P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-05-01 23:03:58 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9268: 2461631

Browse Source
This commit is contained in:
github-actions 2025-05-01 12:53:35 +00:00
parent dd091f606e
commit ac714f6778
79 changed files with 381 additions and 570 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
404.html
View File

@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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
LICENSE-text.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">

44
articles/AMR.html
View File

@ -5,7 +5,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>How to conduct AMR data analysis • AMR (for R)</title>
<title>Conduct AMR data analysis • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
<link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
<link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@ -18,7 +18,7 @@
<link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to conduct AMR data analysis">
<script src="../extra.js"></script><meta property="og:title" content="Conduct AMR data analysis">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -78,7 +78,7 @@
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Conduct AMR data analysis</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
@ -1147,8 +1147,8 @@ incidence and antimicrobial susceptibility patterns.</p>
</tr></thead>
<tbody><tr class="odd">
<td align="left">69.4% (64.3-74.3%)</td>
<td align="left">92.6% (91.2-93.8%)</td>
<td align="left">88.7% (85.9-91.2%)</td>
<td align="left">92.6% (91.1-93.9%)</td>
<td align="left">88.7% (85.8-91.2%)</td>
</tr></tbody>
</table>
<p>WISCA uses a <strong>Bayesian decision model</strong> to integrate
@ -1190,57 +1190,57 @@ function on a grouped <code>tibble</code>, i.e., using
<td align="left">0-24</td>
<td align="left">F</td>
<td align="left">56.6% (25.2-83.9%)</td>
<td align="left">74% (50.5-91.9%)</td>
<td align="left">68% (39.7-88.9%)</td>
<td align="left">73.6% (48-91.6%)</td>
<td align="left">68.6% (42.9-89.5%)</td>
</tr>
<tr class="even">
<td align="left">0-24</td>
<td align="left">M</td>
<td align="left">60.3% (28.4-87.1%)</td>
<td align="left">79.3% (59.5-94.2%)</td>
<td align="left">60.1% (29.3-87.5%)</td>
<td align="left">79.7% (57.6-94.2%)</td>
<td align="left">60.1% (29.5-87.7%)</td>
</tr>
<tr class="odd">
<td align="left">25-49</td>
<td align="left">F</td>
<td align="left">66.6% (45.6-85.5%)</td>
<td align="left">91.8% (85.1-96.5%)</td>
<td align="left">82.6% (66.7-93.9%)</td>
<td align="left">91.7% (84.6-96.7%)</td>
<td align="left">83% (67.9-94%)</td>
</tr>
<tr class="even">
<td align="left">25-49</td>
<td align="left">M</td>
<td align="left">56.4% (29.1-81.7%)</td>
<td align="left">89.5% (80-95.6%)</td>
<td align="left">72.2% (47.1-90%)</td>
<td align="left">89.2% (80.3-95.7%)</td>
<td align="left">72.4% (49.7-90%)</td>
</tr>
<tr class="odd">
<td align="left">50-74</td>
<td align="left">F</td>
<td align="left">67.8% (55.8-80.1%)</td>
<td align="left">95.6% (93.2-97.7%)</td>
<td align="left">88% (80.2-94.2%)</td>
<td align="left">95.6% (93.2-97.5%)</td>
<td align="left">88.1% (80.4-94.6%)</td>
</tr>
<tr class="even">
<td align="left">50-74</td>
<td align="left">M</td>
<td align="left">66.2% (54.8-75.8%)</td>
<td align="left">95.3% (92.5-97.4%)</td>
<td align="left">84.2% (75.2-92.4%)</td>
<td align="left">95.2% (92.4-97.4%)</td>
<td align="left">84.4% (74.4-92.5%)</td>
</tr>
<tr class="odd">
<td align="left">75+</td>
<td align="left">F</td>
<td align="left">71.7% (61-81.7%)</td>
<td align="left">96.5% (94.4-98.2%)</td>
<td align="left">90.7% (84.4-95.7%)</td>
<td align="left">96.6% (94.4-98.2%)</td>
<td align="left">90.6% (84.6-95.3%)</td>
</tr>
<tr class="even">
<td align="left">75+</td>
<td align="left">M</td>
<td align="left">72.9% (63.8-82%)</td>
<td align="left">96.6% (94.5-98.1%)</td>
<td align="left">92.8% (87.6-96.3%)</td>
<td align="left">96.6% (94.6-98.1%)</td>
<td align="left">92.8% (87.8-96.5%)</td>
</tr>
</tbody>
</table>

2
articles/AMR_for_Python.html
View File

@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">

6
articles/AMR_with_tidymodels.html
View File

@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -89,8 +89,8 @@
<blockquote>
<p>This page was entirely written by our <a href="https://chat.amr-for-r.org" class="external-link">AMR for R Assistant</a>, a ChatGPT
manually-trained model able to answer any question about the AMR
package.</p>
manually-trained model able to answer any question about the
<code>AMR</code> package.</p>
</blockquote>
<p>Antimicrobial resistance (AMR) is a global health crisis, and
understanding resistance patterns is crucial for managing effective

8
articles/EUCAST.html
View File

@ -5,7 +5,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>How to apply EUCAST rules • AMR (for R)</title>
<title>Apply EUCAST rules • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
<link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
<link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@ -18,7 +18,7 @@
<link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to apply EUCAST rules">
<script src="../extra.js"></script><meta property="og:title" content="Apply EUCAST rules">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -78,7 +78,7 @@
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>How to apply EUCAST rules</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Apply EUCAST rules</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>

8
articles/MDR.html
View File

@ -5,7 +5,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>How to determine multi-drug resistance (MDR) • AMR (for R)</title>
<title>Determine multi-drug resistance (MDR) • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
<link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
<link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@ -18,7 +18,7 @@
<link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to determine multi-drug resistance (MDR)">
<script src="../extra.js"></script><meta property="og:title" content="Determine multi-drug resistance (MDR)">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -78,7 +78,7 @@
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>How to determine multi-drug resistance (MDR)</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Determine multi-drug resistance (MDR)</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>

8
articles/PCA.html
View File

@ -5,7 +5,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>How to conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
<title>Conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
<link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
<link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@ -18,7 +18,7 @@
<link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to conduct principal component analysis (PCA) for AMR">
<script src="../extra.js"></script><meta property="og:title" content="Conduct principal component analysis (PCA) for AMR">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -78,7 +78,7 @@
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct principal component analysis (PCA) for AMR</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Conduct principal component analysis (PCA) for AMR</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>

8
articles/WHONET.html
View File

@ -5,7 +5,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>How to work with WHONET data • AMR (for R)</title>
<title>Work with WHONET data • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
<link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
<link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@ -18,7 +18,7 @@
<link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to work with WHONET data">
<script src="../extra.js"></script><meta property="og:title" content="Work with WHONET data">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -78,7 +78,7 @@
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>How to work with WHONET data</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Work with WHONET data</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WHONET.Rmd" class="external-link"><code>vignettes/WHONET.Rmd</code></a></small>

662
articles/WISCA.html
View File

@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -87,6 +87,11 @@
<blockquote>
<p>This explainer was largely written by our <a href="https://chat.amr-for-r.org" class="external-link">AMR for R Assistant</a>, a ChatGPT
manually-trained model able to answer any question about the
<code>AMR</code> package.</p>
</blockquote>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -94,33 +99,40 @@
<em>probabilistic reasoning</em>: what is the chance that a regimen will
cover the likely infecting organisms, before culture results are
available?</p>
<p>This is the purpose of <strong>WISCA</strong>, or:</p>
<blockquote>
<p><strong>Weighted-Incidence Syndromic Combination
Antibiogram</strong></p>
</blockquote>
<p>WISCA is a Bayesian approach that integrates: - <strong>Pathogen
prevalence</strong> (how often each species causes the syndrome), -
<p>This is the purpose of <strong>WISCA</strong>, or
<strong>Weighted-Incidence Syndromic Combination
Antibiogram</strong>.</p>
<p>WISCA is a Bayesian approach that integrates:</p>
<ul>
<li>
<strong>Pathogen prevalence</strong> (how often each species causes
the syndrome),</li>
<li>
<strong>Regimen susceptibility</strong> (how often a regimen works
<em>if</em> the pathogen is known),</p>
<em>if</em> the pathogen is known),</li>
</ul>
<p>to estimate the <strong>overall empirical coverage</strong> of
antimicrobial regimens — with quantified uncertainty.</p>
antimicrobial regimens, with quantified uncertainty.</p>
<p>This vignette explains how WISCA works, why it is useful, and how to
apply it in <strong>AMR</strong>.</p>
<hr>
apply it using the <code>AMR</code> package.</p>
</div>
<div class="section level2">
<h2 id="why-traditional-antibiograms-fall-short">Why traditional antibiograms fall short<a class="anchor" aria-label="anchor" href="#why-traditional-antibiograms-fall-short"></a>
</h2>
<p>A standard antibiogram gives you:</p>
<p>``` Species → Antibiotic → Susceptibility %</p>
<pre><code>Species → Antibiotic → Susceptibility %</code></pre>
<p>But clinicians don’t know the species <em>a priori</em>. They need to
choose a regimen that covers the <strong>likely pathogens</strong> —
choose a regimen that covers the <strong>likely pathogens</strong>,
without knowing which one is present.</p>
<p>Traditional antibiograms: - Fragment information by organism, - Do
not weight by real-world prevalence, - Do not account for combination
therapy or sample size, - Do not provide uncertainty.</p>
<hr>
<p>Traditional antibiograms calculate the susceptibility % as just the
number of resistant isolates divided by the total number of tested
isolates. Therefore, traditional antibiograms:</p>
<ul>
<li>Fragment information by organism,</li>
<li>Do not weight by real-world prevalence,</li>
<li>Do not account for combination therapy or sample size,</li>
<li>Do not provide uncertainty.</li>
</ul>
</div>
<div class="section level2">
<h2 id="the-idea-of-wisca">The idea of WISCA<a class="anchor" aria-label="anchor" href="#the-idea-of-wisca"></a>
@ -130,21 +142,31 @@ therapy or sample size, - Do not provide uncertainty.</p>
<p>“What is the <strong>probability</strong> that this regimen
<strong>will cover</strong> the pathogen, given the syndrome?”</p>
</blockquote>
<p>This means combining two things: - <strong>Incidence</strong> of each
pathogen in the syndrome, - <strong>Susceptibility</strong> of each
pathogen to the regimen.</p>
<p>This means combining two things:</p>
<ul>
<li>
<strong>Incidence</strong> of each pathogen in the syndrome,</li>
<li>
<strong>Susceptibility</strong> of each pathogen to the
regimen.</li>
</ul>
<p>We can write this as:</p>
<p>``` coverage = ∑ (pathogen incidence × susceptibility)</p>
<p>For example, suppose: - E. coli causes 60% of cases, and 90% of
<em>E. coli</em> are susceptible to a drug. - Klebsiella causes 40% of
cases, and 70% of <em>Klebsiella</em> are susceptible.</p>
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munder><mo>∑</mo><mi>i</mi></munder><mrow><mo stretchy="true" form="prefix">(</mo><msub><mtext mathvariant="normal">Incidence</mtext><mi>i</mi></msub><mo>×</mo><msub><mtext mathvariant="normal">Susceptibility</mtext><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_i (\text{Incidence}_i \times \text{Susceptibility}_i)</annotation></semantics></math></p>
<p>For example, suppose:</p>
<ul>
<li>
<em>E. coli</em> causes 60% of cases, and 90% of <em>E. coli</em>
are susceptible to a drug.</li>
<li>
<em>Klebsiella</em> causes 40% of cases, and 70% of
<em>Klebsiella</em> are susceptible.</li>
</ul>
<p>Then:</p>
<p>``` coverage = (0.6 × 0.9) + (0.4 × 0.7) = 0.82</p>
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.6</mn><mo>×</mo><mn>0.9</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>+</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.4</mn><mo>×</mo><mn>0.7</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>0.82</mn></mrow><annotation encoding="application/x-tex">\text{Coverage} = (0.6 \times 0.9) + (0.4 \times 0.7) = 0.82</annotation></semantics></math></p>
<p>But in real data, incidence and susceptibility are <strong>estimated
from samples</strong> — so they carry uncertainty. WISCA models this
from samples</strong>, so they carry uncertainty. WISCA models this
<strong>probabilistically</strong>, using conjugate Bayesian
distributions.</p>
<hr>
</div>
<div class="section level2">
<h2 id="the-bayesian-engine-behind-wisca">The Bayesian engine behind WISCA<a class="anchor" aria-label="anchor" href="#the-bayesian-engine-behind-wisca"></a>
@ -152,486 +174,270 @@ distributions.</p>
<div class="section level3">
<h3 id="pathogen-incidence">Pathogen incidence<a class="anchor" aria-label="anchor" href="#pathogen-incidence"></a>
</h3>
<p>Let: - K be the number of pathogens, -
<code>α = (1, 1, ..., 1) be a **Dirichlet** prior (uniform), -</code> n
= (n₁, …, nₖ) be the observed counts per species.</p>
<p>Then the posterior incidence follows:</p>
<p>``` incidence ∼ Dirichlet(α + n)</p>
<p>In simulations, we draw from this posterior using:</p>
<p>``` xᵢ ∼ Gamma(αᵢ + nᵢ, 1)</p>
<p>``` incidenceᵢ = xᵢ / ∑ xⱼ</p>
<hr>
<p>Let:</p>
<ul>
<li>
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>K</mi><annotation encoding="application/x-tex">K</annotation></semantics></math>
be the number of pathogens,</li>
<li>
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>α</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>,</mo><mn>1</mn><mo>,</mo><mi>…</mi><mo>,</mo><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\alpha = (1, 1, \ldots, 1)</annotation></semantics></math>
be a <strong>Dirichlet</strong> prior (uniform),</li>
<li>
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>n</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">n = (n_1, \ldots, n_K)</annotation></semantics></math>
be the observed counts per species.</li>
</ul>
<p>Then the posterior incidence is:</p>
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>p</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>1</mn></msub><mo>+</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>α</mi><mi>K</mi></msub><mo>+</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">p \sim \text{Dirichlet}(\alpha_1 + n_1, \ldots, \alpha_K + n_K)</annotation></semantics></math></p>
<p>To simulate from this, we use:</p>
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>x</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Gamma</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mi>i</mi></msub><mo>+</mo><msub><mi>n</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>,</mo><mspace width="1.0em"></mspace><msub><mi>p</mi><mi>i</mi></msub><mo>=</mo><mfrac><msub><mi>x</mi><mi>i</mi></msub><mrow><munderover><mo>∑</mo><mrow><mi>j</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>x</mi><mi>j</mi></msub></mrow></mfrac></mrow><annotation encoding="application/x-tex">x_i \sim \text{Gamma}(\alpha_i + n_i,\ 1), \quad p_i = \frac{x_i}{\sum_{j=1}^{K} x_j}</annotation></semantics></math></p>
</div>
<div class="section level3">
<h3 id="susceptibility">Susceptibility<a class="anchor" aria-label="anchor" href="#susceptibility"></a>
</h3>
<p>Each pathogen–regimen pair has: - <code>prior: Beta(1, 1) -</code>
data: S susceptible out of N tested</p>
<p>Then:</p>
<p>``` susceptibility ∼ Beta(1 + S, 1 + (N - S))</p>
<p>In each simulation, we draw random susceptibility per species from
this Beta distribution.</p>
<hr>
<p>Each pathogen–regimen pair has a prior and data:</p>
<ul>
<li>Prior:
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>,</mo><msub><mi>β</mi><mn>0</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Beta}(\alpha_0, \beta_0)</annotation></semantics></math>,
with default
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>α</mi><mn>0</mn></msub><mo>=</mo><msub><mi>β</mi><mn>0</mn></msub><mo>=</mo><mn>1</mn></mrow><annotation encoding="application/x-tex">\alpha_0 = \beta_0 = 1</annotation></semantics></math>
</li>
<li>Data:
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
susceptible out of
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>N</mi><annotation encoding="application/x-tex">N</annotation></semantics></math>
tested</li>
</ul>
<p>The
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
category could also include values SDD (susceptible, dose-dependent) and
I (intermediate [CLSI], or susceptible, increased exposure
[EUCAST]).</p>
<p>Then the posterior is:</p>
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>θ</mi><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>+</mo><mi>S</mi><mo>,</mo><mspace width="0.222em"></mspace><msub><mi>β</mi><mn>0</mn></msub><mo>+</mo><mi>N</mi><mo>−</mo><mi>S</mi><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta \sim \text{Beta}(\alpha_0 + S,\ \beta_0 + N - S)</annotation></semantics></math></p>
</div>
<div class="section level3">
<h3 id="final-coverage-estimate">Final coverage estimate<a class="anchor" aria-label="anchor" href="#final-coverage-estimate"></a>
</h3>
<p>Putting it together:</p>
<p>``` For each simulation: - Draw incidence ∼ Dirichlet - Draw
susceptibility ∼ Beta - Multiply → coverage estimate</p>
<p>We repeat this (e.g. 1000×) and summarise: - <strong>Mean</strong>:
expected coverage - <strong>Quantiles</strong>: credible interval
(default 95%)</p>
<hr>
<ol style="list-style-type: decimal">
<li>Simulate pathogen incidence:
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>𝐩</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext></mrow><annotation encoding="application/x-tex">\boldsymbol{p} \sim \text{Dirichlet}</annotation></semantics></math>
</li>
<li>Simulate susceptibility:
<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>θ</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>+</mo><msub><mi>S</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo>+</mo><msub><mi>R</mi><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta_i \sim \text{Beta}(1 + S_i,\ 1 + R_i)</annotation></semantics></math>
</li>
<li>Combine:</li>
</ol>
<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munderover><mo>∑</mo><mrow><mi>i</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>p</mi><mi>i</mi></msub><mo>⋅</mo><msub><mi>θ</mi><mi>i</mi></msub></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_{i=1}^{K} p_i \cdot \theta_i</annotation></semantics></math></p>
<p>Repeat this simulation (e.g. 1000×) and summarise:</p>
<ul>
<li>
<strong>Mean</strong> = expected coverage</li>
<li>
<strong>Quantiles</strong> = credible interval</li>
</ul>
</div>
</div>
<div class="section level2">
<h2 id="practical-use-in-amr">Practical use in AMR<a class="anchor" aria-label="anchor" href="#practical-use-in-amr"></a>
<h2 id="practical-use-in-the-amr-package">Practical use in the <code>AMR</code> package<a class="anchor" aria-label="anchor" href="#practical-use-in-the-amr-package"></a>
</h2>
<div class="section level3">
<h3 id="simulate-a-synthetic-syndrome">Simulate a synthetic syndrome<a class="anchor" aria-label="anchor" href="#simulate-a-synthetic-syndrome"></a>
<h3 id="prepare-data-and-simulate-synthetic-syndrome">Prepare data and simulate synthetic syndrome<a class="anchor" aria-label="anchor" href="#prepare-data-and-simulate-synthetic-syndrome"></a>
</h3>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span></span>
<span></span>
<span><span class="co"># Add a fake syndrome column for stratification</span></span>
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"Other"</span><span class="op">)</span></span></code></pre></div>
<span><span class="co"># Structure of our data</span></span>
<span><span class="va">data</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
<span><span class="co">#&gt; date patient age gender ward mo PEN OXA FLC AMX </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&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;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;, MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span></span>
<span></span>
<span><span class="co"># Add a fake syndrome column</span></span>
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"No UTI"</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="basic-wisca-antibiogram">Basic WISCA antibiogram<a class="anchor" aria-label="anchor" href="#basic-wisca-antibiogram"></a>
</h3>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> antimicrobials <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">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="2%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="1%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="2%">
</colgroup>
<thead><tr class="header">
<th align="left">Amikacin</th>
<th align="left">Amoxicillin</th>
<th align="left">Amoxicillin/clavulanic acid</th>
<th align="left">Ampicillin</th>
<th align="left">Azithromycin</th>
<th align="left">Benzylpenicillin</th>
<th align="left">Cefazolin</th>
<th align="left">Cefepime</th>
<th align="left">Cefotaxime</th>
<th align="left">Cefoxitin</th>
<th align="left">Ceftazidime</th>
<th align="left">Ceftriaxone</th>
<th align="left">Cefuroxime</th>
<th align="left">Chloramphenicol</th>
<th align="left">Ciprofloxacin</th>
<th align="left">Clindamycin</th>
<th align="left">Colistin</th>
<th align="left">Doxycycline</th>
<th align="left">Erythromycin</th>
<th align="left">Flucloxacillin</th>
<th align="left">Fosfomycin</th>
<th align="left">Gentamicin</th>
<th align="left">Imipenem</th>
<th align="left">Kanamycin</th>
<th align="left">Linezolid</th>
<th align="left">Meropenem</th>
<th align="left">Metronidazole</th>
<th align="left">Moxifloxacin</th>
<th align="left">Mupirocin</th>
<th align="left">Nitrofurantoin</th>
<th align="left">Oxacillin</th>
<th align="left">Piperacillin/tazobactam</th>
<th align="left">Rifampicin</th>
<th align="left">Teicoplanin</th>
<th align="left">Tetracycline</th>
<th align="left">Tigecycline</th>
<th align="left">Tobramycin</th>
<th align="left">Trimethoprim</th>
<th align="left">Trimethoprim/sulfamethoxazole</th>
<th align="left">Vancomycin</th>
</tr></thead>
<tbody><tr class="odd">
<td align="left">41.7% (37.2-47.5%)</td>
<td align="left">35.7% (33.3-38.2%)</td>
<td align="left">73.7% (71.7-75.8%)</td>
<td align="left">35.8% (33.6-38.1%)</td>
<td align="left">43.8% (41.5-46%)</td>
<td align="left">28.2% (25.8-30.8%)</td>
<td align="left">69.3% (64.9-73.8%)</td>
<td align="left">74.8% (70.5-78.8%)</td>
<td align="left">73.3% (69.2-77.3%)</td>
<td align="left">69.6% (65.5-73.7%)</td>
<td align="left">35.9% (33.6-38.2%)</td>
<td align="left">73.3% (68.9-77.2%)</td>
<td align="left">71.9% (69.8-74%)</td>
<td align="left">64.9% (51.7-78.5%)</td>
<td align="left">77% (74.5-79.6%)</td>
<td align="left">47.3% (44.7-49.6%)</td>
<td align="left">33% (30.8-35.1%)</td>
<td align="left">63.6% (52.1-74.9%)</td>
<td align="left">43.7% (41.6-46%)</td>
<td align="left">59.3% (47-71%)</td>
<td align="left">60.5% (55.5-65.8%)</td>
<td align="left">72.7% (70.7-74.8%)</td>
<td align="left">78.2% (74-82.2%)</td>
<td align="left">25.6% (13.5-37.7%)</td>
<td align="left">54.9% (50.4-59%)</td>
<td align="left">77.1% (72.8-81.2%)</td>
<td align="left">56.1% (39.5-70.7%)</td>
<td align="left">49.6% (43.6-55.6%)</td>
<td align="left">65.2% (52.7-78.1%)</td>
<td align="left">76.5% (69.4-82.3%)</td>
<td align="left">57.8% (45.4-69.6%)</td>
<td align="left">69.4% (64.2-74.2%)</td>
<td align="left">52.4% (47.6-56.8%)</td>
<td align="left">48.1% (43.4-52.9%)</td>
<td align="left">61.4% (53.6-70.5%)</td>
<td align="left">81.9% (78.1-85.5%)</td>
<td align="left">60.7% (57.8-63.5%)</td>
<td align="left">61% (58.8-63.5%)</td>
<td align="left">76.5% (74.5-78.5%)</td>
<td align="left">61.9% (59.8-64.2%)</td>
<td align="left">77% (74.3-79.4%)</td>
<td align="left">72.8% (70.7-74.8%)</td>
</tr></tbody>
</table>
</div>
<div class="section level3">
<h3 id="use-combination-regimens">Use combination regimens<a class="anchor" aria-label="anchor" href="#use-combination-regimens"></a>
</h3>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> antimicrobials <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">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="24%">
<col width="38%">
<col width="36%">
</colgroup>
<thead><tr class="header">
<th align="left">Amoxicillin/clavulanic acid</th>
<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
</tr></thead>
<tbody><tr class="odd">
<td align="left">73.8% (71.8-75.7%)</td>
<td align="left">87.5% (85.9-89%)</td>
<td align="left">89.7% (88.2-91.1%)</td>
</tr></tbody>
</table>
</div>
<div class="section level3">
<h3 id="stratify-by-syndrome">Stratify by syndrome<a class="anchor" aria-label="anchor" href="#stratify-by-syndrome"></a>
</h3>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span>,</span>
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> antimicrobials <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">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="2%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="12%">
<col width="21%">
<col width="34%">
<col width="31%">
</colgroup>
<thead><tr class="header">
<th align="left">Syndromic Group</th>
<th align="left">Amikacin</th>
<th align="left">Amoxicillin</th>
<th align="left">Amoxicillin/clavulanic acid</th>
<th align="left">Ampicillin</th>
<th align="left">Azithromycin</th>
<th align="left">Benzylpenicillin</th>
<th align="left">Cefazolin</th>
<th align="left">Cefepime</th>
<th align="left">Cefotaxime</th>
<th align="left">Cefoxitin</th>
<th align="left">Ceftazidime</th>
<th align="left">Ceftriaxone</th>
<th align="left">Cefuroxime</th>
<th align="left">Chloramphenicol</th>
<th align="left">Ciprofloxacin</th>
<th align="left">Clindamycin</th>
<th align="left">Colistin</th>
<th align="left">Doxycycline</th>
<th align="left">Erythromycin</th>
<th align="left">Flucloxacillin</th>
<th align="left">Fosfomycin</th>
<th align="left">Gentamicin</th>
<th align="left">Imipenem</th>
<th align="left">Kanamycin</th>
<th align="left">Linezolid</th>
<th align="left">Meropenem</th>
<th align="left">Metronidazole</th>
<th align="left">Moxifloxacin</th>
<th align="left">Mupirocin</th>
<th align="left">Nitrofurantoin</th>
<th align="left">Oxacillin</th>
<th align="left">Piperacillin/tazobactam</th>
<th align="left">Rifampicin</th>
<th align="left">Teicoplanin</th>
<th align="left">Tetracycline</th>
<th align="left">Tigecycline</th>
<th align="left">Tobramycin</th>
<th align="left">Trimethoprim</th>
<th align="left">Trimethoprim/sulfamethoxazole</th>
<th align="left">Vancomycin</th>
<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Other</td>
<td align="left">25% (20.2-31.7%)</td>
<td align="left">31.6% (28.7-34%)</td>
<td align="left">70.1% (67.7-72.4%)</td>
<td align="left">31.6% (29.1-34.1%)</td>
<td align="left">56.4% (53.8-58.8%)</td>
<td align="left">36.3% (33.1-39.4%)</td>
<td align="left">61.5% (55.7-66.5%)</td>
<td align="left">68.5% (63.4-73.8%)</td>
<td align="left">66.7% (61.4-71.9%)</td>
<td align="left">63% (57.7-68.6%)</td>
<td align="left">18.3% (15.9-20.8%)</td>
<td align="left">66.6% (61.4-71.5%)</td>
<td align="left">65.5% (62.7-68%)</td>
<td align="left">69.6% (60-77.2%)</td>
<td align="left">74% (70.8-77.2%)</td>
<td align="left">60.9% (58.1-63.6%)</td>
<td align="left">13.9% (11.8-15.8%)</td>
<td align="left">67.4% (63.7-70.9%)</td>
<td align="left">56.4% (54-58.9%)</td>
<td align="left">61.4% (56-67.6%)</td>
<td align="left">49.6% (43.2-56.3%)</td>
<td align="left">65.6% (62.8-68.1%)</td>
<td align="left">71.8% (66.7-77%)</td>
<td align="left">18.6% (13.1-25.9%)</td>
<td align="left">70.8% (65.1-75.8%)</td>
<td align="left">70.6% (65.1-75.7%)</td>
<td align="left">49.8% (34.2-66.6%)</td>
<td align="left">63.3% (56.2-70.3%)</td>
<td align="left">69.8% (62.6-76.4%)</td>
<td align="left">70.5% (61.2-77.5%)</td>
<td align="left">60% (54.4-65.4%)</td>
<td align="left">62.4% (56.4-68.6%)</td>
<td align="left">67.6% (61.9-73.2%)</td>
<td align="left">61.9% (55.4-67.6%)</td>
<td align="left">67.8% (64.8-70.6%)</td>
<td align="left">77% (72.3-81.8%)</td>
<td align="left">50.1% (46.7-53.6%)</td>
<td align="left">61.1% (58.4-64%)</td>
<td align="left">78.8% (76.4-80.9%)</td>
<td align="left">79.6% (77.4-81.8%)</td>
<td align="left">No UTI</td>
<td align="left">70.1% (67.8-72.3%)</td>
<td align="left">85.2% (83.1-87.2%)</td>
<td align="left">87.1% (85.3-88.7%)</td>
</tr>
<tr class="even">
<td align="left">UTI</td>
<td align="left">91.5% (88.8-93.5%)</td>
<td align="left">50% (45.5-54.6%)</td>
<td align="left">80.9% (77.8-84%)</td>
<td align="left">49.9% (45.6-54.3%)</td>
<td align="left">8.2% (6.4-10.5%)</td>
<td align="left">8.2% (6.3-10.3%)</td>
<td align="left">88.9% (84.2-92.3%)</td>
<td align="left">89.4% (86.5-91.8%)</td>
<td align="left">89.9% (87.4-92.1%)</td>
<td align="left">86.1% (82.9-88.9%)</td>
<td align="left">89.8% (87.2-91.9%)</td>
<td align="left">89.8% (87.1-92.1%)</td>
<td align="left">87.4% (84.5-89.8%)</td>
<td align="left">NA</td>
<td align="left">81.4% (78.3-84.3%)</td>
<td align="left">8.2% (6.3-10.4%)</td>
<td align="left">91.7% (89.6-93.8%)</td>
<td align="left">NA</td>
<td align="left">8.1% (6.3-10.4%)</td>
<td align="left">NA</td>
<td align="left">90.6% (86.5-93.3%)</td>
<td align="left">90.2% (87.9-92.2%)</td>
<td align="left">91.8% (89.7-93.8%)</td>
<td align="left">NA</td>
<td align="left">8.1% (6.1-10.2%)</td>
<td align="left">91.8% (89.6-93.8%)</td>
<td align="left">71.4% (31.8-91.6%)</td>
<td align="left">9.3% (6.7-13.3%)</td>
<td align="left">NA</td>
<td align="left">89.4% (86.9-91.7%)</td>
<td align="left">NA</td>
<td align="left">87.2% (84.4-89.6%)</td>
<td align="left">8.2% (6.3-10.4%)</td>
<td align="left">8.2% (6.3-10.3%)</td>
<td align="left">41.2% (14.3-74.4%)</td>
<td align="left">90.9% (87.7-93.3%)</td>
<td align="left">89.6% (87.1-91.8%)</td>
<td align="left">59.1% (54.7-63.4%)</td>
<td align="left">65.3% (61.3-69.2%)</td>
<td align="left">8.2% (6.2-10.3%)</td>
<td align="left">80.9% (77.7-83.8%)</td>
<td align="left">88.2% (85.7-90.5%)</td>
<td align="left">90.9% (88.7-93%)</td>
</tr>
</tbody>
</table>
</div>
<div class="section level3">
<h3 id="use-combination-regimens">Use combination regimens<a class="anchor" aria-label="anchor" href="#use-combination-regimens"></a>
</h3>
<p>The <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function supports combination
regimens:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> antimicrobials <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">"AMC"</span>, <span class="st">"GEN"</span>, <span class="st">"AMC + GEN"</span>, <span class="st">"CIP"</span><span class="op">)</span>,</span>
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
<p>The <code>AMR</code> package is available in 20 languages, which can
all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></code> function too:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> antimicrobials <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">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"UTI"</span>, <span class="st">"UCI"</span>, <span class="va">data</span><span class="op">$</span><span class="va">syndrome</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="st">"Spanish"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="26%">
<col width="39%">
<col width="16%">
<col width="18%">
<col width="12%">
<col width="21%">
<col width="34%">
<col width="31%">
</colgroup>
<thead><tr class="header">
<th align="left">Amoxicillin/clavulanic acid</th>
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
<th align="left">Ciprofloxacin</th>
<th align="left">Gentamicin</th>
</tr></thead>
<tbody><tr class="odd">
<td align="left">73.8% (71.7-75.8%)</td>
<td align="left">89.7% (88.2-91.2%)</td>
<td align="left">77% (74.3-79.6%)</td>
<td align="left">72.8% (70.6-74.9%)</td>
</tr></tbody>
</table>
<hr>
</div>
</div>
<div class="section level2">
<h2 id="interpretation">Interpretation<a class="anchor" aria-label="anchor" href="#interpretation"></a>
</h2>
<p>Suppose you get this output:</p>
<table class="table">
<thead><tr class="header">
<th>Regimen</th>
<th>Coverage</th>
<th>Lower_CI</th>
<th>Upper_CI</th>
<th align="left">Grupo sindrómico</th>
<th align="left">Amoxicilina/ácido clavulánico</th>
<th align="left">Amoxicilina/ácido clavulánico + Ciprofloxacina</th>
<th align="left">Amoxicilina/ácido clavulánico + Gentamicina</th>
</tr></thead>
<tbody>
<tr class="odd">
<td>AMC</td>
<td>0.72</td>
<td>0.65</td>
<td>0.78</td>
<td align="left">No UCI</td>
<td align="left">70% (67.8-72.4%)</td>
<td align="left">85.3% (83.3-87.2%)</td>
<td align="left">87% (85.3-88.8%)</td>
</tr>
<tr class="even">
<td>AMC + GEN</td>
<td>0.88</td>
<td>0.83</td>
<td>0.93</td>
<td align="left">UCI</td>
<td align="left">80.9% (77.7-83.9%)</td>
<td align="left">88.2% (85.5-90.6%)</td>
<td align="left">90.9% (88.7-93%)</td>
</tr>
</tbody>
</table>
<p>Interpretation:</p>
<blockquote>
<p><em>“AMC + GEN covers 88% of expected pathogens for this syndrome,
with 95% certainty that the true coverage lies between 83% and
93%.”</em></p>
</blockquote>
<p>Regimens with few tested isolates will show <strong>wider
intervals</strong>.</p>
<hr>
</div>
</div>
<div class="section level2">
<h2 id="sensible-defaults-but-you-can-customise">Sensible defaults, but you can customise<a class="anchor" aria-label="anchor" href="#sensible-defaults-but-you-can-customise"></a>
<h2 id="sensible-defaults-which-can-be-customised">Sensible defaults, which can be customised<a class="anchor" aria-label="anchor" href="#sensible-defaults-which-can-be-customised"></a>
</h2>
<ul>
<li>
<code>minimum = 30</code>: exclude regimens with &lt;30 isolates
tested.</li>
<code>simulations = 1000</code>: number of Monte Carlo draws</li>
<li>
<code>simulations = 1000</code>: number of Monte Carlo samples.</li>
<code>conf_interval = 0.95</code>: coverage interval width</li>
<li>
<code>conf_interval = 0.95</code>: coverage interval width.</li>
<li>
<code>combine_SI = TRUE</code>: count “I”/“SDD” as susceptible.</li>
<code>combine_SI = TRUE</code>: count “I” and “SDD” as
susceptible</li>
</ul>
<hr>
</div>
<div class="section level2">
<h2 id="limitations">Limitations<a class="anchor" aria-label="anchor" href="#limitations"></a>
</h2>
<ul>
<li>WISCA does not model time trends or temporal resistance shifts.</li>
<li>It assumes data are representative of current clinical
practice.</li>
<li>It does not account for patient-level covariates (yet).</li>
<li>Species-specific data are abstracted into syndrome-level
estimates.</li>
<li>It assumes your data are representative</li>
<li>No adjustment for patient-level covariates, although these could be
passed onto the <code>syndromic_group</code> argument</li>
<li>WISCA does not model resistance over time, you might want to use
<code>tidymodels</code> for that, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a
basic introduction</a>
</li>
</ul>
<hr>
</div>
<div class="section level2">
<h2 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
</h2>
<p>WISCA enables:</p>
<ul>
<li>Empirical regimen comparison,</li>
<li>Syndrome-specific coverage estimation,</li>
<li>Fully probabilistic interpretation.</li>
</ul>
<p>It is available in the <code>AMR</code> package via either:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">...</span>, wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="reference">Reference<a class="anchor" aria-label="anchor" href="#reference"></a>
</h2>
<p>Bielicki JA et al. (2016).<br><em>Weighted-incidence syndromic combination antibiograms to guide
empiric treatment in pediatric bloodstream infections.</em><br><strong>J Antimicrob Chemother</strong>, 71(2):529–536. <a href="doi:10.1093/jac/dkv397" class="uri">doi:10.1093/jac/dkv397</a></p>
<hr>
</div>
<div class="section level2">
<h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
</h2>
<p>WISCA shifts empirical therapy from simple percent susceptible toward
<strong>probabilistic, syndrome-based decision support</strong>. It is a
statistically principled, clinically intuitive method to guide regimen
selection — and easy to use via the <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function
in the <strong>AMR</strong> package.</p>
<p>For antimicrobial stewardship teams, it enables
<strong>disease-specific, reproducible, and data-driven
guidance</strong> — even in the face of sparse data.</p>
<p>Bielicki, JA, et al. (2016). <em>Selecting appropriate empirical
antibiotic regimens for paediatric bloodstream infections: application
of a Bayesian decision model to local and pooled antimicrobial
resistance surveillance data.</em> <strong>J Antimicrob
Chemother</strong>. 71(3):794-802. <a href="https://doi.org/10.1093/jac/dkv397" class="external-link uri">https://doi.org/10.1093/jac/dkv397</a></p>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside>

8
articles/datasets.html
View File

@ -5,7 +5,7 @@
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Data sets for download / own use • AMR (for R)</title>
<title>Download data sets for download / own use • AMR (for R)</title>
<!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png">
<link rel="icon" type="”image/svg+xml”" href="../favicon.svg">
<link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png">
@ -18,7 +18,7 @@
<link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="Data sets for download / own use">
<script src="../extra.js"></script><meta property="og:title" content="Download data sets for download / own use">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
</head>
@ -30,7 +30,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -78,7 +78,7 @@
<div class="row">
<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>
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">01 May 2025</h4>

14
articles/index.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -55,17 +55,17 @@
<dd>
</dd><dt><a href="AMR_with_tidymodels.html">AMR with tidymodels</a></dt>
<dd>
</dd><dt><a href="AMR.html">How to conduct AMR data analysis</a></dt>
</dd><dt><a href="AMR.html">Conduct AMR data analysis</a></dt>
<dd>
</dd><dt><a href="datasets.html">Data sets for download / own use</a></dt>
</dd><dt><a href="datasets.html">Download data sets for download / own use</a></dt>
<dd>
</dd><dt><a href="EUCAST.html">How to apply EUCAST rules</a></dt>
</dd><dt><a href="EUCAST.html">Apply EUCAST rules</a></dt>
<dd>
</dd><dt><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></dt>
</dd><dt><a href="MDR.html">Determine multi-drug resistance (MDR)</a></dt>
<dd>
</dd><dt><a href="PCA.html">How to conduct principal component analysis (PCA) for AMR</a></dt>
</dd><dt><a href="PCA.html">Conduct principal component analysis (PCA) for AMR</a></dt>
<dd>
</dd><dt><a href="WHONET.html">How to work with WHONET data</a></dt>
</dd><dt><a href="WHONET.html">Work with WHONET data</a></dt>
<dd>
</dd><dt><a href="WISCA.html">Estimating Empirical Coverage with WISCA</a></dt>
<dd>

2
authors.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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
index.html
View File

@ -33,7 +33,7 @@
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">

18
news/index.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -49,11 +49,11 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9267" id="amr-2119267">AMR 2.1.1.9267<a class="anchor" aria-label="anchor" href="#amr-2119267"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9268" id="amr-2119268">AMR 2.1.1.9268<a class="anchor" aria-label="anchor" href="#amr-2119268"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://amr-for-r.org/#get-this-package">the instructions here</a>.)</em></p>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
<div class="section level3">
<h3 id="tldr-2-1-1-9267">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9267"></a></h3>
<h3 id="tldr-2-1-1-9268">tl;dr<a class="anchor" aria-label="anchor" href="#tldr-2-1-1-9268"></a></h3>
<ul><li>
<strong>Scope Expansion</strong>: One Health support (Human + Veterinary + Environmental microbiology).</li>
<li>
@ -113,15 +113,15 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="full-changelog-2-1-1-9267">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9267"></a></h3>
<h3 id="full-changelog-2-1-1-9268">Full Changelog<a class="anchor" aria-label="anchor" href="#full-changelog-2-1-1-9268"></a></h3>
<div class="section level4">
<h4 id="breaking-2-1-1-9267">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9267"></a></h4>
<h4 id="breaking-2-1-1-9268">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9268"></a></h4>
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<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 two years ago.</li>
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> are now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
</ul></div>
<div class="section level4">
<h4 id="new-2-1-1-9267">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9267"></a></h4>
<h4 id="new-2-1-1-9268">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9268"></a></h4>
<ul><li>
<strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -176,7 +176,7 @@
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="changed-2-1-1-9267">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9267"></a></h4>
<h4 id="changed-2-1-1-9268">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9268"></a></h4>
<ul><li>SIR interpretation
<ul><li>Support for parallel computing to greatly improve speed using the <code>parallel</code> package (part of base R). Use <code>as.sir(your_data, parallel = TRUE)</code> to run SIR interpretation using multiple cores.</li>
<li>It is now possible to use column names for arguments <code>guideline</code>, <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>
@ -258,7 +258,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level4">
<h4 id="other-2-1-1-9267">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9267"></a></h4>
<h4 id="other-2-1-1-9268">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9268"></a></h4>
<ul><li>New website domain: <a href="https://amr-for-r.org" class="uri">https://amr-for-r.org</a>! The old domain (<a href="http://amr-for-r.org/" class="external-link uri">http://amr-for-r.org/</a>) will remain to work.</li>
<li>Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
@ -269,7 +269,7 @@
</ul></div>
</div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9267">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9267"></a></h3>
<h3 id="older-versions-2-1-1-9268">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9268"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (March 2025) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

2
pkgdown.yml
View File

@ -11,7 +11,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2025-05-01T09:52Z
last_built: 2025-05-01T12:49Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

2
reference/AMR-deprecated.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/AMR-options.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/AMR.html
View File

@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/WHOCC.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/WHONET.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/ab_from_text.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/ab_property.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/add_custom_antimicrobials.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/add_custom_microorganisms.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/age.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/age_groups.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">

23
reference/antibiogram.html
View File

@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -63,16 +63,17 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, wisca <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, sort_columns <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> wisca <span class="op">=</span> <span class="cn">FALSE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>,</span>
<span> interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antimicrobials <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.sir</span><span class="op">)</span>, ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fl">1</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>, <span class="fl">14</span><span class="op">)</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> sep <span class="op">=</span> <span class="st">" + "</span>, simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>,</span>
<span> interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span> sep <span class="op">=</span> <span class="st">" + "</span>, sort_columns <span class="op">=</span> <span class="cn">TRUE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span>
<span> conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">retrieve_wisca_parameters</span><span class="op">(</span><span class="va">wisca_model</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
@ -168,6 +169,10 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dd><p>A separating character for antimicrobial columns in combination antibiograms.</p></dd>
<dt id="arg-sort-columns">sort_columns<a class="anchor" aria-label="anchor" href="#arg-sort-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the antimicrobial columns must be sorted on name.</p></dd>
<dt id="arg-wisca">wisca<a class="anchor" aria-label="anchor" href="#arg-wisca"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is <code>FALSE</code>). This will use a Bayesian decision model to estimate regimen coverage probabilities using <a href="https://en.wikipedia.org/wiki/Monte_Carlo_method" class="external-link">Monte Carlo simulations</a>. Set <code>simulations</code>, <code>conf_interval</code>, and <code>interval_side</code> to adjust.</p></dd>
@ -572,9 +577,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 73.4% (68.3-78.6%) 92.4% (90.7-93.8%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 57.4% (49.7-65.4%) 85% (82.1-87.9%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 57% (47.4-66.7%) 74.4% (68.6-79.5%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 73.4% (68.3-78.6%) 92.3% (90.7-93.7%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 57.4% (49.7-65.4%) 84.9% (82.1-87.6%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 57% (47.4-66.7%) 74.6% (68.8-79.8%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>

2
reference/antimicrobial_selectors.html
View File

@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/antimicrobials.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/as.ab.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/as.av.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/as.disk.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/as.mic.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/as.mo.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">

10
reference/as.sir.html
View File

@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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">
@ -409,10 +409,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</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;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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-05-01 <span style="color: #949494;">12:50:15</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

2
reference/atc_online.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/bug_drug_combinations.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/clinical_breakpoints.html
View File

@ -21,7 +21,7 @@ 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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/count.html
View File

@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/custom_eucast_rules.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/dosage.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/eucast_rules.html
View File

@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/example_isolates.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/example_isolates_unclean.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/export_ncbi_biosample.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/first_isolate.html
View File

@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/g.test.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/get_episode.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/ggplot_pca.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/ggplot_sir.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/guess_ab_col.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/index.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/intrinsic_resistant.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/italicise_taxonomy.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/join.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/key_antimicrobials.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/kurtosis.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/like.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/mdro.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/mean_amr_distance.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/microorganisms.codes.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/microorganisms.groups.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/microorganisms.html
View File

@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/mo_matching_score.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/mo_property.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/mo_source.html
View File

@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/pca.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/plot.html
View File

@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/proportion.html
View File

@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/random.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/resistance_predict.html
View File

@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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
View File

@ -9,7 +9,7 @@ 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="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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/top_n_microorganisms.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9268</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
View File

File diff suppressed because one or more lines are too long