P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:47:54 +02:00
Code Releases Activity

Built site for AMR: 2.0.0.9024@f065945

Browse Source
This commit is contained in:
github-actions
2023-06-22 13:20:36 +00:00
parent a061a2a482
commit 9fabe8ad02
117 changed files with 476 additions and 407 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
articles/AMR.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@ -204,7 +204,7 @@
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 27 May 2023.</p>
generated on 22 June 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-05-27</td>
<td align="center">2023-06-22</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">2023-05-27</td>
<td align="center">2023-06-22</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">2023-05-27</td>
<td align="center">2023-06-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -405,11 +405,11 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
<span><span class="co">#&gt; Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
<span><span class="co">#&gt; argenteus (0.625), Staphylococcus aureus anaerobius (0.625),</span></span>
<span><span class="co">#&gt; Streptomyces argenteolus (0.483), Streptomyces aureus (0.474),</span></span>
<span><span class="co">#&gt; Streptomyces azureus (0.467), Streptomyces aureorectus (0.444),</span></span>
<span><span class="co">#&gt; Streptomyces auratus (0.433), Streptomyces aurantiogriseus (0.429), and</span></span>
<span><span class="co">#&gt; Streptomyces aureocirculatus (0.429)</span></span>
<span><span class="co">#&gt; argenteus (0.625), Staphylococcus aureus anaerobius (0.625), Salmonella</span></span>
<span><span class="co">#&gt; Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella Amounderness</span></span>
<span><span class="co">#&gt; (0.587), Selenomonas artemidis (0.571), Salmonella choleraesuis</span></span>
<span><span class="co">#&gt; arizonae (0.562), Streptococcus anginosus anginosus (0.561), and</span></span>
<span><span class="co">#&gt; Salmonella Abaetetuba (0.548)</span></span>
<span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
<span><span class="co">#&gt; "S. pneumoniae" -&gt; Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
<span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Serratia</span></span>

4
articles/EUCAST.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@ -216,7 +216,7 @@ recommendations for reporting particular resistances.</em></p>
<p>In Europe, a lot of medical microbiological laboratories already
apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown
<em>et al.</em>, 2015</a>). Our package features their latest insights
on intrinsic resistance and unusual phenotypes (v3.3, 2021).</p>
on intrinsic resistance and unusual phenotypes (v3.1, 2016).</p>
<p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this
purpose can also apply additional rules, like forcing
<help title="ATC: J01CA01">ampicillin</help> = R in isolates when

62
articles/MDR.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@ -402,19 +402,19 @@ 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 R S S R R S</span></span>
<span><span class="co">#&gt; 2 R R I I S S</span></span>
<span><span class="co">#&gt; 3 S R S S I S</span></span>
<span><span class="co">#&gt; 4 R R S R R R</span></span>
<span><span class="co">#&gt; 5 I I I S R R</span></span>
<span><span class="co">#&gt; 6 S I R R S R</span></span>
<span><span class="co">#&gt; 1 R S R I I R</span></span>
<span><span class="co">#&gt; 2 I I I R S I</span></span>
<span><span class="co">#&gt; 3 R S I R I R</span></span>
<span><span class="co">#&gt; 4 S S I I S I</span></span>
<span><span class="co">#&gt; 5 I S R S I R</span></span>
<span><span class="co">#&gt; 6 R R I S S I</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 I</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<span><span class="co">#&gt; 1 I</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 R</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 S</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">
@ -455,40 +455,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3225</td>
<td align="right">64.50%</td>
<td align="right">3225</td>
<td align="right">64.50%</td>
<td align="right">3262</td>
<td align="right">65.24%</td>
<td align="right">3262</td>
<td align="right">65.24%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">963</td>
<td align="right">19.26%</td>
<td align="right">4188</td>
<td align="right">83.76%</td>
<td align="right">923</td>
<td align="right">18.46%</td>
<td align="right">4185</td>
<td align="right">83.70%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">478</td>
<td align="right">9.56%</td>
<td align="right">4666</td>
<td align="right">93.32%</td>
<td align="right">446</td>
<td align="right">8.92%</td>
<td align="right">4631</td>
<td align="right">92.62%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">228</td>
<td align="right">4.56%</td>
<td align="right">4894</td>
<td align="right">97.88%</td>
<td align="right">258</td>
<td align="right">5.16%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">106</td>
<td align="right">2.12%</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
articles/PCA.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@ -307,7 +307,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

2
articles/WHONET.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

94
articles/datasets.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@ -193,7 +193,7 @@
<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">27 May 2023</h4>
<h4 data-toc-skip class="date">22 June 2023</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>
@ -913,68 +913,70 @@ 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 18 271 rows and 11 columns, containing the following
<p>A data set with 42 599 rows and 12 columns, containing the following
column names:<br><em>guideline</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>
<em>breakpoint_S</em>, <em>breakpoint_R</em>, <em>ecoff</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 20 April 2023 13:20:41 UTC. Find more info
<p>It was last updated on 22 June 2023 13:10:59 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> (43 kB)<br>
R Data Structure (RDS) file</a> (82 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> (1.9 MB)<br>
text file</a> (4.4 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> (0.8 MB)<br>
Excel workbook</a> (1.8 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> (0.7 MB)<br>
Feather file</a> (1.6 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> (88 kB)<br>
Parquet file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sas" class="external-link">SAS
data (SAS) file</a> (3.6 MB)<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> (3.4 MB)<br>
transport (XPT) file</a> (10.6 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> (2.3 MB)<br>
SPSS Statistics data file</a> (5.8 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> (3.3 MB)</li>
DTA file</a> (10.5 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 (2013-2022) and EUCAST
(2013-2022).</p>
diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
(2011-2023).</p>
</div>
<div class="section level3">
<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
</h3>
<table style="width:100%;" class="table">
<colgroup>
<col width="8%">
<col width="5%">
<col width="7%">
<col width="4%">
<col width="3%">
<col width="8%">
<col width="14%">
<col width="7%">
<col width="3%">
<col width="10%">
<col width="8%">
<col width="9%">
<col width="7%">
<col width="6%">
<col width="8%">
<col width="8%">
<col width="4%">
<col width="4%">
</colgroup>
<thead><tr class="header">
<th align="center">guideline</th>
@ -989,11 +991,12 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<th align="center">disk_dose</th>
<th align="center">breakpoint_S</th>
<th align="center">breakpoint_R</th>
<th align="center">ecoff</th>
<th align="center">uti</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_ASPRG_MGTS</td>
@ -1005,10 +1008,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_ASPRG_NIGR</td>
@ -1020,10 +1024,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_ALBC</td>
@ -1035,10 +1040,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_DBLN</td>
@ -1050,10 +1056,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_GLBR</td>
@ -1065,10 +1072,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2022</td>
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_KRUS</td>
@ -1080,6 +1088,7 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">FALSE</td>
</tr>
</tbody>
@ -1380,13 +1389,13 @@ v3.3</a> (2021).</p>
<h2 id="dosage-dosage-guidelines-from-eucast">
<code>dosage</code>: Dosage Guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-dosage-guidelines-from-eucast"></a>
</h2>
<p>A data set with 336 rows and 9 columns, containing the following
<p>A data set with 503 rows and 9 columns, containing the following
column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
<em>dose_times</em>, <em>administration</em>, <em>notes</em>,
<em>original_txt</em>, and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you
load the <code>AMR</code> package.</p>
<p>It was last updated on 14 November 2022 14:20:39 UTC. Find more info
<p>It was last updated on 22 June 2023 13:10:59 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -1394,28 +1403,28 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
R Data Structure (RDS) file</a> (3 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">tab-separated
text file</a> (29 kB)<br>
text file</a> (43 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Microsoft
Excel workbook</a> (19 kB)<br>
Excel workbook</a> (25 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache
Feather file</a> (16 kB)<br>
Feather file</a> (21 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache
Parquet file</a> (8 kB)<br>
Parquet file</a> (9 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
data (SAS) file</a> (92 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xpt" class="external-link">SAS
transport (XPT) file</a> (79 kB)<br>
transport (XPT) file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM
SPSS Statistics data file</a> (43 kB)<br>
SPSS Statistics data file</a> (64 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
DTA file</a> (82 kB)</li>
DTA file</a> (0.1 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
@ -1423,8 +1432,9 @@ DTA file</a> (82 kB)</li>
<p>EUCAST breakpoints used in this package are based on the dosages in
this data set.</p>
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v11.0</a> (2021) and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v12.0</a> (2022).</p>
Breakpoint Tables’ v11.0</a> (2021), <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v12.0</a> (2022), and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v13.0</a> (2023).</p>
</div>
<div class="section level3">
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
@ -1462,7 +1472,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">25-30 mg/kg x 1 iv</td>
<td align="center">12</td>
<td align="center">13</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1473,7 +1483,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">2 g x 6 iv</td>
<td align="center">12</td>
<td align="center">13</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1484,7 +1494,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<td align="center">iv</td>
<td align="center"></td>
<td align="center">1 g x 3-4 iv</td>
<td align="center">12</td>
<td align="center">13</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1495,7 +1505,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.75-1 g x 3 oral</td>
<td align="center">12</td>
<td align="center">13</td>
</tr>
<tr class="odd">
<td align="center">AMX</td>
@ -1506,7 +1516,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">12</td>
<td align="center">13</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
@ -1517,7 +1527,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<td align="center">oral</td>
<td align="center"></td>
<td align="center">0.5 g x 3 oral</td>
<td align="center">12</td>
<td align="center">13</td>
</tr>
</tbody>
</table>

2
articles/index.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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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
articles/other_pkg.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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
articles/resistance_predict.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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
articles/welcome_to_AMR.html
View File

@ -38,7 +38,7 @@
<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="">2.0.0.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">