P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 14:27:53 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9080: a558f4c

Browse Source
This commit is contained in:
github-actions
2024-09-24 20:49:01 +00:00
parent 62f6837a98
commit 1c32c669a0
85 changed files with 321 additions and 297 deletions
Download Patch File Download Diff File Expand all files Collapse all files

27
reference/clinical_breakpoints.html
View File

@ -1,10 +1,18 @@
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/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 Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2024 and CLSI 2011-2024.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2024 and CLSI 2019-2024.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2024 and CLSI 2011-2024.
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2024 and CLSI 2019-2024.
These breakpoints are currently implemented:
For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
@ -13,7 +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="">2.1.1.9078</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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">
@ -61,9 +69,10 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="ref-description section level2">
<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.</p>
<p>Currently available breakpoint guidelines for <strong>clinical microbiology</strong> are EUCAST 2011-2024 and CLSI 2011-2024.</p>
<p>Currently available breakpoint guidelines for <strong>veterinary microbiology</strong> are EUCAST 2021-2024 and CLSI 2019-2024.</p>
<p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024;</p></li>
<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024;</p></li>
<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.</p></li>
</ul><p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
</div>
<div class="section level2">
@ -96,7 +105,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<p>Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.</p>
<p>The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. Use <code><a href="as.sir.html">as.sir(..., breakpoint_type = ...)</a></code> to interpret raw data using a specific breakpoint type, e.g. <code>as.sir(..., breakpoint_type = "ECOFF")</code> to use ECOFFs.</p>
<p>The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. Use <code><a href="as.sir.html">as.sir(..., breakpoint_type = ...)</a></code> to interpret raw data using a specific breakpoint type, e.g. <code>as.sir(..., breakpoint_type = "ECOFF")</code> to use ECOFFs.</p>
</div>
<div class="section">