-24 <span style="color: #949494;">17:56:30</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> 2024-02-24 <span style="color: #949494;">17:56:30</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> 2024-02-24 <span style="color: #949494;">17:56:30</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> 2024-02-24 <span style="color: #949494;">17:56:29</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> 2024-02-24 <span style="color: #949494;">17:56:29</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> 2024-02-24 <span style="color: #949494;">17:56:29</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> 2024-02-24 <span style="color: #949494;">18:30:30</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> 2024-02-24 <span style="color: #949494;">18:30:30</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> 2024-02-24 <span style="color: #949494;">18:30:30</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> 2024-02-24 <span style="color: #949494;">18:30:30</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:25</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> 2024-02-24 <span style="color: #949494;">18:30:24</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>

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="">2.1.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9009</small>
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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>
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2
reference/av_property.html
View File

@ -10,7 +10,7 @@
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2
reference/availability.html
View File

@ -10,7 +10,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9008</small>
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reference/bug_drug_combinations.html
View File

@ -10,7 +10,7 @@
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2
reference/clinical_breakpoints.html
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@ -16,7 +16,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/count.html
View File

@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/dosage.html
View File

@ -10,7 +10,7 @@
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2
reference/eucast_rules.html
View File

@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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2
reference/example_isolates.html
View File

@ -10,7 +10,7 @@
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2
reference/example_isolates_unclean.html
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@ -10,7 +10,7 @@
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2
reference/first_isolate.html
View File

@ -12,7 +12,7 @@
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2
reference/g.test.html
View File

@ -10,7 +10,7 @@
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2
reference/get_episode.html
View File

@ -10,7 +10,7 @@
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reference/ggplot_pca.html
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@ -10,7 +10,7 @@
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reference/ggplot_sir.html
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@ -10,7 +10,7 @@
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reference/guess_ab_col.html
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@ -10,7 +10,7 @@
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reference/index.html
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@ -10,7 +10,7 @@
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reference/intrinsic_resistant.html
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@ -10,7 +10,7 @@
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reference/italicise_taxonomy.html
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@ -10,7 +10,7 @@
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reference/join.html
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@ -10,7 +10,7 @@
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reference/key_antimicrobials.html
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@ -10,7 +10,7 @@
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reference/kurtosis.html
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@ -10,7 +10,7 @@
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reference/like.html
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@ -10,7 +10,7 @@
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reference/mdro.html
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reference/mean_amr_distance.html
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@ -10,7 +10,7 @@
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reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
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reference/microorganisms.groups.html
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@ -10,7 +10,7 @@
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reference/microorganisms.html
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@ -10,7 +10,7 @@
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reference/mo_matching_score.html
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@ -10,7 +10,7 @@
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reference/mo_property.html
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@ -10,7 +10,7 @@
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reference/mo_source.html
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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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reference/pca.html
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@ -10,7 +10,7 @@
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reference/plot.html
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@ -12,7 +12,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@ -10,7 +10,7 @@
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reference/resistance_predict.html
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@ -10,7 +10,7 @@
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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
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reference/translate.html
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search.json
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